BioCel User Guide - Velocity 11BioCel User Guide 6 Reporting BioCel Problems Sending Us an Email If...

BioCel® User Guide

November 2004

VWorks3 version 13.1

Copyright 2004 Velocity11

The information provided in this guide is intended to be accurate and reliable. However, Velocity11 does not assume responsibility for its use or for any infringements upon the rights of third parties that may result from its use.

The transfer of this guide, in any manner or form, to a representative of another company is strictly forbidden.

BioCel, PlateLoc, VCode, Velocity11, VPrep and VStack are registered trademarks of Velocity11.

PlatePierce, VSpin, VWorks and VersaScan are trademarks of Velocity11.

Microsoft and Windows are registered trademarks of the Microsoft Corporation in the United States and other countries.

All other trademarks are the sole property of their respective owners.

Chapter 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1What Is Covered by This Guide? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2Other User Guides to Read . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3What’s New in This Version . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4Reporting BioCel Problems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6Reporting User Guide Errors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8General BioCel Hazard Warnings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Chapter 2. BioCel Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Basic Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14Main External Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Utilities Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16Power Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17Hardware Control Components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Power System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20Air System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24Clean-Room Filtration System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25Computers and Networking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27Adjusting the Keyboard Shelf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27BioCel Modules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28Optional BioCel Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Chapter 3. Preparing for a Run . . . . . . . . . . . . . . . . . . . . . . . . . . 35Preparing a Run: Workflow Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36Turning On the BioCel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37BioCel Ready State Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Logging In To the Operating System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39Starting VWorks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40Logging In To VWorks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41About Tasks, Processes and Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42About Protocol Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45Opening a Protocol in VWorks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47Setting General Options. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48Setting Error Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51Setting Protocol Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53Pipetting Order Rule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54About Log and Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Contents

Setting Log Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60Importing a Log File to Excel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63Adding an Alarm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65Understanding the Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68Preparing Plates, Modules and Accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69Placing and Removing Hotel Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76Setting Up a VSpin Counterweight Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Chapter 4. Performing a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79Overview of Performing a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80Performing Pre-Run Checks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81Starting a Run from VWorks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83Starting a Run from a Command Line. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86About Starting Runs Automatically . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87Working with Runsets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88Runset Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91Stopping a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95Monitoring a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99Working with the Log Toolbar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104Performing Post-Run Clean-Up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106Shutting Down the BioCel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107

Chapter 5. Creating a Protocol: Basics . . . . . . . . . . . . . . . . . 109Creating a Protocol: Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110Setting Up a Plate Instance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112Setting the Number of Simultaneous Plates . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116Adding and Deleting Tasks and Pipette Tasks. . . . . . . . . . . . . . . . . . . . . . . . . . . 117Compiling and Saving Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118About Setting Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120About Setting Pipette Process Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 121Checking a Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

Chapter 6. Setting Task Parameters . . . . . . . . . . . . . . . . . . . 125Setting AliQuot Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126Setting Apply Label Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127Setting Bio-Tek Washer Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133Setting Centrifuge Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134Setting Delid/Relid Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135Setting Echo 550 Transfer Task Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . 136Setting Envision Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138Setting Incubate Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139Setting MultiDrop Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141Setting Nanodrop Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143Setting Pierce Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144Setting Place Plate Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145

Setting QFill Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146Setting Remp CSP Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147Setting Restack Task Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147Setting Seal Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151Setting Stacker Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152Setting StoreX Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154Setting Teleshake Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156Setting User Message Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157Setting Vacuum Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159Setting Waitfor Task and Signal Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . 160Setting Zeiss Task Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161Specifying Task Order Across Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162

Chapter 7. Setting Pipette Task Parameters . . . . . . . . . . . 163Configuring a Pipette Process: Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164Adding and Configuring a Pipette Process Task . . . . . . . . . . . . . . . . . . . . . . . . . . 169Configuring a VPrep Shelf As a Device . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171Setting Aspirate Pipette Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173Setting Change Instance Pipette Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . 175Setting Change Tips Pipette Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 177Setting Dispense Pipette Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180Setting Dry Tips Pipette Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183Setting Loop Pipette Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184Setting Mix Pipette Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185Setting Pump Reagent Pipette Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . 188Setting Wash Tips Pipette Task Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189

Chapter 8. Creating a Protocol: Advanced Topics . . . . . . 193Setting Up VWorks Plug-Ins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194About the FileReader Plug-In. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196Setting up the FileReader Plug-in . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199Using JavaScript in VWorks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202The JavaScript Task Object and Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208Understanding the Configuration Settings in a Pipette Task . . . . . . . . . . . . . . . . . 219Working With Device Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221About Bar Code Reading and Tracking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223Using Bar Code Input Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225Using Bar Code Data Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 228About Setting Up a StoreX Transfer Station . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230Inventory Management Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231Inventory Manager Views and Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 234About Linker Groups and Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235Working with Linker Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238Using Bar Code Input Files with Linker Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247Using Inventory Labware Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249Adding StoreX Plates Manually . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250

Reinventorying the Plate Management System . . . . . . . . . . . . . . . . . . . . . . . . . . 252

Chapter 9. Administrator Procedures . . . . . . . . . . . . . . . . . . 253Creating a User Account . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254Setting Labware and Liquid Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255Ultramark Plate Reader Data File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256Network Cards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257

Chapter 10. Using Diagnostics Software . . . . . . . . . . . . . . . 259About Diagnostics Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260Using AliQuot Diagnostics Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262Using Bio-Tek Diagnostics Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266About Bio I/O Diagnostics Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270Using the Echo 550 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270Using Envision Diagnostics Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272Using iSeries Diagnostics Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275Using Lid Hotel Diagnostics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278Using Multidrop Diagnostics Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279Using Nanodrop Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282Using QFill Diagnostics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286Using Robot Diagnostics Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288Fine-Tuning Robot Teachpoints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 296Using StoreX Diagnostics Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301Using Teleshake Diagnostics Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306

Chapter 11. Maintenance and Troubleshooting . . . . . . . . 307Routine Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308About Error Handling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309Compilation Warnings and Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 310Resolving Device Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 310Resolving Robot Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311Overriding the Safety Interlock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 314Resolving BioCel Bar Code Reader Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315VCode Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 316Resolving Environmental Control Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317Resolving Plate Placing Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318Resolving Inventory Management Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318Resolving Lid Removal Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320

Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321

This chapter describes the user guides that support the BioCel®, explains how to report software and document errors, and provides general safety information.

Introduction 1

Chapter 1: IntroductionBioCel User Guide

2

What Is Covered by This Guide?VWorks Version This guide supports VWorks3 (file version 13.x) and the following major

software components.

Note: Your BioCel may not have all of the components listed in the following table or may have components not listed here.

To find version information for your software:

1. Start VWorks™.

For more information, see “Starting VWorks” on page 40.

2. Select Help > About VWorks.

Component Version Component Version

Aliquot Device 2.2 SpectrafluorDevice 2.0

BenchCelDevice 5.0 ST6StackerDevice 4.0

BioIO.ocx 4.0 StackerDevice 7.0

BioTekWasherDevice 2.0 StoreXDevice 1.5

deviceenumerator.dll 5.0 TeleshakeDevice 2.1

Echo550Device 1.0 UltramarkDevice 3.0

FlexispenseDevice 1.0 VCode.ocx 2.1

MultidropDevice 3.1 VCode3KDevice 5.0

NanodropDevice 1.0 VersaScanDevice 2.2

OriginalVCodeDevice 3.1 VLidDevice 1.0

PlateLocDevice 6.1 VPrepDevice 13.0

PlatePierceDevice 4.0 VSpinDevice 4.1

QFillDevice 3.0 VStackBionet.ocx 4.0

RempCSPDevice 2.0 WeighPadDevice 1.0

RobotDevice 7.0 WellMateDevice 1.0

ShuttleRobotDevice 1.0 ZeissReaderDevice 2.0

3Chapter 1: IntroductionBioCel User Guide

What This Guide Does Not Cover

This guide does not cover the operation of:

❑ Velocity11® modules, such as the PlateLoc® and VPrep®, when used in stand-alone mode.

❑ Third-party modules.

The exception to this is the use of diagnostics software that is developed by Velocity11 for third-party devices.

For operational instructions, see the user guides for the relevant modules.

BioCel Customization

Because the BioCel is a customized platform with many options, this guide describes features that are not included in your BioCel.

Other User Guides to ReadRead These Guides In addition to this guide, also read the following guides:

Guide Contents

Getting Started ❑ Basic information about Velocity11

❑ Document support, including Online Help

❑ General safety information

❑ Product warranty

Database and Security User Guide ❑ Security login settings

❑ Labware database settings

❑ Liquid library database settings


4

What’s New in This VersionIntroduction The following table describes the main new features of VWorks3, version

13.x and the BioCel hardware that it supports.

New Features

Feature Description See...

Nanodrop Newly supported module ❑ “Setting Nanodrop Task Parameters” on page 143

❑ “Using Nanodrop Diagnostics” on page 282

Aliquot Newly supported module ❑ “Setting AliQuot Task Parameters” on page 126

❑ “Using AliQuot Diagnostics Software” on page 262

Echo 550 Newly supported module ❑ “Setting Echo 550 Transfer Task Parameters” on page 136

❑ “Using the Echo 550” on page 270

StoreX Additional software features ❑ “Setting StoreX Task Parameters” on page 154

❑ “About Setting Up a StoreX Transfer Station” on page 230

❑ “Adding StoreX Plates Manually” on page 250

❑ “Using StoreX Diagnostics Software” on page 301

Inventory Management and linker files

❑ Tracks the plates stored in incubators

❑ Used to define which plates are used with a StoreX task

❑ Used to define which plates are used in protocols scheduled in runsets

❑ “Inventory Management Overview” on page 231

❑ “About Linker Groups and Files” on page 235

❑ “Working with Linker Files” on page 238

❑ “Using Bar Code Input Files with Linker Files” on page 247

❑ “Using Inventory Labware Selection” on page 249

❑ “Reinventorying the Plate Management System” on page 252


Runset manager Controls the automated scheduling of groups of runs

❑ “About Starting Runs Automatically” on page 87

❑ “Working with Runsets” on page 88

❑ “Runset Examples” on page 91

JavaScript methods task.repeat() method added “Using JavaScript in VWorks” on page 202

Reset script context protocol rule

New rule that changes the context of global variables

“Using JavaScript in VWorks” on page 202

Save All command New ability to save the current protocol file, linker file and device file at the same time

“Compiling and Saving Protocols” on page 118

Bar code error handling New tab on Task Parameters Toolbar of plate instance

“Setting Up a Plate Instance” on page 112

Bar code task Renamed to Apply label task “Using Bar Code Data Files” on page 228

Alarm Settings All alarms are now set in one place “Adding an Alarm” on page 65

Rotate plates at VCode® feature

If a downstacked plate is turned 180 degrees from its correct orientation it can be reoriented on a VCode.

“Setting Error Options” on page 51

Attempt to put plates away if deadlock occurs

If a deadlock occurs, the plates are moved to the positions they would be in at the end of a successful protocol run.

“Setting Error Options” on page 51

Change Instance pipette task

New task performs replicate dispense operations

“Setting Change Instance Pipette Task Parameters” on page 175

Light Configuration Select the type of error lights that your BioCel has.

“Setting General Options” on page 48

Feature Description See...


6

Reporting BioCel ProblemsSending Us an Email If you find a bug in the Velocity11 software or are unable to solve a

technical problem, despite reading “Maintenance and Troubleshooting” on page 307, please let us know by sending us an email using the bug reporting feature of VWorks.

Requirements Before you can send a bug report:

❑ The BioCel computer must be connected to a network with internet access.

For more information about the network connection, see “Computers and Networking” on page 27.

❑ The outgoing email server must be set up on the system’s computer by a BioCel or network administrator.

Setting Up Email To set up the outgoing email server:

1. Select Tools > Options.

2. In the VWorks Options dialog box, click the Email Setup tab.

3. In the Mail Server Setup group box, enter the name of your SMTP (outgoing) email server.

4. If the server requires a user name and password:

a. Select the Server requires authentication check box.

b. Enter the User name and Password that you use to access email on the network.

This information only needs to be set up once, provided the email account remains active. All email sent from your BioCel is authenticated using this account.

Sending a Bug Report

A bug report is an email that you create and send from within VWorks. The email automatically identifies your BioCel and is sent directly to Velocity11.

To send a bug report:

1. Select Help > Report a bug.

2. Type a description of the error in the text box.

In your description, provide a summary of the error and, in the case of a software bug, a description of how we can reproduce it. Also include a phone number in case we need to contact you.

3. Attach the following files, which can help us to troubleshoot the problem:


a. Select the Attach log files check box.

b. Click the ellipsis button.

c. Browse to one of the files listed above and click Open.

d. Repeat step a and step b to attach each remaining file.

4. Click Email Velocity11 and wait until a Message Sent message box opens.

Registry File We may also ask you to send the Velocity11 registry file from the Windows® registry. In this case, follow the directions in the Database and Security User Guide for exporting a registry key to create a file. Export the key:

HKEY_LOCAL_MACHINE\SOFTWARE\Velocity11

File Find in...

Protocol file you were running when the problem occurred

The location set by your administrator when saving protocols.

The default location is C:\VWorks Workspace\protocols.

See “File Name Format” on page 45.

Device file The location set by your administrator when saving device files.

See “Saving a Device File” on page 221 for information about where to find a device file.

protocol log file The location set in log file options.

See “Setting Log Options” on page 60.

For general information, see “Protocol Log File” on page 57.


8

Reporting User Guide ErrorsAbout Feedback We greatly appreciate any feedback you can give us on our user guides.

We are especially happy to receive information about inaccuracies and missing features, but all comments are welcome.

Your comments will be reviewed promptly and referenced as the next version of the guide is developed.

Online Help Feedback

It only takes a minute or two to provide feedback using the feedback button in the Online Help.

Email You can also send an email directly to [email protected].

mailto:[email protected]


General BioCel Hazard WarningsIntroduction This topic gives more information about general hazards that are not

related to any particular procedure.

Before Using the BioCel

Before using the BioCel, your organization should make sure that you are properly trained in:

❑ General laboratory safety

❑ The correct and safe operation of the BioCel

❑ The correct and safe operation of the modules used with the BioCel

If you are the person in your organization responsible for training others on this product and you have a safety question relating to the BioCel, please take the time to ask us.

Overhead Door Injury Hazards

!! INJURY HAZARD !! Opened overhead doors are approximately 6 feet 2 inches (188 cm) above the floor. To avoid injury, be aware of the door height and position at all times when working around the BioCel.

!! INJURY HAZARD !! The pneumatic braces on overhead doors should be adjusted so you can comfortably open and close the doors. If you have to strain to open a door, please contact the Velocity11 Service Center and ask to have the braces adjusted.

Side Door Injury Hazard

!! INJURY HAZARD !! Always close the side doors when you finish the operation that led you to open them. Leaving side doors open creates a tripping hazard. It can also block escape routes in a laboratory.

0000

7

6 feet 2 in.188 cm


10

Overhead Door Damage Hazard

!! DAMAGE HAZARD !! Always open and close overhead doors using their handles. Opening and closing overhead doors by pulling and pushing on their corners may crack the glass and damage the pneumatic braces.

Computer Monitor Damage Hazard

!! DAMAGE HAZARD !! To avoid damage to the computer monitor, make sure that you move the monitor out of the way as you close the overhead doors.

12

Interlock Override Injury Hazard

!! INJURY HAZARD !! Only fully trained BioCel administrators should have access to, and use of, the safety interlock key. Use the override only when you know how the robot and VPrep modules will move during the protocol, when the robot speed is slow, and when you have taken measures to keep away from the areas in which the robot and VPrep parts will be moving.

With the interlock overridden, it is possible to be hit by the robot when it is moving. If this happens, the robot will immediately stop, minimizing injury, and the likely outcome is minor bruising. However, not all circumstances can be foreseen and more serious injury is possible. It is the responsibility of every operator to use the built-in BioCel safety features, follow warnings and safety labels and keep out of the robot’s radius whenever it is likely to move.

00008


Laser Warnings BioCel LasersYour BioCel contains lasers used to read bar codes. One bar code reader, attached underneath the robot arm, is used to read plates as they are picked up. Other bar code readers may be included on your system, attached to platepad readers, VPrep shelves or VCode printers.

!! INJURY HAZARD !! The BioCel bar code readers use class 2 lasers. Before using the BioCel, you should be trained in the safe use of these lasers.

The laser beam will not harm your skin so there is no danger in exposing your arms or hands to the beam. However, you could damage your eyes if you stare directly into the beam.

Bar code readers emit light for up to 0.5 seconds only when taking a reading so they are only a hazard during protocol runs. When a plate is being read, the beam should not pass beyond the plate. If you are operating the BioCel without plates, and with the overhead doors open, the risk of exposure is increased.

Before using the BioCel you should identify the locations of all bar code readers and establish the directions in which they point. All readers point downwards to minimize the potential exposure at eye level. The robot bar code reader represents the greatest hazard because of its height above the table. This bar code reader is angled downwards at 15 degrees and has a maximum illumination arc of 60 degrees, centered perpendicularly to the reader. With these measurements you can establish the space that is illuminated on occasions when there is no plate in the robot gripper.

!! INJURY HAZARD !! Class 2 laser hazard. Do not look directly at the laser beam. Looking directly at the laser beam may result in serious eye injury.!! INJURY HAZARD !! Do not disassemble the bar code reader sensor heads. Laser emission from the reader is not automatically stopped if the sensor head is disassembled.!! INJURY HAZARD !! Unless following a procedure in a Velocity11 user guide, do not touch the white test button on the side of the sensor head of an auxiliary bar code reader. This button turns on the laser creating the possibility of a long exposure to the beam.

Third-Party Module Lasers

Your BioCel may also contain lasers built in to third-party devices, such as Zeiss Multimode readers and Liconic incubators. For information about laser safety for third-party modules, see the relevant module’s documentation.


12

This chapter:

❑ Introduces the hardware, software and major systems

❑ Lists the modules that can be used with the BioCel® to automate laboratory procedures

BioCel Overview 2

Chapter 2: BioCel OverviewBioCel User Guide

14

Basic DescriptionIntroduction The BioCel is a microplate-processing automation platform that is used

in combination with modules for applications such as:

❑ Compound management

❑ Sample preparation

❑ Plate replication

❑ PCR purification

❑ High throughput screening

To operate the BioCel you should be familiar with the operating procedures in this guide as well as the guides for the modules installed on your BioCel.

Basic BioCel Components

Every BioCel includes:

❑ A frame

❑ A table

❑ A robotic arm

❑ A controlling computer, monitor, keyboard and mouse

❑ A main power panel and electrical supply circuits

❑ Communication hubs and cables

❑ A Bio I/O console for managing sensor information

❑ One or more uninterruptible Power Supplies (UPSs)

❑ An AC/DC converter (DC power supply)

❑ An air system that includes a main air panel, pressure regulators, an air filter and air lines

❑ VWorks™ software

❑ Software for each module

15Chapter 2: BioCel OverviewBioCel User Guide

Main External FeaturesDiagram The main external features of the BioCel are shown in the following

diagram.

Note: The exact locations of the components on your BioCel may be different.

0000

2

External connections

Power panel

Overhead door

Foot

Side door

Status light

Monitor

Keyboard

Frame post


16

Utilities ConnectionsDiagram There are usually four connections to external utilities on the BioCel, as

shown in the following diagram:

Utilities Location The connections are located on top of the BioCel above the power panel.

Direct Plumbing Your BioCel may also have direct plumbing lines for water and waste instead of reservoirs and waste containers.

0000

1

Main air line

Ethernet cable

Main power line

Main vacuum line


Power PanelDiagram The following diagram shows the power panel for a BioCel that is

equipped with a clean-room environment. The power panel on your BioCel may not include all of the features shown in this diagram.

Power Panel Functions

You can use the power panel to perform the following procedures:

About Opening the Power Panel

!! INJURY HAZARD !! The power panel should only be opened by a Velocity11® service technician or a BioCel administrator, working under the guidance of Velocity11 service staff. Do not force open the power panel door. It has a safety device to prevent it from opening when the main power switch on the power panel is turned on.

INTERLOCK RESET AIR

0

MAIN POWER

HOOD LIGHTS

0

EMERGENCY

STOP

00096

0

UV LIGHTS

0

Procedure See...

Turn on and off the main power and air supplies to the BioCel

“Turning On the BioCel” on page 37

Override the safety interlock “Overriding the Safety Interlock” on page 314

Activate an emergency stop “Stopping a Run” on page 95

Reset the safety interlock after an emergency stop has been activated

“Emergency Stop Error Recovery” on page 311

Check the status of the BioCel “Monitoring a Run” on page 99


18

Hardware Control ComponentsOverview Diagram The main hardware control components are shown in the following

diagram.

Note: The exact locations of the components on your BioCel may be different.

The components located behind the other side doors vary with the modules used on your BioCel.

Communication Hubs

The Ethernet and RS-232 hubs form communications connections between a single cable connected to the computer and multiple cables going to devices. This allows the BioCel’s computer to communicate with many devices at once.

You should not need to touch the communication hubs.

Bio I/O Console The Bio I/O console:

❑ Makes information from analog and digital sensors available to the computer.

❑ Initiates actions such as turning on the status lights, and opening and closing optional trash and enclosure doors.

Many of the thin, gray, low-voltage cables that run through the BioCel go to the Bio I/O.

You should not need to touch the Bio I/O.

EXHAUST FAN INTAKE FAN RECIRCULATING FAN

00097

Power strip

Computer

DC power supply

UPS

Ethernet hub

RS-232 hub

Air panel

Bio I/O

Robot and system power switches

Fan controls


Air Panel Diagram

Function

The air panel contains components that control the flow of air to all parts of the BioCel.

Component Description

The main air pressure regulator and main shutoff valve lie in between the main air line that provides house air and the AIR switch on the power panel.

Note: The AIR switch is usually used to turn the air supply on and off. You should not need to use the main shutoff valve.

The interlock air shutoff valve shuts off air to moving parts when the interlock circuit is interrupted.

The air filter provides an extra purification step for house air. You should not need to adjust the air gauges.

PlateLoc Air Filter

!! IMPORTANT !! PlateLoc® modules intended for use with the BioCel do not contain an air filter. If you plan to remove a BioCel PlateLoc for use in stand-alone mode, you must contact Velocity11 and arrange to have a filter installed. Without a filter your PlateLoc may become damaged.

More Information

For more information about the functions of air on the BioCel, see “Air System” on page 23.

0001

0

Robot air pressure regulator

Optional enclosure door air pressure regulator

Interlock air shutoff valve

Main shutoff valve

Optional waste door air pressure regulator

Main air pressure regulator

Air filter


20

Power SystemIntroduction This topic summarizes the power system of the BioCel. Becoming

familiar with how your BioCel is wired will help you to understand the behavior of your BioCel and troubleshoot problems.

Overview Diagram The power system is summarized in the following diagram.

Ethernet hub

VPrep Pump

Optional enclosure

door controllerModuleDevice

Monitor

PC

RS-232 hub

UPS

Robot DC

power

supply

Robot

Bio I/O console

Device

Post-emergency stop power strip

Emergency

stop

relay

Pre-emergency

stop block

AC power in

Cooling fans

Main

switch

Fuse

Door

interlocks

Interlock switch

Emergency

stop

button

System DC

power

supply

Emergency

stop

buttonReset

ButtonInterlock

override

VPrep

Pre-emergency stop power strip

Post-emergency stop power strip

Clean room intake

and recirculation fans

ModuleModuleModuleDevice

iSeries control console

Clean room output fan

UV lights

Incubator environmental control

Power panel


In the diagram, dotted lines are control “enable” circuits and solid lines are AC and DC power circuits. The dot-dash line indicates those elements that lie inside the power panel. The dotted line between the robot DC power supply and system DC power supply indicates that the two power supplies are housed in the same box.

Main Power The main AC power enters at the external connections and travels down inside the corner post to the power panel. It passes through a main fuse, through the main switch, and out of the power panel to the UPS.

Pre-UPS, Pre-Emergency Stop Current

If your BioCel includes environmental control or a clean-room, one or more electrical lines branch off before the UPS. These lines supply current to the following options:

❑ Environmental controller console that houses the iSeries controllers for the main BioCel (not for any separate environmental enclosures)

❑ Liconic incubators (environmental control, not transfer mechanism)

❑ UV lights and hood lights

❑ Clean-room output fan

These options therefore receive pre-UPS, pre-emergency stop current. They are not affected by emergency stops or interlocks but are also not buffered by the UPS from power outages.

UPS Connections If there is more than one UPS, they are connected in series so that current output from UPS 1 supplies the current input for UPS 2. The UPS, or UPSs, provide current backup to the monitor, PC and communications hubs. If there is more than one computer and more than one UPS, one computer is fed from one UPS and the other computer is fed from the other UPS.

From the UPS, current is passed back into the power panel and through the main switch to the rest of the BioCel. This means that when you turn off the main switch current is cut to the UPS, but it is also cut between the UPS and the main part of the BioCel, preventing the BioCel and its modules from draining the UPS. The UPS will continue to be drained by the computer, monitor and communication hubs, which is why the shutdown procedure includes a step for turning off the UPS. For more information, see “Shutting Down the BioCel” on page 107.

Pre-Emergency Stop After the main switch, the electrical line enters a bank of connections in the power panel known as the pre-emergency stop block. A pre-emergency stop power strip is connected to this block. Modules and devices wired from the pre-emergency stop power strip do not have their power cut when an emergency stop is activated. For example, the robot retains power after activation of an emergency stop because its DC power is supplied by the robot DC power supply fed from the pre-emergency stop block.


22

Emergency Stop and Interlocks

An electrical line from the pre-emergency stop block enters the emergency stop relay which controls the emergency stop circuit. One output from the emergency stop relay powers an interlock circuit switch. Another output supplies the BioCel power strips from which most of the BioCel modules, devices and system components receive current (exceptions to this are the VPrep, VPrep pumps, Ethernet hub, and clean-room intake and recirculation fans). These modules, devices and system components are all wired after the emergency stop and therefore receive no current when an emergency stop is activated. This includes the Bio I/O and cooling fans, which use DC electricity produced by the system DC power supply.

If an emergency stop is activated, the reset button must be pushed to reset the emergency stop relay to a position that allows current to flow.

The door interlock system is fed AC electricity from the emergency stop relay. If an overhead door is opened during a run, the interlock switch cuts power to the enable wires that lead to the robot, VPrep, VPrep pumps, and clean-room intake and recirculation fans. This stops the robot and VPrep motors and turns on their respective z-axis brakes. The brakes make sure that the VPrep head and robot do not drop, preventing damage and eliminating a crushing hazard.

The interlock switch is bypassed when the interlock override switch is activated by turning a key on the power panel. This maintains current in the enable wires even when the overhead doors are open.

For more information about how individual components are affected by activation of emergency stop and interlocks, see “Stopping a Run” on page 95.


Air SystemAir and Power Interaction

The following diagram shows how the air and power systems interact. Becoming familiar with these systems will help you to understand the behavior of your BioCel and troubleshoot problems.

For more information, see “Power System” on page 20.

Air System Description

Air is used on the BioCel to:

❑ Move parts, such as the robot gripper, VStack® grippers and VPrep shelves

❑ Create vacuums, such as for the suction-based lid remover

The flow of air through the system is controlled by air pressure regulators. Many modules have their own, built-in regulators. Air pressure to other parts is controlled by regulators in the air panel of the BioCel.

The diagram above shows how air to the BioCel can be cut off during a run by:

❑ Pressing an emergency stop button

❑ Turning off the AIR switch on the power panel

❑ Turning off the main air shutoff valve in the air panel

❑ Turning off the main power in the power panel

Module

Module

Module

Module

Module

Secondary

distribution

manifold

Main

distribution

manifold

Robot

Optional

waste door

AC power in

Main regulator

Main air

shut-off valve

Interlock air

shut-off solenoid

Regulators

Main

switch

Emergency

stop circuit

Air

switch

Power panel

Main air line

Optional environmental

enclosure door

Secondary

distribution

manifold

Air panel


24

Vacuum SystemVacuum Flow Diagram

The following diagram shows the vacuum flow in the optional vacuum system.

Vacuum System Description

A vacuum may be used on the BioCel for:

❑ Filtration stations

❑ Suction to hold plates flat on a VPrep shelf or VStack stage

The vacuum can be supplied by a pump or house vacuum system. If a house vacuum system is used, the main vacuum line enters the BioCel with the other external connections. For more information, see “Utilities Connections” on page 16. If a pump is used, it will be located on the floor of the BioCel.

A reserve vacuum tank may be used to ensure an instantaneous vacuum supply.

Waste liquid produced by filtration stations is collected in one or more waste containers.

Vacuums are also created in modules and accessories using vacuum ejectors that create the vacuum at the site where it is required, such as at the suction-based lid remover. For more information, see “Lid-Removal Devices” on page 31.

Main vacuum line

Reserve tank

Distribution manifold

VPrep VStack

Pinchvalve

Filtration station

Pump

Wastebottle(s)


Clean-Room Filtration SystemIntroduction This topic is relevant to you if your BioCel is equipped with a clean-room

filtration system.

System Description Air enters the BioCel through a small intake fan. It is then sucked into a vertical duct at one corner post and either expelled to the outside by a small exhaust fan or returned to the BioCel by a large recirculating fan. All fans are mounted in the ceiling and include ULPA clean-room 1000-class filters that remove airborne particles.

The speed of each fan is controlled by dials on the fan console (see “Hardware Control Components” on page 18 for more information). Adjust the fans to create the flow of air that you want. You can make adjustments to create a positive or negative air flow.

The input and recirculation fans turn off when the overhead doors are opened, but the output fan remains on. For more information, see “Power System” on page 20.

Standards Testing Your BioCel has been tested to make sure that the environment enclosed by the overhead doors meets or exceeds Class 6 of the ISO 14644-1 clean-room standard, and USA Federal Standard 209.

The USA clean-room 1000 standard requires that there are no more than 1000 particles per cubic foot that exceed 0.5 µm in diameter.

During testing, the concentration of airborne particles in the BioCel was measured using a discrete-particle-counting instrument, model HHPC-2 purchased from Hach Ultra Analytics. We recommend that you purchase your own counter and periodically test the system. For more information, see:

http://www.hachultra.com/

Replacement Filters Replacement filters can be obtained from:

http://www.precisionaire.com.

The filters are minipleat ULPA filters that remove 99.99% of particles with diameters greater than, or equal to, 0.12µm, and meet 1000 clean-room standards.

Filter Size Dimensions (inches) Part Number

Large 24 x 48 AP591-2448

Small 24 x 24 AP591-2424

http://www.precisionaire.com

http://www.hachultra.com/


26

Fan Specifications The recirculating fan is large, and the input and exhaust fans are small.

Property Large Fan Small Fan

Air flow (cfm) (L/s) 1177 (530) 170 (76.5)

Power (W) 163 40

Noise Intensity (dB) 67 60


Computers and NetworkingComputer Functions The BioCel computer is used to:

❑ Control the BioCel and its modules.

❑ Input bar code labelling instructions.

❑ Store and export log files.

❑ Store and export data collected by plate readers.

Note: Some plate readers have their own computer for storing data.

❑ Communicate with other computers on your organization’s network for the exchange of files, reporting of errors and accessing email.

Network Cards If you are an administrator and you need information about the network cards in the BioCel, see “Network Cards” on page 257.

Module Computers If your BioCel has a module that includes its own computer, such as the Zeiss Multimode plate reader, the same monitor is used for both computers. You can switch the monitor display between the two computers.

This feature is a property of the monitor switching device.

To switch the monitor display between two computers:

1. Rapidly press the SCROLL LOCK key on the keyboard twice.

Adjusting the Keyboard ShelfGeneral Information You can adjust the computer shelf to position the keyboard, monitor

and mouse to suit your requirements. To make the adjustments, swivel the shelf at the appropriate shelf joints. You can loosen or tighten the joints by prying off the joint covers and making the adjustments with a wrench.


28

BioCel ModulesDefinition Modules are individual pieces of equipment that sit on the BioCel table

and manipulate microplates. Every module is also a device, although not every device is a module. For a definition of devices, see “Working With Device Files” on page 221.

Velocity11 Module List

The following Velocity11 modules can be used on a BioCel.

Third-Party Modules The following third-party modules can be used on a BioCel.

Module Description and Comments

PlateLoc Thermal plate sealer

PlatePierce™ Seal piercing station

VCode® Bar code print and apply station

VPrep® Pipetting station

VSpin™ Microplate centrifuge

VStack Labware stacker

VersaScan™ Microplate reader


ASYS Hitech GmbH

FlexiSpense

Automated liquid dispenser

BioRad Ultramark Plate reader

Bio-Tek ELx405 Washer Automated microplate washer

Genetix aliQuot Low volume liquid dispenser

Genetix QFill2 Dispenser

Automated liquid dispenser

Innovadyne Nanodrop Automated liquid pipettor

H+P Labortechnik AG

Teleshake

Plate shaker

Labcyte Echo 550 Compound reformatter

Liconic StoreX Plate incubator

PerkinElmer Envision Plate reader

RempCSP Plate sealer


If there is product that you would like to add to your BioCel, please contact Velocity11 for customization information.

Thermo-Electron Multiskan Ascent

Plate reader

Thermo Labsystems Multidrop

Automated microplate filler

Zeiss Multimode Plate reader



30

Optional BioCel ComponentsAvailable Accessories

One or more of the following optional components may be present on your BioCel.

Plate Hotel A plate hotel stores a smaller number of plates than a VStack, but unlike the VStack, the robot has immediate, random access to all plates.

You can remove the hotel from the BioCel to access plates from the front, or leave the hotel in the BioCel and access plates from the back. For more information, see “Placing and Removing Hotel Plates” on page 76.

Accessory Description and Comments

Auxiliary bar code reader

One or more bar code readers attached to a platepad or other device

Environmental Enclosure

Glass-enclosed area for controlling temperature and humidity

Suction-based lid remover

A static arm with suction cups that removes lids from plates and drops them into the waste bin

Lid hotel A tower that removes and holds up to 10 plate lids with random access to the lids.

Module shelf Semi-circular shelf for holding a second tier of modules

Plate hotel Plate stacking shelves that allow random, access to any plate in the stack

Refrigeration block Lidded table position for cooling microplates

VShuttle A device with one or more pairs of rotating platepads that are used to transfer a plate between two robots.

Weigh Pad A base that sits underneath a liquid container and reports the percentage of liquid in the container.


Transfer Station The transfer station is a special platepad used to transfer a plate between the StoreX and the BioCel robot. Some transfer stations, such as the one shown in the following diagram include two platepads.

Lid-Removal Devices The BioCel supports two types of lid-removal device.

Suction-Based Lid Remover

The suction-based lid remover sits over the waste opening in the table. It uses one or more suction cups to remove plate lids. The vacuum used to hold the lids is created by a vacuum ejector, which uses an air line rather than a vacuum line.

Lid Hotel

The lid hotel† is able to store lids so they can be returned to the plates that they were removed from. It includes a sensor at each lid position so the system knows which positions contain lids. Unlike with a plate hotel, a lid hotel cannot be removed from the BioCel table.

Lidded plates are brought to the lid hotel, so that the lids are held by the rollers. The robot then pulls the plate down, leaving the lid behind.

00088plate hotel

00

08

8

00105transfer station

0010

5


32

†Concept developed by Novartis Pharma AG, NIBR/DT/IAT, Basel, Switzerland.

VShuttle The VShuttle shown below has two decks, each with a pair of rotating plate pads. It allows plates to move between robots while maintaining the same orientation.

00087plate hotel

0008

7

00109


Weigh Pad Weigh Pads are available in different sizes. They report the percentage of a liquid in a container that sits on the Weigh Pad.

00110Weighpads


34

This chapter describes how to start the BioCel® and prepare it to run an existing protocol. All of the procedures in this chapter can be performed by someone with Operator privileges.

Preparing for a Run 3

Chapter 3: Preparing for a RunBioCel User Guide

36

Preparing a Run: Workflow OverviewWorkflow Steps The general workflow for starting the BioCel and preparing for a run is

given in the following table:

Step Topic

1. “Turning On the BioCel” on page 37

2. “Logging In To the Operating System” on page 39

3. “Starting VWorks” on page 40

4. “Logging In To VWorks” on page 41

5. “Opening a Protocol in VWorks” on page 47

6. “Setting General Options” on page 48

7. “Setting Error Options” on page 51

8. “Setting Protocol Options” on page 53

9. “Pipetting Order Rule” on page 54

10. “Setting Log Options” on page 60

11. “Understanding the Protocol” on page 68

12. “Adding an Alarm” on page 65

13. “Preparing Plates, Modules and Accessories” on page 69

14. “Placing and Removing Hotel Plates” on page 76

15. “Setting Up a VSpin Counterweight Plate” on page 77

37Chapter 3: Preparing for a RunBioCel User Guide

Turning On the BioCelIntroduction If your BioCel is not already on, turning it on is the first step.

Procedure To better understand what is happening as you turn on the BioCel, refer to the description of the “Power System” on page 20.

To turn on the BioCel (part one):

1. Make sure that the main power line, air line, vacuum line (optional) and Ethernet cable (optional) are plugged in, as shown in “Utilities Connections” on page 16.

2. Make sure that external drains and water lines are attached if your BioCel uses them.

3. On the power panel, turn the main power switch to the ON position.

The main power indicator light on the power panel remains off and this action does not appear to do anything. This is correct. For a diagram, see “Power Panel” on page 17.

4. Open the side door to the controls.

5. Push the UPS (uninterruptible power supply) power button to allow the UPS to supply electricity.

The UPS LEDs illuminate to indicate the UPS power status.

If you have more than one UPS on your BioCel, make sure you turn them all on. The UPSs are connected in series, so turn on the UPS that is connected to the main power first followed by the remaining UPSs in the order in which they are connected together.

For more information about operation of the UPS and meaning of the status lights, see the third-party UPS documentation provided with your BioCel.

6. Turn on the DC power supply switches labelled Robot and System, as shown in “Hardware Control Components” on page 18.

The switch lights turn on.

To turn on the BioCel (part two):

1. Check that the lights on the Ethernet and RS-232 communication hubs are on.

Refer to “Hardware Control Components” on page 18 for a diagram.

2. If the monitor is off, turn it on.

3. Make sure that all modules are turned on.

4. Push the computer on/off button to start the computer.


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The computer performs self-tests, starts the operating system, and opens the Welcome to Windows screen.

5. Close the door.

See “General BioCel Hazard Warnings” on page 9 for injury hazards associated with the BioCel side doors.

6. Make sure that the emergency stop button on the power panel and the emergency stop buttons on the tabletop are in the out position.

For more information about emergency stops, see “Stopping a Run” on page 95.

7. Close the overhead doors.

See “General BioCel Hazard Warnings” on page 9 for damage and injury hazards associated with the BioCel overhead doors.

To turn on the BioCel (part three):

1. On the power panel:

a. Check that the INTERLOCK light is on.

This indicates that the overhead doors are closed, provided the interlock override is not in use.

b. Press the RESET button and check that its indicator light is on.

This resets the emergency stop circuit.

c. Turn the AIR switch counterclockwise and check that the indicator light is on.

This turns on air to the modules.

2. If you use modules or devices that require a vacuum created by a vacuum pump:

a. Check that the gauge on the vacuum pump indicates a vacuum pressure.

b. Make sure that the vacuum system is connected correctly.

For more information, see “Vacuum System” on page 24.

3. If you use modules that require a gas supply, such as a StoreX incubator, make sure that the supply is turned on.

4. Make sure that all four lights on the power panel are on.

For more information, see “Power Panel” on page 17.

If you have not previously selected the option to sense the air pressure automatically (see “Setting General Options” on page 48) check that the operating pressure is 90–100 psi (0.62–0.69 MPa) for

On/off button


the main regulator and 40–50 psi (0.27–0.34 MPa) for the robot regulator.

5. Turn on the modules if they are not already on.

For more information, see the module’s user guide.

BioCel Ready State CheckReady State Conditions

When the BioCel is on and ready for a protocol to be opened:

❑ The status lights are off.

❑ All devices are on, pneumatic devices are supplied with air, and a vacuum is supplied where used.

❑ The computer is on and ready for a user to log in to the operating system.

❑ The UPSs are charged, ready to provide battery backup if the main AC power supply is cut.

❑ All doors are closed.

❑ The interlock override is off so that opening an overhead door or pressing an emergency button will activate the emergency stop circuit.

Logging In To the Operating SystemOverall Process Log in to the Windows® operating system on the computer after

following the directions in “Turning On the BioCel” on page 37.

To see how this procedure fits in to the overall process of performing a run, see “Preparing a Run: Workflow Overview” on page 36.

Procedure To log in to the Windows operating system:

1. At the Welcome to Windows screen, press CTRL + ALT + DELETE.

2. At the Log On to Windows screen, type your user name and password.

3. If necessary, in the Log on to text box, type the name of the network domain to which your BioCel is connected.

Contact your network administrator if you do not know your network domain name. You should only need to type in this name once as the system will remember it.

4. Click OK.


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Starting VWorksOverall Process To see how this procedure fits in to the overall process of performing a

run, see “Preparing a Run: Workflow Overview” on page 36.

Starting VWorks To start VWorks:

1. Make sure that everyone is clear of the table and there are no objects on the table that could obstruct the robot.

!! INJURY HAZARD !! When VWorks™ starts, the robot and module parts may move to their home positions.

2. Double-click the shortcut to VWorks on the Windows® desktop.

Note: If the shortcut has been deleted, open the folder C:\VWorks Workspace\bin and create a new shortcut from the executable file VWorks<version>.exe.

If you receive an error at this point, refer to “Maintenance and Troubleshooting” on page 307.

The VWorks splash screen opens, which you can dismiss by clicking the mouse or pressing any button.

VWorks opens at the Progress tab.


Logging In To VWorksUser Account To log in to VWorks you need a VWorks user account, created by an

administrator.

For information about user accounts, see the Database and Security User Guide.

Logging In To log in to VWorks:

1. Click the Log In button.

2. Select your account user name from the list box.

3. Type your password and click OK.


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About Tasks, Processes and ProtocolsIntroduction Before you can read protocols, you need to know the definitions of the

terms in this topic.

Plate Instance Defined

A plate instance represents the basic information about a plate or collection of plates and is the first icon in a process displayed in the protocol editor. The information it represents includes the type of labware used in the process, how many plates are available for processing at one time, whether the plates have lids, and so on.

The following icon represents a plate instance for a tipbox.

For information about creating a plate instance, see “Setting Up a Plate Instance” on page 112.

Task Defined A task is an operation that is performed on one or more plates and is represented by an icon in the protocol editor. It has associated parameters that are defined in the Protocol Task Parameters toolbar.

The following icon represents a task for downstacking plates.

Process Defined A process is a sequence of tasks that are performed on a plate instance.

The following diagram shows a process with one plate instance icon and four task icons.

How a Plate Instance and Task Differ

Although the icon for a plate instance looks like a task icon its function is different because it does not represent an action in a protocol. This distinction becomes important when you are interpreting error messages. Consider the following example:


This error refers to task 2, which is the Pipette Process task in the following diagram, and not the downstack task. The first icon is the plate instance.

Protocol Defined A protocol is a collection of processes that run at the same time, as defined in the protocol editor.

The following diagram shows one protocol with two processes.

Pipette Process Task Defined

A Pipette Process task is the parent of a sequence of pipette tasks that perform liquid handling procedures using a VPrep®. A pipette process is sufficiently complex that it has to be defined by a group of separate sub-tasks, each with its own parameters.

An icon for a Pipette Process task is shown below.

Pipette Process Link Icon

The pipette process link icon is always the first icon in a pipette process. The icon performs a similar function to a plate instance in that it does not represent a task itself and is the first icon in a protocol. However, the pipette process link icon only has one parameter, which is used to link a Pipette Process task in the protocol editor to a pipette process in the pipette process editor.


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Pipette Task Defined A pipette task is an operation that is performed on one or more plates by a VPrep. It is represented by an icon in the pipette process editor.

The following diagram shows a pipette task.

Pipette Process Defined

A pipette process is a sequence of pipette tasks that a specific plate performs, as defined in the protocol editor. It is a subroutine of a Pipette Process task.

The following diagram describes the relationship between a task, pipette task and a pipette process.

Run Defined A run is a single protocol that cycles one or more times in a series.

When you start a run, you are prompted to enter the number of plates that you want to run. The value that you enter represents the number of times the protocol executes before the run ends. For example, a value of four means that the protocol will run four times in the series.

Task Pipette process Pipette task


About Protocol FilesFile Name Format The configuration settings associated with a protocol are stored in a

protocol file that is named <file name>.pro. Protocol files are stored in a folder location determined by an administrator at the time they are saved.

XML Format Protocol files are written in XML (Extensible Markup Language), in which markup tags indicate the protocol’s properties, and text within the markup tags gives the properties’ values.

A protocol file viewed in an XML editor that color-codes text is shown below.

You can also open a protocol file in any browser that contains an XML parser, such as Internet Explorer, version 4 or later.

Most users will create and edit protocols through VWorks. Advanced users have the option of creating and editing protocols directly in XML.

XML Schema To create and edit protocols directly in XML, you need to know the XML schema that defines the logical rules of a VWorks protocol. If you are interested in using XML directly, please contact the Velocity11 Service Center.


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More InformationFor more information about... See...

The data stored in a protocol “Understanding the Configuration Settings in a Pipette Task” on page 219

Protocol-related terms “About Tasks, Processes and Protocols” on page 42

Instructions for creating a protocol

“Creating a Protocol: Workflow” on page 110

Opening a protocol “Opening a Protocol in VWorks” on page 47


Opening a Protocol in VWorksWhen to Use Use the procedure in this topic to open a protocol that has already been

created.

To see how this procedure fits into the overall process of performing a run, see “Preparing a Run: Workflow Overview” on page 36.

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Procedure To open a protocol:

1. Select File > Protocol File > Open.

2. Navigate to the folder containing the protocol file.

The default folder is C:\VWorks Workspace\protocols, but this may have been changed by an administrator.

3. Select the protocol file and click OK.

Note: You can also open a protocol by navigating to the .pro file in Windows and double-clicking it. This will launch VWorks™ and open the protocol.


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Setting General OptionsIntroduction General options include:

❑ General device settings

❑ The location of the bar code data file

❑ The maximum robot speed option

❑ The task icon visibility option

❑ UPS settings

Procedure You may decide to keep many of the options the same for every run. If you use bar code input or data files, though, remember to select the correct file for every run.

To set general options:


The Options page of the VWorks Options dialog box opens.

2. In the Device Settings group box, select from the following options:

Option When selected...

Check for minimum air pressure The system air pressure is continuously monitored.

If the pressure falls below the value specified in the text box, an error is generated.

The units of pressure specified in the text box are pounds per square inch.

Enable BioIO on COM port The Bio I/O functions work.

The COM port text box identifies the communications port to which the Bio I/O serial cable is connected. You should not need to change this number.

Check trash receptacle on BioIO input

The waste-fill sensor is activated, if your BioCel has one.

The input text box specifies the number of the Bio I/O input port to which the sensor is connected.

The selected high or low radio button determines whether a high or low signal from the sensor corresponds to a full waste bin.

You should not need to change these settings.


3. If you are using a bar code input file or bar code database file, select its location:

a. In the Bar Code Settings group box, click the Bar code input file or Bar code database file ellipsis button.

b. In the browse dialog box, navigate to the folder that contains the bar code input file.

c. Select the file (with a .bar or .dat file name extension) and click Open.

4. In the Robot Settings group box, select the maximum relative speed at which the robot will move.

!! DAMAGE HAZARD !! If you are testing a new protocol or learning to use the BioCel, run the robot at a slow or medium speed to reduce the risk of damage in the event of a crash.

5. If you want to hide task icons that are not relevant to your BioCel module configuration, select the check box in the Protocol Editor Settings group box.

This makes it easier to locate and drag task icons when creating a protocol.

6. In the UPS Settings group box, select from the following options:

Light configuration Selects the type of lights on your BioCel: standard blue or red-yellow-green.

You should not need to change this setting.

Enable measurements and alarms

Allows the BioCel to read data from iSeries and StoreX environmental control systems and set alarms at defined thresholds.



Use UPS on COM... Identifies the communications port to which the UPS serial cable is connected. If more than one UPS is connected, it identifies the port for the primary UPS.

You should not need to change this number.

Use additional UPS on COM... Identifies the communications port to which a secondary UPS serial cable is connected.

You should not need to change this number.


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7. Click OK to close the VWorks Options dialog box.

Halt scheduler when battery level drops below...

The scheduler stops scheduling tasks when the battery power falls below the percentage specified in the text box.

If your BioCel has two UPSs, the value in this text box should be half of the value you would use with a single UPS. For example, if you want the scheduler to stop when the battery power drops below 80% of the total available power, type 40 into this text box.

Power down system when battery level falls below critical power level

When the battery power falls below the level specified in this text box, the BioCel and computer are powered down.

Additionally power down this remote system

Allows a remote computer, such as that used by a plate reader, to be shut down in the event of a power outage.

UPS diags Provides information about the primary UPS, including the source of power, UPS temperature, remaining charge and power draw.

UPS2 diags Provides information about a secondary UPS, including the source of power, UPS temperature, remaining charge and power draw.



Setting Error OptionsIntroduction Error options include:

❑ General error options

Error reporting options

Error handling options

Scheduler error behavior options

❑ Protocol Error Handling options

Setting General Error Options

To set general error options:


2. Click the Error Handling tab of the VWorks Options dialog box.

3. In the Error Reporting group box, select the modules for which you want to report errors.

Typically, all of the modules are selected for a run. If you want to perform a test run without plates, clear the options for modules used in the protocol that would otherwise report errors.

!! DAMAGE HAZARD !! A robot collision may occur if any of these options are cleared during a protocol run.

4. Select from the following options in the Error Handling group box.

Option When checked...

Sound alarm on output... An alarm will sound in the event of an error. The alarm generates a sound, opens a message box, and causes the status lights to flash.

The number in the text box refers to the output connection on the Bio I/O console to which the alarm is connected. You should not need to change this number.

Send Email when errors occur The email address listed in the Email tab of the VWorks Options dialog box will receive an email for every error notification.

For more information, see “Notification of Errors by Pager or Email” on page 103.

Halt on bar code misreads The robot will complete currently scheduled steps and then stop. The type of error that causes this is a bar code misread.

For more information, see “Types of Bar Code Misread Errors” on page 315.


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5. In the Scheduler Error Behavior group box, select one of the following options:

6. Click OK to close the VWorks Options dialog box.

Halt on bar code database lookup errors

An error message will open if there is a mismatch between the bar code’s fields on the reference west or south side and the bar code data file.

Launch program if error occurs...

A program that you specify is launched. You must specify the program by clicking the ellipsis button (...) and browsing to the program’s executable (.exe) file. With the appropriate script, this function can be used to send a page or an email.

If you want to pass the text of the error message to the program, select the “Add error text as command line argument” check box.

Halt if available disk space... The robot will complete the currently scheduled step and then stop if the percentage of available hard disk space is less than the percentage specified in the text box.

Option When checked...

Option When selected, in the event of an error...

Process as many plates as possible

As many tasks as possible, given the error, will be completed.

Continue processing without starting any new plates

Tasks involving plates that are currently available to the robot will continue. Other tasks will not be scheduled.

Stop scheduler The scheduler will stop scheduling new tasks, even if plates are currently available to the robot. The current task continues to completion.


Setting Protocol OptionsIntroduction Protocol options are set in the Protocol Options dialog box. There are

four groups of protocol options.

Setting Protocol Error Handling Options

To set protocol error handling options:

1. Navigate to Tools > Protocol Options.

2. In the Error Handling group box, select either or both of the following options:

Protocol Option See...

Device File “Working With Device Files” on page 221

Description/Notes “Compiling and Saving Protocols” on page 118

Rules “Pipetting Order Rule” on page 54

Error Handling This topic

Option Description

Rotate plates at VCode feature If a downstacked plate is turned 180 degrees from its correct orientation it can be reoriented on a VCode.

This only applies to VCode3 models.

Attempt to put plates away if deadlock occurs?

If a deadlock occurs, the lids are replaced and the plates are moved to the positions they would be in at the end of a successful protocol run.


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Pipetting Order RuleIntroduction There are two rules in the Protocol Options dialog box:

❑ Pipette plates in instance order, which is explained below

❑ Reset script context (erases all variables) before protocol executes, which is explained in “Using JavaScript in VWorks” on page 202

Pipette Plates in Instance Order

Default Setting

The default setting for the Pipette plates in instance order rule is for it to be checked, and it should be left checked for most protocols.

When to Clear the Rule

If your protocol has all of the following attributes, consider clearing the rule check box:

❑ The protocol will run for more than one cycle, which you define in the Number of Cycles dialog box after starting the run.

❑ The protocol has more than one pipette process that uses the same VPrep.

❑ The duration of one of the pipetting operations is much longer than another.

Explanation

Consider an example in which a protocol has two processes and both have a pipetting operation that uses the same VPrep. When the check box is selected, the pipetting operations for one process are completed before the pipetting operations begin for the other process.

Now consider what happens when the first pipetting operation takes significantly longer to complete than the second operation, and the protocol is run several times in succession. The overall time taken for the protocol to complete is much greater than it needs to be because during each cycle the system had to wait for the slower pipetting operations to complete for all the plates in the process before it could continue.

If the rule is turned off, a plate from the fast pipetting process can be delivered to the VPrep after a plate from the slow pipetting process, followed by another plate from the slow pipette process, and so on. This reduces the bottleneck at the VPrep because it allows the faster process to continue, and its second cycle in the series to start before the first cycle is complete.


Procedure To pipette plates in the order of the plate instance:

1. Select Tools > Protocol Options.

The Protocol Options dialog box opens.

2. In the Rules group box, select the Pipette plates in instance order check box.


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About Log and Data FilesIntroduction This topic describes the different types of log and data files that the

BioCel creates.

For directions for how to set up log files, see “Setting Log Options” on page 60.

Types of Log and Data Files

Log files record event and error information in text files that can be useful for troubleshooting. Data files record data collected by modules such as plate readers.

The locations of five log files, a data file, and a folder are set in the Log Options page of the VWorks Options dialog box.

These are listed in the following table, and described in more detail later in this topic.

Note: You can change the default file names to suit your own needs.

File or folder Default File or Folder Name

Protocol log file log.txt

Pipettor transfer log file piplog.txt

Bar code log file barcodelog.txt

Reader output file Reader.dat

Measurements output file environment.txt

Image file root folder A folder that you select


About Opening Log Files

You can open a log file in any text editor, but we recommend that you use the Windows application Notepad because you can open the file during a run as the file is being written.

Protocol Log File The protocol log file records all available event and error information.

A protocol log file, opened in Notepad, is shown in the following diagram.

During a run, you can type notes that are added to this log file. For more information, see “Working with the Log Toolbar” on page 104.

Pipettor Transfer Log File

The pipettor transfer log file is a tab-delimited text file that records VPrep pipetting information.

Note: This log is not the same as the log generated by the VPrep.

The pipettor transfer log contains the following information, separated by tabs:

❑ Timestamp

❑ Pipettor name, and number of channels on the head, given in parentheses

❑ Name of the position pipetted from in the process


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❑ North bar code

❑ East bar code

❑ South bar code

❑ West bar code

❑ Quadrant of the position aspirated from (number 1–16)

❑ Dispense timestamp

❑ Name of the plate dispensed to

❑ North bar code

❑ East bar code

❑ South bar code

❑ West bar code

❑ Quadrant of the plate dispensed to (number 1–16)

❑ Volume of liquid dispensed in microliters

❑ Status of the dispense

Values are ERROR or OK. These refer to the status of the bar code verification and not the dispense itself.

Note: One pipettor transfer log entry is created for every dispense task pair. For example, if 20 µL are aspirated and half is dispensed to one plate and half to another plate, two entries are created because it is treated as two aspirate-dispense pairs.

Bar Code Log File The bar code log file contains the date and time at which each bar code is applied, and the text of each field. Bar Code fields are displayed in human readable form.

For more information, see “Setting Apply Label Task Parameters” on page 127.

Reader Output File The reader output file defines the location of the data file (<file name>.dat) for the Ultramark plate reader. For more information, see “Ultramark Plate Reader Data File” on page 256.


Measurements Output Log File

What is RecordedThe measurements output log file records measurements made by iSeries, StoreX and Weigh Pad devices.

iSeries Measuring Units

The measuring units displayed in the log file are whatever measuring units are configured on the iSeries device. Typically, the temperature is recorded in degrees Celsius and the humidity is recorded as a relative humidity percentage.

Weigh Pad Measuring Units

The Weigh Pad records liquid volumes as percentage of the maximum.

StoreX Measuring Units

The measuring units recorded by a StoreX device are temperature, in degrees Celsius, humidity in relative humidity percentage, and gas concentrations in percent (by volume).

VersaScan Image File Root Folder

The image file root folder sets the folder in which images from a VersaScan™ are automatically stored.


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Setting Log OptionsIntroduction This topic explains how to configure the log options page of the VWorks

Options dialog box. You may not need to configure these options for every run.

Available Options There are three types of log options on the BioCel:

❑ The type of log information to show in the log toolbar of VWorks.

❑ General settings that pertain to log and data file maintenance.

❑ The folders in which to store log and data files.

For an explanation of log and data files, see “About Log and Data Files” on page 56.

The first three of these log options are described in this topic. Setting the output folder for plate reader data is described in “Ultramark Plate Reader Data File” on page 256.

How Messages Displayed in the Log Toolbar Are Controlled

Event and error messages are displayed in the log toolbar of the VWorks window. With all message options turned on, a large number of messages are displayed. For simplicity, you can hide types of messages that are not important to you.

The messages that are displayed during a run are controlled by:


❑ Selecting screen settings options before a run (see Setting Log Options Procedure in this topic).

❑ Clicking tabs in the log toolbar during a run (see “Working with the Log Toolbar” on page 104).

Note: Screen display settings do not affect the information saved in log files. All error and event information is always saved to log files.

Setting Log Options Procedure

To set log file options:


2. In the VWorks Options dialog box, click the Log Options tab.

3. In the Screen settings group box, select one or more of the following options, as needed:

4. In the File Settings group box:

a. In the Max number of each log file to maintain text box, type the maximum number of log files that you want to store.

!! IMPORTANT !! After this number has been reached, each new log files replaces the oldest existing log file.

b. Select one or more of the following options, as needed:

Log Option Description

Log “task begin” events on screen

Displays messages at the time that process tasks are scheduled (not at the time that they are performed).

This applies only to the protocol log file.

Log “task complete” events on screen

Displays messages that confirm when process tasks are completed.


Log robot motions on screen Displays robot motion events as they happen.


Log pipettor debug messages Displays event messages that are generated by VPrep pipettors.


Log Options Description

Create new logs for every run A separate log file is created for every run.

If the check box is cleared, each run appends data to the same log file and a new log file is created when VWorks is started.

This affects all log files.


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c. Click the ellipsis button for a log file or folder.

For more information about the options, see “About Log and Data Files” on page 56.

d. Navigate to the folder to which you want to save the log file.

e. Repeat step c and step d as necessary.

f. Click Save.

5. In the VWorks Options dialog box, click OK.

Append timestamps to log file names

The date and time of the run is appended to the name of the log file.

This affects all log files.

Log Options Description


Importing a Log File to ExcelIntroduction Because comma-delimited and tab-delimited text files contain

structured data, you can quickly import them into Microsoft® Excel, automatically organizing their data into columns.

This feature is helpful for making it easier to analyze the data in log files.

Procedure To import a log file to Excel:

1. Open Microsoft Excel.

2. Drag the file onto the Excel window.

The data is imported.


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Protocol Log File Information

The information given in a protocol log file is explained in the following table. Refer to the screenshot of the Excel file for the column letters.

Spreadsheet Column Information

A Date and time that the entry was added

B Type of information:

❑ Error

❑ Event

❑ Info

❑ Script

❑ User

C Origin of the information

D Either the:

❑ Name of the plate

❑ Name of the device, if it refers to a reagent

E Description of the log entry


Adding an AlarmIntroduction If your BioCel, or a third-party module contained on your BioCel, is

equipped with the ability to measure temperature, humidity, gas concentrations or liquid volumes, you can set an alarm to inform you when a particular level is reached. The alarm creates an error message and optionally sounds an alarm when an environmental measurement falls outside the range that you specify.

The alarm settings described in “Setting Error Options” on page 51 determine the behavior of the alarm.

Warning for iSeries Environmental Control

!! IMPORTANT !! Although it is possible to change environmental control settings directly using the iSeries controllers, we recommend that you do not do this. Attempting to make changes when VWorks is communicating with the iSeries controllers may corrupt data. Use the procedures in this topic to change the environmental control settings.

Procedure To add an environmental control alarm:

1. Make sure that the Enable measurements and alarms option is turned on.

See “Setting General Options” on page 48.


3. In the Protocol Options dialog box, click the Alarms tab.

4. In the Log measurements every text box, type in the time interval between measurements taken by the BioCel.

If you change this value, the existing time interval instance will expire before the change is implemented. If the existing time interval is long and you want to implement the change as soon as possible, you will need to restart VWorks.


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5. Click the Create a new alarm button.

A row with default values is added to the Measurement Alarms table. Click to select the row and then click a value to edit it, using the following table as a guide.

An example of a field ready to be edited is shown below.

Field Comments

Alarm name A name of your choice.

Enabled? Yes turns the alarm on.

Device The name of the device on which the alarm is set.

Alarm type The parameter that is being measured. It could be temperature, relative humidity, mass, volume, and so on.

Process value The current measurement, with units being dependent on the alarm type.

Low Alarm The low value at which you want the alarm to be turned on.

High alarm The high value at which you want the alarm to be turned on.

Alarm Timer [minutes] The time interval between the alarm being registered and the alarm being turned on. For example, if the temperature High Alarm is 40 ºC and the Alarm Timer is 5 min, a measurement is recorded at 40 ºC and the alarm is triggered five minutes after remaining above 40 ºC, causing an error condition to be triggered.



Monitoring environmental conditions during a run

“Monitoring a Run” on page 99.

The log file to which measurements are recorded

“About Log and Data Files” on page 56.

iSeries environmental control “Using iSeries Diagnostics Software” on page 275.

StoreX environmental control “Using StoreX Diagnostics Software” on page 301.


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Understanding the ProtocolIntroduction If you are not already familiar with the protocol you intend to run you

will need to take some time to understand it.

What You Should Know

You should minimally know:

❑ Which modules you need to prepare

❑ Where you should position the plates before the run and where they are moved to during the run

❑ Whether User Message tasks prompt you to perform certain actions after you start the run or whether you must perform the actions before you start the run

❑ Whether you will need to replace fluids and empty waste during the run

❑ Whether you will need to remove and add plates during the run

❑ Which liquids to prepare, where they should be placed, and in what kind of reservoir

Printing a Protocol It may help you to refer to a printout of the protocol steps as you analyze the protocol.

To print a protocol:

1. Select File > Print.

2. Select your required options from your printer’s print options dialog box.

3. Click Print.

An example of a printed process that includes a pipette process is shown here.

Note: If you try to print a protocol before a network printer driver is installed on the BioCel computer, you will receive an error. If this happens, contact your network administrator for help.


Preparing Plates, Modules and AccessoriesIntroduction This topic provides a quick reference for use when preparing modules

and accessories for use on the BioCel.

Note: For complete information, see the manuals for the individual modules.

The procedures in this topic assume that the modules are already turned on and that you are familiar with the operation of the modules on your BioCel.

When to Use Prepare modules and accessories after you have become familiar with the protocol.

See also “Preparing a Run: Workflow Overview” on page 36.

Set Up Order You would typically prepare the BioCel modules and accessories in the order presented in this topic. Using this order you first set up modules and accessories that have no time-sensitive elements. These could be set up the night before the run. Leave the more complex preparations, which may use expensive and unstable reagents, until last.

Note: If the protocol includes User Message tasks to prompt you to perform some setup steps, such as placing counterweight plates, do not include these steps in the setup. For more information, see “Setting User Message Task Parameters” on page 157.

About Placing Plates Depending on the protocol you intend to run, you may need to manually place plates, tipboxes, reservoirs, or counterweights onto platepads, hotel shelves, VStack® racks, VSpin™ rotors, or VPrep shelves.

Always place plates so that the A1 well is in the top, left corner, as viewed by the robot. The following illustration is from the operator’s perspective.


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Waste Bin Set Up Empty the waste bin and replace it under the waste opening in the BioCel table.

!! INJURY HAZARD !! If your BioCel has an automatic door over the waste bin, use caution when removing or replacing the waste bin. If a protocol is running, the automatic door for the waste opening may open or close at any time. Low force is used to open and close the door, so the risk of serious injury is low. However, protect yourself by keeping away from the door mechanism at all times.

To remove the waste bin from its hanger:

1. Open the side door nearest to the bin.

2. Hold the bin at the top right corner with your right hand.

3. Lifting the front side of the bin upwards with your right hand, place your left hand underneath at the bottom left corner.

4. Supporting the bin with both hands, lift it up and off the hanger, resting it on the BioCel floor.

5. Slide the bin out of the BioCel.

6. Close the side door.

To replace the waste bin on its hanger:

1. Open the side door nearest the bin.

2. Slide the empty bin into the BioCel until it lies underneath the waste opening, with the side of the bin resting against the hanger.

3. Lifting the front side of the bin upwards with your right hand, place your left hand underneath at the bottom left corner.

Robot arm and plate

00

01

5

A

B

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123456789101112131415161718192021222324

A1 well


4. Using both hands, lift the bin up, over the hanger, and down so the hanger supports the underside of the lip.

5. Close the side doors.

Teleshake Set Up No setup is required for a Teleshake module.

VStack Set Up The general process for loading a VStack with plates for a run is described here. For more detailed procedures, see the VStack User Guide.

1. Press the load/release button to upstack the bottom plate in the rack and release the grippers.

Note that a rack must be present in the VStack for the load/release button to work.

2. Remove the rack.

3. Fill with the correct labware.

4. Return the rack to a VStack that will deliver plates, according to the protocol you will run.

As the racks can be positioned either way round, make sure that the A1 wells of the plates are in the top, left corner, as viewed by the robot.

5. Press the load/release button to set the gripper.

PlateLoc Set Up The general process of preparing a PlateLoc® is described here. For more detailed procedures, see the PlateLoc User Guide.

1. Make sure that there is enough seal stock on the roll for the run.

2. Make sure that the right support insert is installed for the plates you are using.

3. Open the PlateLoc Diagnostics software.

See “Opening Diagnostics Software” on page 260.


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VCode Set Up The general process of preparing a VCode® for a run is described here. For more detailed procedures, see the VCode User Guide.

1. Make sure that there is enough label stock in the label source roll.

2. Make sure that there is enough media stock in the media source roll.

3. If the radius width of the label backing on the take-up roll is more than 1 inch (2.5 cm) wide, remove the label backing from the take-up roll, cut it and reattach the end.

Too much label backing on the take-up roll can interfere with operation of the VCode.

4. Use VCode Diagnostics software to perform a plate labelling test.

For more information, see the VCode User Guide.

VSpin Set Up For more detailed information about manual operation of the VSpin, see the VSpin User Guide.

In stand-alone mode, the VSpin can spin two sample plates at the same time. When used on the BioCel, it can spin one sample plate at a time and always requires a counterweight plate.

The counterweight can be added manually or robotically.

1. If you are using a manually-loaded centrifuge counterweight, place the counterweight into bucket 2, using VSpin diagnostics software to open and close the VSpin door.


2. If you are using robot-loaded counterweights, make sure you have correctly set up counterweights in VWorks™ and placed the counterweights in the correct plate positions.

For more information, see “Setting Up a VSpin Counterweight Plate” on page 77.

!! DAMAGE HAZARD !! To avoid a robot crash, always place the counterweight into bucket 2 and leave the door open with bucket 1 at the front. The sample plate will always be moved to bucket 1 by the robot.

UltraMark Set Up The general process for preparing an UltraMark for a run is described here. For more detailed procedures, see the documentation that accompanies the UltraMark.

1. Make sure that the plate carrier is in the out position.

2. Make sure that the correct filter set is used.


Bio-Tek Washer Set Up

The general process of preparing a Bio-Tek washer ELx405 for a run is described here. For more detailed procedures, see the documentation that accompanies the Bio-Tek washer.

1. Empty the waste container.

2. Fill the source reservoir.

3. Make sure that the vacuum to the washer is set up.

4. Prime the washer, either manually or using the Bio-Tek Diagnostics software.

5. Press the Main Menu button to return the Bio-Tek Washer display console to the main menu.

!! IMPORTANT !! If you do not do this, the protocol will not run.

!! IMPORTANT !! Do not use any of the Bio-Tek Washer sensors. The sensor information interferes with the Velocity11® diagnostics software. See the ELx405 Washer Operator’s Manual for more information.

StoreX Set Up The general process of preparing a StoreX incubator for a run is described here. For more detailed procedures, see the documentation that accompanies the StoreX.

1. Turn on the StoreX.

2. Add any plates to the StoreX that are required in the protocol.

For more information, see “Setting StoreX Task Parameters” on page 154.

3. Make sure that the door is closed.

4. Make sure that the water tray is full if using humidity control.

5. Make sure that the external carbon dioxide tanks are open if using carbon dioxide control.

Echo550 Set Up 1. Create a protocol for the operation you want to perform on the Echo550, following the directions in the Labcyte technical documents.

2. Select the profile that you want to use in the device manager.

3. Make sure that the:

a. Coupler pump fluid bottle is full.

b. Vacuum is on.


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c. Cooling system is on.

For information about creating profiles, see “Using the Echo 550” on page 270.

QFill2 and AliQuot Set Up

The general process of preparing a QFill2 or aliQuot for a run is described here. For more detailed procedures, see the QFill2 or aliQuot user manual.

1. Fill the dispensing bottle with the liquid you want to use.

2. Connect the tubing.

3. Press the Purge button to prime the tubing with liquid.

4. Return to the main screen on the QFill2 or aliQuot.

5. Make sure that the correct manifold is installed for the type of plate you are using.

Different manifolds dispense to different numbers of wells.

Nanodrop Set Up The general process of preparing an Nanodrop for a run is described here. For more detailed procedures, see the Nanodrop user documents.

1. Make sure that the system liquid bottle is full.

2. Make sure that the warm up protocol has been run.

Multidrop Set Up The general process for preparing a Multidrop for a run is described here. For more detailed procedures, see the operational checklist in the Multidrop User Manual that accompanies the product.

1. Set up the reagents to be used.

2. Switch on the instrument.

3. Insert the priming vessel and the dispensing cassette.

4. Pull the rotor cover over the rotor.

5. Insert the correct plate adapter, according to the size of the plates you are using.

6. Prime all eight channels so that there are no air bubbles in the tubes.

Zeiss Multimode Set Up

For information about setting up a Zeiss Reader, see the user documents that accompany the reader.

VPrep Set Up The general process of preparing a VPrep for a run is described here. For more detailed procedures, see the VPrep User Guide.

Note: On the BioCel, the robot has access to VPrep shelves 2, 4, 6 and 8, meaning that only these shelves can hold sample plates. Shelves 1, 3, 5 and 7 are reserved for reservoirs and tipboxes.

1. If you are changing the reagent type in a particular reservoir:

a. Remove and wash any reservoirs.


b. Detach and wash reservoir tubing.

c. Replace the tubing and reinstall the reservoir.

d. Remove and wash any MicroWash trays.

e. Detach and wash MicroWash tray tubing.

f. Replace the tubing and reinstall the tray.

2. Make sure that the reservoir and tray tubing allows the shelves to move to their fully engaged position.

3. Install tubing into the correct pumps.

4. Fill the fluid reservoir bottle, replace the cap, and attach the fluid line to the cap connector.

Make sure you attach the fluid line that pumps towards the VPrep.

5. Empty the waste container, replace the cap and attach the fluid line to the cap connector.

Make sure that you attach the fluid line that pumps away from the VPrep.

6. Use the VPrep Diagnostics software to prime the fluid lines between the pump and VPrep reservoirs by filling the lines with the appropriate fluid.


7. If your VPrep has a WeighShelf, calibrate the WeighShelf if:

You are changing the liquid type used in the reservoir on the WeighShelf.

The pump module connected to the WeighShelf has been turned off.

If you haven’t calibrated it for a while.

8. If you are using disposable tips, you may need to attach them before starting the run. If so:

a. Place a tipbox on the tipbox shelf.

b. Use the VPrep Diagnostics software to install the tips.

c. Remove the tipbox.

Note: Attaching tips is an important step. Please refer to the VPrep User Guide for more information.


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Placing and Removing Hotel PlatesIntroduction You can place plates into a plate hotel and remove plates from a plate

hotel by:

❑ Removing the hotel from the BioCel first.

❑ Leaving the hotel on the table.

In general, it is better to add and remove plates while leaving the hotels in place. Doing it this way you are less likely to spill liquids in the plate wells, and it will reduce wear on the registration pins and hotel bases.

For a general description of plate hotels, see “Plate Hotel” on page 30.

For a description of how to orient plates, see “About Placing Plates” on page 69.

Removing and Replacing a Hotel

!! IMPORTANT !! If you remove a plate hotel, you must put it back in the same place to maintain accurate teachpoints.

To remove a plate hotel:

1. Holding the top handle, lift directly upwards.

The plate hotel lifts off its base.

To replace a plate hotel:

1. Holding the top handle, position the plate hotel above the base so that the dowels are aligned with the dowel holes.

2. Slowly lower the plate hotel onto its base.


Setting Up a VSpin Counterweight PlateIntroduction A counterweight plate is always required to balance a sample plate

when centrifuging in a VSpin module on a BioCel. This means that only one sample plate can be centrifuged at one time.

A counterweight plate is the same as a sample plate except that it is empty, or contains water to provide a more accurate balance. If a counterweight is not used, a load imbalance error will result. The load imbalance tolerance is 10 grams.

Using a counterweight plate and centrifuging one sample plate at a time does not typically increase the length of a protocol run, compared to spinning two sample plates at a time. This is because the centrifuge task is not typically the time-limiting step of a protocol.

Options For Loading Plates

If three different types of plates are centrifuged during a protocol, three different counterweights are required.

You can load counterweights into a VSpin:

❑ By hand, using VSpin Diagnostics software to open and close the centrifuge door and move the rotor.

❑ With the robot, using a combination of Robot Diagnostics and VSpin Diagnostics.

❑ Automatically, using the robot during a normal run.

Some set up is required by administrators before you can load counterweights robotically.

Manually Loading Counterweights

To load a counterweight by hand:

1. Open VSpin Diagnostics software.


The VSpin Control dialog box opens.

2. Follow the directions in the VSpin User Guide to open the VSpin door and load the counterweight.

!! DAMAGE HAZARD !! To avoid a robot crash, always place the counterweight into bucket 2 and leave the door open with bucket 1 at the front. The sample plate will always be moved to bucket 1 by the robot.

About Robotically Loaded Counterweights

For the robot to be able to load a counterweight:

❑ The platepad containing the counterweight must be associated in VWorks with the type of labware used for the counterweight so the robot knows how to pick it up.

This association is created by an administrator in the manage counterweights database when creating the protocol. For more information, see “Managing Counterweights” on page 134.


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❑ The Centrifuge task that uses the counterweight must specify from which device to pick up the counterweight.

This is specified by an administrator when creating the Centrifuge task for the protocol. For more information, see “Setting Centrifuge Task Parameters” on page 134.

❑ The counterweight plate must be placed by the operator on the platepad specified in the Centrifuge task.

!! IMPORTANT !! It is the operator’s responsibility to make sure that the counterweight on the pickup platepad is of the correct type to balance the sample plate. VWorks does not generate an error if the type of counterweight picked up does not match the type of sample plate.

Note: The administrator who creates a protocol can add user messages to the protocol to remind the operator before a run which types of plate to put on which platepad. For more information about user messages, see “Setting User Message Task Parameters” on page 157.

Setting Up Robotically Loaded Counterweights

To set up robotically loaded counterweights:

1. Identify a process that includes a Centrifuge task, look at the plate instance and note the type of plate used for the process.

2. In the same process pane, click the Centrifuge task in the process.

3. In the Protocol Task Parameters toolbar, note the name of the device defined in the Select counterweight to use list box.

If you are unable to select a device, the administrator has not yet defined a counterweight. See “Managing Counterweights” on page 134 for more information.

Note: If you have just added a counterweight and it does not appear in the list box, click a different task and click back on the Centrifuge task.

4. Repeat the procedure for the remaining Centrifuge tasks in the protocol.

It may help to create a table that looks like this one, which replicates the relevant information from the manage counterweights database:

5. Place the counterweights on the platepads with which they are associated.

Plate Type Platepad

w 1

x 2

y 3

This chapter describes how to set up and start an existing protocol run or runset. All of the procedures in this chapter can be performed by someone with Operator privileges.

Performing a Run 4

Chapter 4: Performing a RunBioCel User Guide

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Overview of Performing a RunWays to Set Up a Run

There are three ways to set up and start a run.

Overview Whichever way you choose to start a run, you would typically perform a number of pre-run checks. These are described in “About Starting Runs Automatically” on page 87.

What you do next depends on whether you are going to run a single protocol or a runset.

If you are going to run a single protocol, at this point the protocol you plan to run has been created and opened in VWorks. The next step is to start the run, as described in “Starting a Run from VWorks” on page 83.

If you are going to run a runset, you first have to create it. The following topics explain how to do this.




During the run you might monitor the progress, as described in “Monitoring a Run” on page 99 and “Working with the Log Toolbar” on page 104.

If you need to stop the run when it is in progress, follow the directions in “Stopping a Run” on page 95.

When the run has ended, you would clean up, according to “Performing Post-Run Clean-Up” on page 106.

Method See...

Set up a single protocol run and manually start it by clicking the Start button in the VWorks

“Starting a Run from VWorks” on page 83

Set up a single protocol in advance and manually start it from a command line

“Starting a Run from a Command Line” on page 86

Set up a runset, which consists of one or more protocol runs that are started automatically, based on times that you set in advance




81Chapter 4: Performing a RunBioCel User Guide

Performing Pre-Run ChecksIntroduction To see how this procedure fits into the overall process of performing a

run, see “Overview of Performing a Run” on page 80.

Procedure To check that the BioCel is ready for a run:

1. Make sure that reservoirs and Micro Wash trays are on the correct shelves of the VPrep®.

2. Make sure that there are no stray plates or lids in robot-accessible places, which include:

Platepads

VPrep shelves

VStack® presentation stages

VSpin buckets

VCode® plate stages

PlateLoc® plate stages

Plate hotel shelves

Lid hotel bays

Lid removal devices

Third-party devices

As a second check, you can also set the robot to check all accessible positions immediately after starting a run. For more information, see “Setting General Options” on page 48.

!! DAMAGE HAZARD !! Leaving a stray plate on the table may cause the robot arm holding a plate to crash into the stray plate. A typical robot crash will damage the plates, spill samples and stop the robot. It may also damage the robot gripper pads.

3. If you are using VSpin counterweight plates, make sure that they are on the correct platepads, according to the protocol you will run, and oriented correctly.

4. Check each VStack to make sure that the stackers are loaded and that the labware and plate name displayed on the display panel match:

The actual labware in the stacker

The labware and plate name in the protocol

5. Make sure that the module air pressures regulators lie within the following ranges:

Module Air Pressure (psi) Air Pressure (MPa)

PlateLoc 85–90 0.56–0.62


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To find the current incoming air pressure for the PlatePierce, open the PlatePierce Diagnostics software. For more information, see the PlatePierce User Guide.

6. For each VStack, open the VStack BioNet Diagnostics software to check that the grip pressure is appropriate for the type of plates that you are using.

For more information about adjusting the grip pressure, see the VStack User Guide.

7. If your BioCel® is equipped with environmental control, check that environmental settings are within acceptable ranges for the run.

8. Close all doors.

!! DAMAGE HAZARD !! Make sure that you move the computer monitor out of the way as you close the overhead doors. For more information, see “General BioCel Hazard Warnings” on page 9.

9. If the interlock override is on, put the key into the interlock override keyhole in the power panel and turn it to the 12 o’clock position.

This disables the interlock override.

VCode 85–90 0.56–0.62

VPrep 90–95 0.62–0.65

VStack 40–50 0.28–0.34

PlatePierce™ 75–80 0.65–0.55

Module Air Pressure (psi) Air Pressure (MPa)


Starting a Run from VWorksIntroduction This topic explains how to start an individual protocol run. Runset runs

do not need to be started with the procedure in this topic because they are scheduled to start at a particular time.

Procedure To start a run:

1. Make sure that all modules used in the protocol are in their home positions.

Refer to the relevant module’s user manual for more information about homing.

2. In VWorks, click Start.

At this point, VWorks reads the protocol, checks it for inconsistencies and reports any warnings and errors. If there are no protocol compilation errors and if you are not using the FileReader plug-in, the Number of Cycles dialog box opens. For more information about compilation errors, see “Compilation Warnings and Errors” on page 310.

3. If you are using the FileReader plug-in to populate Apply label task fields:

a. Select the plug-in text file that contains the data from the dialog box that opens.

b. In the new dialog box that opens, check the list of names of the columns of the text file and the total number of rows in the file.

In the following screenshot, the first six columns of the plug-in file are repeated for each side of the plate. For more information, see “Repeating Columns” on page 198.


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c. Click OK.

If the file is not the one you intend to use, you can cancel the run at the next step if needed.

4. In the Number of Cycles dialog box, type in the number of times that you want to execute the protocol during the run.

If your protocol includes a Restack task, this number must be equal to the total number of plates you want to restack. For more information, see “Setting Stacker Task Parameters” on page 152.

5. Click OK.

The run starts.

6. If User Message tasks are included in the protocol, you are prompted to respond to them as they execute.

If there are no User Message tasks for this purpose, set laboratory countdown timers for when you need to empty liquid waste containers and refill liquid source bottles.

For more information about User Message tasks, see “Setting Stacker Task Parameters” on page 152.

What Happens After a Run Starts

After you start the run, the following events occur:

❑ The Start button becomes unavailable and the Stop button becomes active.

❑ Log messages on the log toolbar indicate the start of the run. Also, Log files record events as they are performed on all plates in the Run, according to the selected log file options.

For more information about log file options, see “Setting Log Options” on page 60.

❑ Monitoring of the environment (if selected in general options), UPS and disk space begins.


❑ If you selected the option for the robot to check all plate positions for plates, this operation will now be performed. If an error is found, correct the problem and click Retry. For more information about this option, see “Setting General Options” on page 48.

❑ The first instructions of the protocol are executed.

❑ If User Message tasks are included in the protocol, you are prompted to respond to them.

For more information about User Message tasks, see “Setting User Message Task Parameters” on page 157.


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Starting a Run from a Command LineIntroduction You can start VWorks and initiate a run directly from a command line.

Procedure To start VWorks from a command line:

1. In Windows®, navigate to Start > Run.

2. In the Run text box, type cmd and Click OK.

The command prompt opens.

3. At the command prompt, change the current directory to vworks workspace by typing:

cd \vworks workspace\bin

4. Press ENTER.

5. Type the name of the VWorks executable followed by values for the switches that specify:

The protocol to run

Your user name

Your password

The number of cycles for which to run the protocol,

An example is:

vworks3 myprotocol.pro /user:<your user name> /password:<your password> /runs:<number of run cycles>

6. Press ENTER to start the run.

The following screenshot shows a generic example of the completed command prompt.


About Starting Runs AutomaticallyIntroduction For an overview of setting up runs, see “Ways to Set Up a Run” on

page 80.

Runset Defined A runset is a collection of runs that are scheduled in advance to run without operator intervention.

The runset is defined in the Runset Manager toolbar, which is displayed on the Progress page of VWorks.

Typical Use Runsets are typically used with BioCel systems that store many plates in incubators and run subsets of the plates through protocols in batches.

Runset File The data displayed in the runset manager is stored as an XML file with the file name extension .rst, in a location selected by your BioCel administrator.

Runset Privileges You can only save runset files if you are logged in as a Technician or an Administrator.

Run Options When setting up a runset, for each run you define either:

❑ How many times the run should cycle

❑ Which subset of available plates will be run

The subset of plates that is to be run as a batch is defined by inclusion of a linker file.

For more information about linker files, see “About Linker Groups and Files” on page 235.

Run Scheduling Logic

You can create a runset while a manually set-up protocol is running.

If the time to start a run scheduled by the runset manager arrives while another run is being performed, the start will be delayed. Then, when the running protocol finishes, the earliest-scheduled run in the runset will start.


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Working with RunsetsProtocol Notes If you want to add notes to a protocol that will appear in the Protocol

Notes column of the Runset Manager toolbar, see “Adding Notes About the Protocol” on page 118.

Adding a Run To add a run to the runset:

1. In the Runset Manager toolbar, click Add Run.

2. In the Select a protocol file to use for this scheduled run browser box, navigate to, and select, the protocol file that you want to add.

3. Click Open.

A new row is added to the Runset Manager toolbar table, with a default time scheduled 5 minutes into the future.

4. If you want to schedule the run for a different day:

a. Click in the Date column.

b. Click a second time in the Date column to make the date editable.

c. Click the drop-down arrow to open a calendar and select the date.

d. If you want all other runs in a runset to be modified in relation to the changed day, click Yes in the VWorks dialog box.

5. If you want to schedule the run for a different time:

a. Click in the Time column.

b. Click again in the Time column to make the time editable.

c. Click the group of hours, minutes or seconds to edit.

In the following example, the minutes group is selected.


d. Click the up or down arrows to change the value or type the new value in the field.

6. If you do not intend to use linker files for the runset, in the Runs column, enter a number of cycles that you want the protocol to run.

7. If you do intend to use linker files:

a. Click in the linker column.

b. Click in the linker column a second time to open the Select the linker file to use for this scheduled run.

c. Navigate to the linker file, select it and click Open.

Filtering Runs If you have a long list of runs in a runset, you can apply a filter to display a subset of the runs.

To filter displayed runs:

1. Right-click a cell in the Runset Manager toolbar that you would like to keep in the displayed selection.

2. Select Filter by row from the menu that appears.

3. Select the value that you would like to filter on.

Runs that do not include this value are hidden.

After filtering a runset, you can display all runs again.

To display all runs:

1. Right-click a data-containing row in the Runset Manager toolbar.

2. Select Show all from the menu that appears.

All runs are now displayed.


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Deleting a Run To delete a run:

1. Select a row in the Runset Manager toolbar.

2. Click Delete run.

Saving Runsets To save a runset you must be logged in as a Technician or Administrator.

To save a runset:

1. Select File > Runset File > Save.

To save the file in a different location, select Save As.

Opening a Runset If you open a previously created runset it is likely that some or all of the runs are scheduled to start in the past. In this case, make sure that you set new start dates and times so that they are in the future.

The runset manager allows you to set a new start time for one run and automatically reset the start times of the other runs by the same time increment.

!! IMPORTANT !! The runs that are scheduled in the past will not start automatically.

To open a runset:

1. Select File > Runset File > Open.

2. In the Open browser box, navigate to and select the runset file that you want to open.

3. Click Open.

4. Change the scheduled date and time following step 4 and step 5 in “Adding a Run” on page 88.

Stopping a Runset The procedure for stopping a runset is the same as the procedure for stopping any run. For more information, see “Stopping a Run” on page 95.


Runset ExamplesIntroduction The topic “Working with Runsets” on page 88 explains how to create

runsets and perform basic runset management. This topic describes how runsets are used in the context of actual protocols.

The first example shows how a runset can be set up using linker files. The second example shows a runset that cannot be created in VWorks version 13.x.

Before reading the examples in this topic, you should understand how linker files are set up. For more information, see “Inventory Management Overview” on page 231.

Process Overview The general process of creating a runset using linker files is as follows:

1. Create the first protocol for the runset.

2. Create a linker file for the protocol.

3. Create additional protocols and linker files.

4. Create a runset using the protocols and linker files.

Example In this example there are two single-process protocols.

Protocol X

In protocol X, 10 plates are unloaded from cassette 1, slots 1–10 of the incubator. The same plates are then loaded into slots 11–20.

Protocol Y

In protocol Y, the same 10 plates are unloaded from cassette 1, slots 11–20 and returned to slots 11–20.

To create runset example one:

1. Create protocol X, as shown in the following screenshot.

2. Navigate to Tools > Linker.

The Plate Linker dialog box opens.

3. Follow the directions in “Clearing the Current Linker File” on page 239 to remove any plates currently selected in the Plate Linker group.

4. Set up the Protocol X linker:

a. Make sure that the Input Plates tab is selected.


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The process Protocol X is listed as the only process in the protocol.

b. In the Plate inventory, select a plate in cassette 1, right-click and select Filter by row > cassette=1.

This orders the plates in the list for selection.

c. Click cassette 1 plate 1, then hold down the SHIFT key and click plate 10.

This selects the group.

d. Click Add selected plates.

The plate group is added to the list of Plates currently in the selected group.

e. Click to select the Output Plates tab.

f. Select slots 11–20 in the Plate inventory and click Add selected plates.

The group of slots is added to the list of Plates currently in the selected group.


5. Click OK

Create protocol Y, as shown in the following screenshot.




8. Set up the Protocol Y linker:

a. Select the Input Plates tab.

Select the process processY is selected by default as the only process in the protocol.

b. Filter the plate inventory again.

c. Click plate 1, then hold down the SHIFT key and click plate 10.

This selects the same group of plates that are already selected.

Note: Although the plates will actually be in slots 11-20 when this protocol starts, you select plates 1-10 here. This system tracks the plates as they are moved during the runset.



e. Select the Output Plates tab.

f. Select slots 11–20 and click Add selected plates.


g. Click OK.

9. Click the Progress tab to view the Runset Manager toolbar.

10. Using the procedures in “Working with Runsets” on page 88, create the runset using these two protocols.

11. Start the run.


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Example Error There are some sets of protocols for which you cannot create a runset. When you try to set up a runset, you will get an error if there are no plates in the incubator to select when attempting to create a group.

This example shows a runset that cannot be created and explains why.

Protocol ADownstack the plates and load them into cassette 1, slots 1–10.

Protocol B

Unload 10 plates from cassette 1, slots 1–10 of the incubator and then load them into slots 11–20.

When you try to create the linker to load plates back into slots 11–20 in protocol B there will be no plates in the plate inventory to select.


Stopping a RunWays to Stop a Run You can stop a run in the following ways:

Stopping a Run Using VWorks

Use this procedure to:

❑ Stop and continue a run, for example, when you want to:

Add or remove labware

Clean up a spill

Add buffer to a VPrep reservoir

Diagnose a problem that you notice

Perform an operation that is not part of the protocol

❑ Abort a run in a non-emergency situation

To stop a run using VWorks:

1. In VWorks, click Stop.

The Stop dialog box opens and the currently scheduled task continues to completion. This may take a minute or more. After that, no more tasks are performed.

Method Comments See...

Click Stop in VWorks The currently scheduled task continues to completion.

You can either continue or abort the run after this.

“Stopping a Run Using VWorks” on page 95

Push an emergency stop button

All accessible moving parts stop instantly (does not include cooling fans).

The run cannot be continued. Use this option for emergencies only.

“Using an Emergency Stop Button” on page 96

Lift up an overhead door

All moving parts stop instantly.

This generates a robot error, but you can either continue or abort the run.

“Opening an Overhead Door During a Run” on page 97


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!! INJURY HAZARD !! Do not open overhead doors until the currently scheduled task is complete.

2. You now have three choices:

!! IMPORTANT !! Before continuing with a run, make sure that the system is in a valid state for the protocol. In other words, make sure that you have not made changes that will cause an error or cause samples to be switched around. Errors can be caused, for example, when moving a plate to a position that should not have a plate. Plates can be switched around, for example, when moving a plate from one stacker to another.

Using an Emergency Stop Button

In an emergency situation, you can instantly stop all accessible moving parts by pressing an emergency stop button. Emergency stop buttons are located on the table and the power panel.

!! IMPORTANT !! You cannot continue with a run after using an emergency stop because VWorks must be restarted.

Pressing the emergency button:

❑ Stops power to the robot motor

❑ Stops power to the modules (except for VPrep and VPrep pump main power)

If you want to... Then...

Continue with the run Click Continue.

Troubleshoot a problem or perform a manual operation

Click Diagnostics, and select the module that caused the error. This opens the diagnostics software for that module, allowing you to troubleshoot the problem.

For more information, see “Using Diagnostics Software” on page 259.

Abort the protocol Click Abort Process.


❑ Stops power to the VPrep motors that move the head, and activates the brake on the head to prevent it from falling

❑ Stops air being supplied to the modules

For information about recovering from an emergency stop, see “Emergency Stop Error Recovery” on page 311.

Opening an Overhead Door During a Run

Provided the interlock circuit has not been overridden you can open an overhead door at any time during a run to instantly stop BioCel motion. The interlock light on the power panel will turn off when this happens.

When you close the door, a Robot Error dialog box is displayed. For more information about recovering from in interlock error, see “Door Interlock Error Recovery” on page 311.

If a VPrep was in motion when the door was opened, a VPrep Error dialog box may also be displayed.

!! IMPORTANT !! Do not use the door interlocks to routinely stop a protocol. The door interlocks are designed to be a safety backup system.

Comparing Interlock and Emergency Circuits

If you lift an overhead door during a run, the run will stop. When you close the door, and click the Continue button in the stop dialog box, the run will resume. If you press an emergency stop button during a run, you will have to perform a more invasive recovery procedure and you cannot continue with the protocol.

The following table shows how different components are affected by the door interlock circuit and emergency stop circuit.

0000

5

Component Interlock Cuts?

Emergency Stop Cuts?

Bio I/O power No No

Cooling fan power No No

Device power, such as platepad bar code reader

No Yes


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Module power No Yes (except VPrep)

Robot motor servo power Yes Yes

Robot system power No No

System air No Yes

VPrep motor servo power Yes Yes

VPrep pump module power Yes Yes

iSeries console No No

Liconic incubator environmental control No No

UV lights No No

Clean-room output fan No No

Component Interlock Cuts?

Emergency Stop Cuts?


Monitoring a RunWhat to Monitor After starting a run, the operation of the BioCel should be monitored.

Exactly what you do to monitor a run depends on the protocol that you are using. For example, you might need to:

❑ Compare the motions of the robot to the protocol tasks being completed.

You can identify the task that is currently being performed from the position of the green ball in the process panes. Because VWorks can schedule more than one task at a time, there may be more than one green ball displayed.

❑ Add and remove labware.

For more information about adding and removing labware during a run, see “Stopping a Run” on page 95.

❑ Empty the waste bin.

For more information, see “Waste Bin Set Up” on page 70.

❑ Empty liquid waste containers.

❑ Fill liquid reservoirs.

❑ Replace an empty roll of PlateLoc seal or bar code labels.

!! IMPORTANT !! No errors are reported when a liquid waste container becomes full or a liquid reservoir becomes empty. (Exceptions to this are reservoirs on a VPrep WeighShelf or some third-party modules.) To guard against the problem of a full waste container or empty reservoir container, the protocol writer can incorporate User Message tasks into the protocol to remind the operator at the appropriate steps in the protocol. Alternatively, operators can set their own timer alarms to remind them to fill reservoirs and empty a waste containers at the appropriate time.

For more information about User Message tasks see, “Setting User Message Task Parameters” on page 157.

Monitoring Environmental Conditions

If your BioCel is equipped with temperature and humidity controls you can monitor them during the run by:

❑ Looking at the digital readouts on the iSeries controllers located behind a side door.

❑ Selecting Tools > Options and clicking the Alarms tab.

The Process Value column displays the current value for each alarm that is set.


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❑ Looking at the digital readout in the iSeries Diagnostics dialog box.

For more information about iSeries Diagnostics, see “About Bio I/O Diagnostics Software” on page 270.

❑ Looking at the log toolbar.

Monitoring UPS Status

You can monitor the UPS status during a run, or at any other time.

To monitor the UPS status:


2. In the VWorks Options dialog box, make sure that the Options tab is selected.

3. In the UPS Settings group box, click UPSDiags.

If there are two UPSs on your BioCel, you can click UPS2Diags for the status of the secondary UPS.

This opens the UPS Diagnostics dialog box.

4. Click the close box and then click OK to close the dialog boxes.

Field Description

Battery level Charge in the battery as a percentage of its capacity. An alarm will sound if the power source switches to battery. The system shuts down if the battery power drops below a defined threshold.

For information about setting the alarm threshold, see “Setting General Options” on page 48.

Power load Power drawn from the UPS by the BioCel as a percentage of its capacity.

Internal temperature Temperature of the battery. For UPS temperature specifications, see the supplied user documents.


Monitoring Overall Progress

You can monitor overall progress of the run on the Progress page of VWorks.

Closing Unneeded Toolbars

You can close unneeded toolbars to create more room on the screen for you to monitor a run.

To close a toolbar:

1. Either:

Click the close box in the toolbar.

From the View menu, select Toolbars > <toolbar name>.

Finding Plates During a run you can find out where all of the plates in the system are.

To find plates:

1. Select Tools > Find Plates.

2. Examine the log toolbar.

Each plate in the system is listed, along with the device at which it is located.

Querying Devices During a run you can find out what plates are currently at each device.

To query devices:

1. Select Tools > Query Devices.

2. Examine the log toolbar.

Each device in the system is listed, along with the plate that is currently at that device.


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System Monitoring What is monitored by the BioCel during a run depends on the options selected for the protocol.

Status Lights The blue BioCel status lights give you general information about the status of a run.

Monitored Item See...

System air pressure “Setting General Options” on page 48

Percentage of maximum UPS charge


Hard drive space “Setting Error Options” on page 51

Presence of plates “Setting General Options” on page 48

Label stock in a VCode “Setting Error Options” on page 51

Seal stock in a PlateLoc “Setting Error Options” on page 51

Environmental variables, on systems with environmental control


Bar code verification “Setting Up a Plate Instance” on page 112

Volume of fluid left in reservoirs on Weigh Pads

“Weigh Pad” on page 33.

Volumes of fluids in reservoirs not using a Weigh Pad, for example an AliQuot.

User guide for the relevant module.

Light Pattern Status

All on solid Run progressing normally

All off Not currently running

All blinking simultaneously Run error


Notification of Errors by Pager or Email

You can set up your BioCel so that you are notified of run errors by your pager or email.

To set up error notification:


2. Click the Email Setup tab.

3. In the Error Notifications group box, click Add.

4. Click to select the New email address text.

5. Click once more to make the text editable.

The text is editable when a box appears around it.

6. Type in your full email address.

7. Click OK.

8. Select the Send Email when errors occur option on the Error Handling tab.

For more information about this option, see “Setting Error Options” on page 51.

What to Do When You Get an Error

If you get an error during a run, refer to “Maintenance and Troubleshooting” on page 307 for help.

One light on each post blinking twice, followed by the other light on each post blinking twice

Run progressing normally but with interlock bypass in use

All blinking in circular pattern Run complete

Light Pattern Status


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Working with the Log ToolbarLog Toolbar Event and error messages are displayed in the Log toolbar of the VWorks

window.

Viewing the Log Toolbar:

1. If the toolbar is not showing, from the View menu, select Toolbars > Log.

The toolbar opens at the bottom of the screen.

With all message options turned on, a large number of messages are displayed during a run. For simplicity, you can hide types of messages that are not important to you. The messages displayed during a run are controlled by:

❑ Selecting screen setting options before a run

❑ Clicking tabs at the bottom of the display during a run

For more information about setting screen message options before a run, see “About Log and Data Files” on page 56.

Log Toolbar Options The following options are available for displaying screen messages.

VWorks Log Tab Displays...

All All event and error messages.

This is the same as the data that is recorded in the protocol log file.

Process Event messages, including fluid transfer messages.

Fluid Transfers Event messages reported by one or more VPrep pipettors.

This is the same data that is recorded in the pipettor transfer log file, but presented in a sentence format rather than a tab-delimited format.

The event messages that are displayed depend on whether the “Record in transfer log” option is selected in the aspirate and dispense pipette task parameters. For more information, see “Setting Aspirate Pipette Task Parameters” on page 173 and “Setting Change Tips Pipette Task Parameters” on page 177.

Measurements Temperature and humidity measurements.

Errors Error messages that appear as alert boxes on the screen.

This data is not saved in a separate log, but is included in the protocol log file.

Notes Notes that you add.


Searching the Log Toolbar

You can search for specific text in the log toolbar.

To perform a search in the log toolbar:

1. Select the appropriate tab in the log toolbar.

2. Click in the toolbar pane.

3. Click CTRL + F.

The Find dialog box opens.

Adding a Note You can type notes into the log toolbar during a run. Any notes that you type are also incorporated into the protocol log file.

To add a note to the log toolbar and protocol log file:

1. At the bottom of the log toolbar, click the Notes tab.

2. Click in the toolbar pane at the end of a line.

3. Press ENTER on the keyboard to create a blank line.

4. Type the note.

5. Press ENTER.

A timestamp is appended to the note.


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Performing Post-Run Clean-UpProcedure Perform this procedure immediately after a run ends.

To clean up after a run (part one):

1. If the protocol used robotically-loaded counterweight plates, click Yes in the message that prompts you to unload the last counterweight that was loaded into the VSpin™.

The robot moves the counterweight plate from the VSpin to the platepad with which the counterweight is associated.

2. Click Yes in the dialog box that prompts you to release all VStack module grippers.

3. Remove sample plates that have been used.

4. Remove manually placed plates from platepads, hotel shelves, VPrep module shelves, and so on.

5. If necessary, remove the counterbalance plate from any VSpin modules.

To clean up after a run (part two):

1. Wash all items, such as, reservoirs, tubes and manifolds, that were contacted by liquid.

2. Empty the waste bin.

3. Check run logs.

For more information about run logs, see “About Log and Data Files” on page 56.

4. Turn off environmental controls.

5. If you have Administrator or Technician privileges and you have modified the protocol, including selected options, you can save the protocol.

For more information, see “Compiling and Saving Protocols” on page 118.

6. Log off from VWorks™.

7. Optionally shut down the BioCel.

For more information, see “Shutting Down the BioCel” on page 107.


Shutting Down the BioCelWhen to Use Shut down the BioCel if you intend to:

❑ Move it

❑ Leave it unused overnight

Procedure To shut down the BioCel:

1. Make sure that the post-run clean up procedure was followed after the last run.

See “Performing Post-Run Clean-Up” on page 106.

2. In VWorks, select File > Exit to shut down the application.

3. Shut down the computer from the Windows operating system.

4. Optionally, turn off the monitor using the power button on the monitor.

5. If you use modules or devices that require a vacuum pump, optionally turn off power at the pump if the pump module has an on/off switch.

6. Open side door 2, and optionally, turn off the DC power supply switches labelled “Robot” and “System”.

7. Push the UPS button that turns off power output to all parts of the system.

If you have more than one UPS on your BioCel, make sure that you turn them all off. For more information about turning off the UPS, see the user manual for the UPS.

8. On the power panel, turn the main power switch counterclockwise to the off position.

9. If moving the BioCel, unplug the air, Ethernet and main power cables.

To locate these cables, see “Utilities Connections” on page 16.


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This chapter is intended for people with Technician or Administrator privileges. It describes the basic process of creating a protocol. To fully understand how to create a protocol, you will also need to read the information in the following chapters:

❑ “Setting Task Parameters” on page 125

❑ “Setting Pipette Task Parameters” on page 163

❑ “Creating a Protocol: Advanced Topics” on page 193

Before reading this chapter you should be familiar with the concepts presented in the chapter “Performing a Run” on page 79.

Note: This chapter is not a tutorial on writing protocols — it provides the basic reference information you will need to write protocols.

Creating a Protocol: Basics 5

Chapter 5: Creating a Protocol: BasicsBioCel User Guide

110

Creating a Protocol: WorkflowGeneral Information About Protocols

For general information about protocols, including definitions of terms, see “About Tasks, Processes and Protocols” on page 42.

Who Creates Protocols?

People who have Technician and Administrator user accounts have the necessary privileges to create protocols. For more information about privileges, see the Database and Security User Guide.

Overall Method The overall workflow for creating a protocol is given in the following table.

Step Topic See...

1. Optionally preparing back-end data to use with a plug-in.

“Setting Up VWorks Plug-Ins” on page 194

“About the FileReader Plug-In” on page 196

“Setting up the FileReader Plug-in” on page 199

2. Optionally writing JavaScript scripts to dynamically set task parameters.


“The JavaScript Task Object and Properties” on page 208

111Chapter 5: Creating a Protocol: BasicsBioCel User Guide

3. Creating a Process, which includes:

Setting up a plate instance. “Setting Up a Plate Instance” on page 112

Deciding the number of simultaneous plates to set.

“Setting the Number of Simultaneous Plates” on page 116

Adding tasks. “Adding and Deleting Tasks and Pipette Tasks” on page 117

Setting task parameters. “About Setting Task Parameters” on page 120

“Setting Task Parameters” on page 125

Optionally entering JavaScript scripts to dynamically set task parameters.


“The JavaScript Task Object and Properties” on page 208

4. Optionally creating a pipette process, which includes:

Linking a Pipette Process task icon to a pipette processes.

“About Setting Pipette Process Task Parameters” on page 121

Adding pipette tasks. “Adding and Configuring a Pipette Process Task” on page 169

Setting pipette process task parameters. “Setting Pipette Task Parameters” on page 163

5. Optionally creating additional processes and pipette processes.

This table, step 3 and step 4

6. Compiling and saving the protocol. “Compiling and Saving Protocols” on page 118

7. Testing the protocol with the simulator. “Checking a Protocol” on page 122

Step Topic See...


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Setting Up a Plate InstanceBackground Setting up a plate instance for a process is the first step in creating a

protocol. For a definition of a plate instance, see “About Tasks, Processes and Protocols” on page 42.

Procedure To set up a plate instance:

1. Click the Protocol Editor tab.

This page of VWorks™ is referred to as the protocol editor.

2. Click Add.

A plate instance icon appears in the protocol editor window.

3. If the Protocol Task Parameters toolbar is not showing, select View > Toolbars > Protocol Task Parameters.

The Protocol Task Parameters toolbar opens.

8. Running the protocol. “Performing a Run” on page 79

Step Topic See...


4. In the Task Settings page of the Protocol Task Parameters toolbar:

a. Type a name for the plate in the Plate name text box.

b. In the Plate type list box select the type of plate you want to use.

c. If you want to add or modify a plate definition, click Edit labware settings to open the labware editor.

For more information about labware settings, see the Database and Security User Guide.

d. If you are using a plug-in, select it from the Plugin list box.

If the plug-in is not available for selection, it is because the <file name>.dll file is not in the plug-ins folder, in the same directory as the VWorks executable. For more information about plug-ins, see “Setting Up VWorks Plug-Ins” on page 194.

e. In the Simultaneous plates text box, type the maximum number of plates of this type that you want to be available to the system at one time.

For advice on setting the number of simultaneous plates, see “Setting the Number of Simultaneous Plates” on page 116.

f. If you plan to use lids on the plates, select the Plates have lids check box.


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This option is only available if the plate you selected is capable of using a lid, as defined in the labware editor. For more information, see the Database and Security User Guide.

g. If the sample plates in the protocol have seals when they are placed on the BioCel®, check the Plates enter the system sealed check box.

h. If you are using the FileReader plug-in, select the Use plug-in for bar code data check box and make sure that the plate type you intend to use is selected in the Plate type list box.

5. In the Bar code control sub-page:

a. If the incoming plates have a bar code on the south side, in the Bar Code Control group box, select the first Incoming plates have bar codes check box.

b. If you want to check the south side bar codes on the incoming plates against a series of bar codes in a bar code input file, select the name of the bar code series you want to use.

For more information, see “Using Bar Code Input Files” on page 225.

c. If your BioCel has a VCode® or auxiliary bar code reader and you want to read bar codes on other sides of the plate, configure the relevant remaining options in the Bar Code Control group box.

6. In the Bar code error handling sub page:

a. Select one or more devices that you want to use as quarantine stations and click Add.

The device names are moved to the bottom quarantine list.

A quarantine station is a place that plates will be placed if the plate has a bar code mismatch error.

b. Check, or leave clear, the Quarantine plate after process completed check box, based on the following descriptions.

If the check box is left clear, a plate that gives a bar code misread error is immediately moved to a quarantine station and a new


plate takes the place of the quarantined plate in the processing sequence.

If the check box is selected, plates that give a bar code misread are processed as normal, but are then moved to quarantine instead of moving to the final destination specified in the protocol.


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Setting the Number of Simultaneous PlatesBackground The number of simultaneous plates is the maximum number of plates

belonging to a single process that are in the system at one time.

Plates that are in the system could be in the robot gripper, on platepads, VPrep® module shelves, plate hotels, and so on. Simultaneous plates do not include counterweight plates.

Setting the number of simultaneous plates is part of the process of setting up a plate instance, described in “Setting Up a Plate Instance” on page 112.

Selecting the Number

In general, the number of simultaneous plates to select for a plate instance depends on how many:

❑ Positions there are in the system that will incubate plates.

If your BioCel has five plate hotels and each stores ten plates, you can run more simultaneous plates than if your BioCel has only six platepads.

❑ Tasks there are in the protocol

In general, one simultaneous plate can be used for every task in the protocol. This is because, in general, each task uses one plate position. As an example, a protocol with three tasks can have three plates on the table at once. There are exceptions to this, though, such as cases where the same plate position is used for more than one of the tasks, and when a VPrep is used. Several plates can be positioned on a VPrep at the same time.

❑ Plates there are in a restack task.

If the protocol includes a restack task, the number of simultaneous plates must be equal to, or greater than, the number of plates in the restack task.

If the number of simultaneous plates is set too high, a plate could be introduced into the system when there is no place for it to go. This could result in a deadlock, at which point the protocol will stop.

For information about recovering from a deadlock error, see “Routine Maintenance” on page 308.

If the number of simultaneous plates is set too low, the time for the protocol run could be extended. Optimizing the number of simultaneous plates is therefore critical for maximizing BioCel efficiency.

A typical BioCel protocol has 5–30 simultaneous plates, but it could be many more than that. A safe number to start with when testing a new protocol is 1–2.


Adding and Deleting Tasks and Pipette TasksBackground After you have set up a plate instance for a process, you can start adding

tasks and pipette tasks.

Adding a Task You must always add a task to a process before you can define its task parameters.

To add a task:

1. If the Protocol Tasks toolbar is not showing, select View > Toolbars > Protocol Tasks.

2. In the Protocol Tasks toolbar, click the All tab.

3. Either:

Select a task icon and drag it to the protocol editor window until a vertical, dashed line appears.

Double-click the icon.

If you attempt to add a task that uses a module that is not configured in your device file, you will receive an error message.

Deleting a Task To delete a task:

1. In a protocol editor, select a task that is part of the protocol.

2. Press the DELETE key on the keyboard.

3. Click Yes in the Delete Task dialog box.


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Compiling and Saving ProtocolsCompiling a Protocol When you compile a protocol, VWorks checks to make sure that your

protocol makes logical sense.

If there are errors, it will report them, as described in “Compilation Warnings and Errors” on page 310.

To compile a protocol:

1. In VWorks, click Compile in the control toolbar.

Note: When you start a protocol, VWorks automatically compiles it and checks for errors.

Saving a Protocol To save a protocol you must be logged on with an Administrator or Technician user account. You can either save the protocol file alone, or save the protocol file and the current device file in a single procedure.

!! IMPORTANT !! When you edit a protocol, the changes to properties, other than plate instance properties, take effect immediately. Unless you explicitly save the protocol, the changes are lost when you exit VWorks.

To save a protocol:

1. Select File > Protocol File > Save As.

2. In the Save As dialog box, navigate to the folder in which you want to save the protocol.

3. In the File name text box, replace the selected file name with a name of your choice.

4. Click Save.

To save a protocol and the current device file:

1. Select File > Save All.

Adding Notes About the Protocol

You can add a description of your protocol to remind yourself of its features or for BioCel operators to review before performing a run. These notes will appear in the Protocol Notes column of the Runset Manager toolbar.

To add notes about your protocol:


2. Type your notes into the Description/Notes text box.


When you open a new protocol, its associated description replaces the description of the previous protocol.


120

About Setting Task ParametersBackground After you have added a task, you can set parameters for it. As you set the

parameters, the text underneath the task icons change to reflect the new parameters.

Types of Task For information about specific types of tasks, see the following topics:

Topic See page...

Setting AliQuot Task Parameters 126

Setting Apply Label Task Parameters 127

Setting Bio-Tek Washer Task Parameters 133

Setting Centrifuge Task Parameters 134

Setting Delid/Relid Task Parameters 135

Setting Echo 550 Transfer Task Parameters 136

Setting Envision Task Parameters 138

Setting Incubate Task Parameters 139

Setting MultiDrop Task Parameters 141

Setting Nanodrop Task Parameters 143

Setting Pierce Task Parameters 144

Setting Place Plate Task Parameters 145

Setting QFill Task Parameters 146

Setting Remp CSP Task Parameters 147

Setting Restack Task Parameters 147

Setting Seal Task Parameters 151

Setting Stacker Task Parameters 152

Setting StoreX Task Parameters 154

Setting Teleshake Task Parameters 156

Setting User Message Task Parameters 157

Setting Vacuum Task Parameters 159

Setting Waitfor Task and Signal Task Parameters 160

Setting Zeiss Task Parameters 161


About Setting Pipette Process Task ParametersPipette Tasks Versus Tasks

Pipette tasks differ from tasks in that they:

❑ Are added in the pipette process editor and not the protocol editor

❑ Reference settings in the liquid library editor

❑ May require you to change the VPrep shelf configuration in the device manager

More Information For information about the specific types of pipette tasks, see the following topics:

Topic See page

Setting Aspirate Pipette Task Parameters 173

Setting Change Instance Pipette Task Parameters 175

Setting Change Tips Pipette Task Parameters 177

Setting Dispense Pipette Task Parameters 180

Setting Dry Tips Pipette Task Parameters 183

Setting Loop Pipette Task Parameters 184

Setting Mix Pipette Task Parameters 185

Setting Pump Reagent Pipette Task Parameters 188

Setting Wash Tips Pipette Task Parameters 189


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Checking a ProtocolCompiling the Protocol

After creating a protocol, you can check for logical errors and out-of-range parameters by compiling the protocol.

To compile a protocol:

1. Click Compile.

Errors are reported in the Log toolbar.

Simulating the Run After making sure that there are no compiler errors in the protocol, you can check for other types of problems by running the protocol through the simulator. The simulator will allow you to find problems such as:

❑ Deadlocks

❑ Periods of inefficiency, when the robot is not being used

❑ Plates spending different times at critical steps when they should be run under identical conditions

❑ A number of simultaneous plates that is too high or too low

The simulator does not involve the robot or any modules. It performs a “virtual run” based on the estimated task execution times displayed for each task. You can change the execution times for tasks to make the simulation more accurate for your protocol.

One approach you could use for testing is to:

1. Run the simulator with the default task execution times and the same number of plates expected for a run to identify deadlocks and rate limiting tasks.

2. Resolve any major problems with the protocol.

3. Perform a real, dry run with a plate.

4. Use the times recorded in the Log toolbar to edit the task execution times for each task.

5. Run the simulator with the more accurate task execution times.

6. Fine-tune the protocol based on the results of the simulation.

Not all tasks have adjustable execution times, but for those that do, follow this procedure to change them.


To change the default task execution times:

1. Select a task in the protocol editor.

2. In the Protocol Task Parameters toolbar, click the Advanced Settings tab.

3. At the bottom of the toolbar, enter a new value for the Estimated task-execution time.


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This chapter is intended for people with Technician or Administrator privileges. It gives the procedures for configuring the parameters for individual tasks in a protocol. Before reading this chapter you should be familiar with the concepts presented in the chapter “Creating a Protocol: Basics” on page 109.

Procedures for configuring pipette tasks are given in “Setting Pipette Task Parameters” on page 163.

Setting Task Parameters 6

Chapter 6: Setting Task ParametersBioCel User Guide

126

Setting AliQuot Task ParametersTask Defined The Aliquot task moves a plate to an aliQuot where it liquid is dispensed

into the plate.

Procedure To set Aliquot task parameters:

1. In the process window, click the icon for the Aliquot task.

2. In the Protocol Task Parameters toolbar type the volume of liquid that you want to dispense in the Enter dispense volume text box.

3. In the Available devices list, select the aliQuot device that you want to use for this task and click Add.

The name of the device moves to the Devices to use list. If you want to use aliQuot pooling, you can add more than one aliQuot to the bottom list. This can double the throughput and will allow the protocol to continue if there is a problem with one of the aliQuots.

!! IMPORTANT !! If you are going to use pooling, you must make sure that the same reagent is dispensed to both, that the same manifold is used in both, and if you are using a filter plate, that the same filtering parameters are used.

4. If you have added more than one aliQuot you can change the order in which they are used:

a. Select an aliQuot in the Devices to use list.

b. Click Use Earlier to promote the aliQuot or Use later to demote it.

5. If you intend to use a filter plate:

a. Select the Use filtration check box.

b. Complete the Begin filtration... sentence to enter the remaining parameters.

The After filtration delay is the time after the filtration has stopped before the plate can be picked up.

!! DAMAGE HAZARD !! If the After filtration delay of is too short, the robot may crash.

127Chapter 6: Setting Task ParametersBioCel User Guide

Setting Apply Label Task ParametersBar Code Task Defined

The Apply label task uses a VCode® to print a bar code label and apply it to a plate.

Bar Code Labelling Decisions

Before you add an Apply label task to a protocol, consider your record-keeping and automation needs. For example:

❑ Do you need each bar code label to be unique within a run, but not from run to run?

❑ Do you need each bar code label to be unique across all runs?

❑ Will you be using a Laboratory Information Management System (LIMS) for barcoding information and record-keeping?

❑ What human-readable fields do you want to include on the label?

❑ Do you want to use a bar code input file?

❑ Do you want to use a bar code data file?

Bar Code Format When setting Apply label task parameters you need to select a bar code format, which specifies the type, number, properties and location of fields that are printed on bar code labels.

Some formats are provided with the VCode, but you can define others according to your needs. Each format is identified by a number, which you enter when setting up a Bar Code task.

For more information about formats and bar code symbologies, see the VCode User Guide.

Procedure To set Apply label task parameters:

1. In the process window, click the Apply Label task icon.

2. If necessary, widen the Protocol Task Parameters toolbar by dragging the left side.

3. In the Protocol Task Parameters toolbar, click a tab corresponding to a side of the plate.

The options are South, West, North and East.

4. Select one of the options in the Printing Option list box.

If... Then...

You do not want to place a label on this side of the plate

Select No Label and return to step 3.

You want to print a label that is the same as a label already set up for another side of the plate

Select Use <side> label and continue with step 3.

All other parameters on the page are ignored.


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5. In the Format to use text box, type a number that corresponds to the bar code format that you want.

For more information about formats, see the VCode User Guide.

6. In the Number of Fields text box, type the number of fields that you want to print on the bar code.

The maximum number of fields you can print is limited by the number of fields in the format you selected. For example, if the format specifies three fields you cannot print a bar code with four fields. In this example, if you do enter the number four into the text box, the last field is ignored.

VWorks does not delimit the number that you can type in this field and does not provide an error message, so you must take care to enter a valid number.

7. Click in the Field text box for the first field that you want to use and enter one or more of the following types of information that you want to print in that position on the label:

You want to define a bar code label and place it on this side of the plate

Select Use this label and continue with step 5.

If... Then...

If You Want to Print... Then...

A human-readable text field that does not increment

Type the text in the text box.

A bar code field that is identical to a bar code field on another side of the plate

a. Select the side of the plate from the from <side> side list box, below the Use existing bar code button.

b. Click Use existing bar code. This places the code [BC] in the text box.

Note: This option copies a bar code field from another side of the plate. The similar option selected in the Printing Options list box copies an entire bar code from another side of the plate.


A series of bar codes from a bar code input file

For information about creating a bar code input file, see “Using Bar Code Input Files” on page 225.

a. Make sure that you have set up a bar code input file and selected it in VWorks general options.For more information, see “Setting General Options” on page 48.

b. Make sure that the number of bar codes specified in the series of the bar code input file that you want to use is greater than the number of labels that you want to print.

c. Select the series in the Bar code file entry list box at the bottom of the toolbar. Note: If there are no entries in the Bar code file entry list box other than the default text, you need to set the location of the bar code input file. For more information, see “Setting General Options” on page 48.

d. Click From File. This places the code [FILE] in the text box. Note: If you use this option in two fields, the same data will be printed in both fields. You cannot enter different data into fields using this method.



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A series of bar codes by referencing bar codes on another side of the plate, using a bar code data file

For general information about bar code data files, see “Using Bar Code Data Files” on page 228.

a. Make sure that you have created a bar code database file and selected it in VWorks general options.For more information, see “Setting General Options” on page 48.

b. Make sure that the incoming plates have bar code labels on the south or west side, or a previous Apply label task is set up to print labels on the south or west side.

c. If the incoming plates are labelled, make sure that the system verifies the labels by setting up bar code control on the plate instance. For more information, see “Setting Up a Plate Instance” on page 112.

d. Click From text database.This places the code [DB] in the text box.

e. In the use <side> side list box under the From text database button, select the side of the plate that has the bar codes you want to use as a reference.

Note: Although you can select any side, only the south and west sides can currently be used.



8. Return to step 7 and fill out another field until all required fields are completed.

If you enter information in a field that does not exist in the format you have chosen, the information is ignored.

9. Return to step 3 and define labels to put on other sides of the plate.

Combining Bar Code Modifiers

You can combine bar code modifiers with text in a single field. In the example in this section, Format 2, which has five available fields, is selected as the format to use.

The available fields are:

A series of bar codes that increment, but which are not specified by a bar code input file

a. Type the root data that you want in the Field 1 text box.

b. Click Increment.This adds the code [INC] to the root data.

c. In the Increment chars text box, type the number of alphanumeric characters that you want to be appended to the root data.For example, if you want the series to increment from 01 type 2. If you want it to increment from 001, type 3.

d. In the Starting increment # text box, type the number that you want to be printed on the first label.

e. Select either Numeric or Alphanumeric depending on the increment style you prefer. Alphanumeric increments use 0–9, A–Z, whereas numeric increments use 0–9.

From a plug-in that you have developed

Select From user plug-in.

For more information about plug-ins, see “Setting Up VWorks Plug-Ins” on page 194.


Format Field VWorks Field Symbology/Font

Field 0 Field 1 Swiss Mono 721 Bold

Field 1 Field 2 Code 39

Field 2 Field 3 Dutch Roman 801 prop




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In the screenshot below, you can see that three of the VWorks fields are used: Field 2, Field 3 and Field 4.

Field 2 prints a Code 39 symbology bar code that is incremented for each printing. Field 3 prints the same bar code in the human readable Dutch Roman font. The text entered into Field 3 is the same as that entered into Field 2.

The information entered in Field 3, combined with the information entered into the Increment chars and Starting increment # fields, creates the following human readable bar code sequence:

Tues001

Tues002

Tues003

Tues004

Tues005

Tues006

Tues007...

The Bar Code Log File

Information about the bar codes that are applied during a run is saved in a bar code log file. Because this is a tab-delimited text file, the data can easily be imported into a spreadsheet program.

You can specify the folder in which you want to save the log file. For more information about setting up log files, see “About Log and Data Files” on page 56.


Setting Bio-Tek Washer Task ParametersBio-Tek Washer Task Defined

A Bio-Tek Washer task runs a single Bio-Tek washer program.

Procedure To set Bio-Tek Washer parameters:

1. In the Process window, click the Bio-Tek Washer icon.

2. In the Protocol Task Parameters toolbar, from the list box, select the program that you want to run.

3. If you want to see the parameters used for that program, modify a program, or create a program, click Show Programs.

This opens the Bio-Tek Diagnostics software. For more information, see “Using Bio-Tek Diagnostics Software” on page 266.

4. If your BioCel® has more than one Bio-Tek washer, select the one to use for this task from the Select washer to use list box.

f

More Information For more information, see the Bio-Tek user documents.


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Setting Centrifuge Task ParametersCentrifuge Task Defined

The Centrifuge task centrifuges a plate using a VSpin™.

This topic describes how to set the parameters for the Centrifuge task. Before you can run a protocol that uses a Centrifuge task, you must also set up one or more counterweight plates, so read this topic in conjunction with “Setting Up a VSpin Counterweight Plate” on page 77.

Managing Counterweights

If you intend to use the robot to load counterweights you must associate the device that will house the counterweight during the task with the type of labware that is used for the counterweight. This is so the robot can accurately pick up the plate. The device is usually a platepad.

You must make this association before you set the Centrifuge task parameters.

To associate a device with a counterweight plate type:

1. Identify a type of sample plate to centrifuge.

2. Select Tools > Manage Counterweights.

3. In the Manage Counterweights dialog box, select the device on which you want the operator to place the counterweight.

4. In the Labware type list box, select the same labware type as the plate instance for the process.

5. Repeat step 3 and step 4 to set up other types of counterweight plates.

6. Click OK.

Setting Centrifuge Task Parameters

To set Centrifuge task parameters:

1. In the process window, click the Centrifuge task icon.

2. In the Spin time text box of the Protocol Task Parameters toolbar, select two digits that correspond to the hours, minutes, or seconds that you want to change, and replace the numbers.

3. Repeat step 2 as needed.

4. Use the sliders to select the percentages of maximum velocity, maximum acceleration and maximum breaking deceleration.

5. If there is more than one VSpin on your BioCel, select the one you want to use from the Select VSpin to use list box.

6. Select the counterweight plate that you want to use for this task:

If you intend to manually place a counterweight plate into the centrifuge before starting the run, select manually inserted counterweight.

If you want the robot to deliver a counterweight plate to the centrifuge, select the device that will contain the correct


counterweight plate, according to the associations you made in “Managing Counterweights” on page 134.

More Information For more information, see the VSpin User Guide.

Setting Delid/Relid Task ParametersDelid/Relid Task Defined

The Delid/Relid task removes or replaces a lid on a plate.

Note: Do not confuse this task with the Change Tips pipette task which removes tipbox lids when changing tips on a VPrep®.

How It Is Used There are no task parameters for the Delid/Relid task. The following screenshot shows a typical use for this task.

In the example, a plate is downstacked and the lid is removed. A reagent is pipetted into the plate and the lid is replaced. The plate is then upstacked.

Note: For systems with a lid hotel and vacuum station, the relid task must be included, otherwise the lid will be removed by a vacuum station and dropped into the waste.


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Setting Echo 550 Transfer Task ParametersIntroduction Pairs of Echo550 Transfer tasks are used to move a plate to an Echo 550

compound reformatter and initiate an Echo 550 protocol. The protocol uses an acoustic wave to transfer a droplet of liquid from one plate to another.

Echo550 protocols are created in the Echo550 software which is installed on the BioCel computer.

Protocol Set-Up This section explains how to set up a VWorks™ protocol for an Echo550 transfer. For information about setting up an Echo550 protocol, see the Echo550 user documents.

To perform a droplet transfer with an Echo550 you need to set up two processes in a single protocol. One process is for the source plate and the other is for the destination plate. An example protocol is shown below in which first process is for the source plate.

Procedure To perform an Echo 550 transfer:

1. Make sure you have created the Echo550 protocol that you want to run.

2. Set up a VWorks protocol with processes similar to those shown in the previous section.

3. Configure the Echo550 Transfer task for the source plates:

a. Select the Echo550 source task.

b. If the protocol will perform more than one transfer, select the name of the transfer in the Use process label list box.

Process 1 is the name of the default transfer.

c. If you have more than one Echo550 on your BioCel, select the one you want to use in the Echo550 device list box.

d. Make sure that the Source button is selected.

e. In the Echo550 protocol list box, select the name of the Echo550 protocol that want to run.


f. Select the labware type that you want to use for the source plates in the Echo550 labware list box.

Note: The labware definition you are selecting is an Echo550 definition and not a Velocity11® labware database definition.

g. If you want the stage to stop at every well as it performs the transfer, clear the Use fast fly-by transfer mode check box.

The default alternative is a single “scan” of every row of the plate.

h. If you want to survey a random sample of wells instead of every well, select the Perform a fast survey check box.

A well survey records reflection amplitudes from the microplate and fluid surfaces, the results of which are use to optimize the delivered acoustic transfer wave.

4. Configure the Echo550 Transfer task for the destination plates:

a. Select the Echo550 destination task.

b. Make sure that the name in the Use process label list box is the same as that used for the source plates.

c. Make sure that the name in the Echo550 device list box is the same as that used for the source plates.

d. Select Destination.

More Information For more information, see the Echo550 user documents.


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Setting Envision Task ParametersEnvision Task Defined

The Envision task moves a plate to a PerkinElmer Envision plate reader and instructs the reader to perform an Envision assay protocol.

Envision assay protocols are created using the Envision’s dedicated computer and software. The protocol to use for the task is selected when setting the Envision task.

For information about switching to the Envision’s dedicated computer, see “Computers and Networking” on page 27.

Procedure To set Envision task parameters:

1. In the process window, click to select the Envision task.

2. In the Protocol Task Parameters toolbar, check the name of the currently selected assay protocol, which is displayed in the Assay protocol to run box.

3. If the displayed protocol is not the one you want to run, click Select new assay protocol and select the profile from the Select Envision Assay Protocol list box.

4. Click OK.

More Information For more information, see the Envision user documents.


Setting Incubate Task ParametersIncubate Task Defined

The Incubate task performs a timed incubation of a plate. It is typically used for short incubations.

The number of plates that can be incubated simultaneously is limited by the number of platepads and plate hotels that are available for holding plates.

When to Use If you want to perform a longer incubation of more than one plate and want to reduce evaporation from the plates, see “Setting Restack Task Parameters” on page 147.

Process Overview The overall process for a typical incubation is as follows:

1. Incubation of the plate starts with the addition of an initiating reagent.

This would be performed by a liquid handling task, such as a QFill Task or Pipette Process Task.

2. The plate is moved to a platepad.

When the plate arrives at the platepad, the incubation time parameter that you specify starts timing.

3. The plate is moved from the platepad to a reader.

The plate is moved when the incubation time parameter that you specify ends.

Incubation Time Error

The time parameter that you set for the incubation period is not the actual time of the incubation. It represents the minimum time that the plate will sit on the platepad where the Incubation task is carried out.

The actual incubation period starts when the initiating reagent is added and continues until the plate is transferred to the next step in the process. This means that the actual incubation is longer than the time parameter that you set, by an amount that depends on the scheduling and operating speed of the robot.

If your assays require greater precision in plate incubation times than this method supports you can use internal controls on each plate to allow you to adjust data across plates if you need to.

Procedure To set Incubate task parameters:

1. In the process window, select the Incubate task icon.

2. In the Protocol Task Parameters toolbar, type the length of time for which you want the plate to incubate on the platepad.

3. If you want to perform a time-series incubation, in which each plate is incubated for a time longer than the previous plate, select the Start timer when previous plate finishes incubating check box.


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4. If you want to restrict a device so it is not used as the place where the incubation takes place, in the Available devices box, select the device and click Exclude.

This may be useful if a particular plate pad is used during multiple steps of the protocol.

The name of the device moves to the lower box.

5. If you want to allow a device that is currently excluded, click Allow.

The name of the device moves to the upper box.

Example In the following example, a plate is downstacked, moved to an incubator and incubated for 60 minutes, moved out of the incubator and then upstacked.

!! IMPORTANT !! To create this process, the downstack and upstack tasks must be added to the process first. Then the StoreX task is added between them.

To perform a timed incubation:

1. Set up a protocol like that shown above.

2. Select the StoreX task and configure the task parameters, as described in “Setting StoreX Task Parameters” on page 154.

3. Start the run.

For more information, see “Starting a Run from VWorks” on page 83.


Setting MultiDrop Task ParametersMultidrop Task Defined

The MultiDrop task moves a plate to a Thermo Labsystems Multidrop 384 or 96 dispenser and instructs the dispenser to fill the plate. You can specify whether to include prime, shake or purge operations.

The MultiDrop is capable of dispensing up to eight different liquids into one plate. During a dispense, the plate stage moves in the left-right axis and the wells are filled in columns, starting with column 1. In a 96-well plate there are eight rows, so every well in a column is filled at the same time. In a 384-well plate there are 16 rows, requiring two dispense passes. During the first pass, every second well in a column is filled. The plate stage then moves over by one well so that the dispensers sit above empty wells. In the second pass, the stage returns to the starting position and the remaining wells are filled.

Procedure To set Multidrop parameters:

1. In the process window, click the Multidrop task icon.

2. If your BioCel has more than one Multidrop, select the one you want to use for the task from the Select the Multidrop to work with list box.

3. If you want to prime the Multidrop, enter the volume of liquid to prime with in the Prime volume text box, as a multiple of 5 µL.

Priming moves liquid through the dispensing system into waste to make sure that there is no air in the lines.

4. In the Dispense volume text box, enter the volume of liquid that you want to dispense into each well, as a multiple of 5 µL.

5. To shake the plate after the dispense, enter a value into the Shake time text box.

6. To purge the lines after the dispense, select the Purge x times when complete check box, and enter the number of times to purge.

Purging moves liquid back into the liquid reservoir or reservoirs. If you want to return all liquid, the value of x may need to be greater than one.

7. To dispense into all wells, make sure that the Entire plate option is selected.

A

B

C

D

E

F

G

H

I

J

K

L

M

N

O

P

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

Columns

Rows


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8. To only dispense into some of the wells:

a. Select the Selected columns option.

b. Click Select none.

c. In the number matrix, click the numbers corresponding to the columns to dispense into.

In the following example liquid will be dispensed into columns 2, 4, 6 and 8 of a 384-well plate.

More Information For more information, see the Multidrop user documents.


Setting Nanodrop Task ParametersNanodrop Task Defined

The Nanodrop task moves a plate to a Nanodrop liquid dispenser and runs a pre-defined program, using a calibration file for more accurate dispensing.

Procedure To set Nanodrop task parameters:

1. From the list boxes, select:

a. The program to run.

b. The calibration file to use.

c. The Nanodrop to use, if your BioCel has more than one.

The name of the Nanodrop is defined in the device manager.

More Information For detailed information about the Nanodrop, see the Nanodrop User Manual.


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Setting Pierce Task ParametersPierce Task Defined The Pierce task pierces a plate seal using a PlatePierce™.

When to Use To see how this procedure fits into the overall process of performing a run, see “Overview of Performing a Run” on page 80.

For the steps required before performing this procedure, see “Creating a Protocol: Workflow” on page 110.

Procedure To set Pierce task parameters:

1. In the process window, click the Pierce task icon.

2. In the Protocol Task Parameters toolbar, enter a value in the Piercing Pressure text box.

If you are unsure of the best piercing pressure to use for your application, contact the Velocity11 Service Center.


Setting Place Plate Task ParametersPlace Plate Task Defined

The Place Plate task moves a plate to any location. This task has many uses.

The next task in the process after a Place Plate task will move the plate to another location.

Note: Do not confuse this task with the plate instance, described in “Setting Up a Plate Instance” on page 112.

Place Plate Task and Bar Codes

The Place Plate task can be used in combination with a platepad bar code reader to read a bar code. The requirements for this are:

❑ The platepad reader must be set up in the device manager as a device.

❑ The plate instance for the plate must indicate that the plate has a bar code on the side that the bar code reader reads.

Whenever a plate is placed on this platepad the scheduler tells the bar code reader to read the plate.

Procedure To set Place Plate task parameters:

1. In the process window, select the Place Plate task icon.

2. In the Protocol Task Parameters toolbar, from the list box, select the device to which you want to move the plate.

You may need to scroll down to make your selection. If you are using this task to read a bar code on a platepad, make sure you select the bar code reader device.

3. If the Place Plate task is the first task in the protocol and you want to require that the operator confirms the bar code on the plate that is placed, check the Manually confirm bar code check box.

This can prevent the wrong plate from being used in the protocol, which could be a costly mistake if you are using expensive reagents.

To confirm the bar code, when the plate is picked up, the operator is prompted to enter the bar code of the plate that should be in the placed position. If the two codes do not match, an error is generated.


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Setting QFill Task ParametersQFill Task Defined The QFill task dispenses liquids into plate wells and offers the option of

vacuum filtration.

If you want to use vacuum filtration, your QFill must include the vacuum station option developed by Velocity11.

If your QFill2 does not contain the vacuum station option, you can use a separate vacuum station. For more information about setting up vacuum filtration as a separate task, see “Setting Vacuum Task Parameters” on page 159.

Procedure To set QFill task parameters:

1. Drag a QFill task icon to the process window to add the task.

2. In the Protocol Task Parameters toolbar enter the volume of liquid that you want to dispense into each plate well.

3. In the Available devices box, select the QFill that you want to use for this task.

4. Click Add.

The name of the device moves to the Devices to use list. If you want to use QFill pooling, you can add more than one QFill to the bottom list. This can double the throughput and will allow the protocol to continue if there is a problem with one of the QFills.

!! IMPORTANT !! If you are going to use pooling, you must make sure that the same reagent is dispensed to both, that the same manifold is used in both, and if you are using a filter plate, that the same filtering parameters are used.

5. If you want to use vacuum filtration, in the Filtration group box:

a. Select the Use filtration check box.

b. Complete the Begin filtration sentence, specifying how long before or after filling you want the filtration to start.

c. Type a filtration duration in the Filter for text box.

d. If you want to add a post-filtration delay, type the delay time in the remaining text box.

The delay is the time that elapses before the robot will pick up the plate, allowing the vacuum under the plate to dissipate.

!! IMPORTANT !! If this value is too small the robot may not pick up the plate correctly, causing a robot crash.


Setting Remp CSP Task ParametersRemp CSP Task Defined

The Remp CSP task seals a plate using a Remp sealer.

There are no task parameters to configure for the Remp sealer.

Setting Restack Task ParametersRestack Task Defined

The Restack task collects plates in a VStack®, moves them to another VStack in a definable time, and returns the plates to their original order before moving them to another task.

The Restack task is used as part of a larger process that carries out simultaneous, timed incubations of more than one plate, where the goals are for the:

❑ Time between the start of the incubation and the reading of the plate to be approximately the same for each plate

❑ Evaporation from the plates to be minimized

The minimum incubation time for this task is 30 seconds.

If you want to perform a simple, timed incubation that takes place on platepads or plate hotels, and which is useful for short incubations and when fewer plates are used, see “Setting Incubate Task Parameters” on page 139.



Process Overview To understand the concept of a Restack task consider the following simple restacking protocol as an example.

The overall flow of events in the protocol, in which individual steps do not necessarily correspond to individual protocol tasks is as follows:

1. The plates are in a VStack (Stacker 1) ready for the run.


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2. The plates are downstacked and moved to a VPrep where a reagent is added to initiate the incubation. The restack task begins when the plates are then moved to an empty rack (Stacker 2).

When the first plate enters the empty stacker the incubation time parameter that you specify starts timing. However, the actual incubation started when the initiating reagent was added. The time between the actual incubation start and the time at which the incubation time parameter starts depends on the scheduling and operation speed of the robot, so it may not be consistent from one plate to another.

3. The remaining plates are moved to the receiving stacker. The last plate to start incubating is now on the bottom.

If plates are moved directly to a reader from this position the plate that has incubated for the least time is read first, leading to a large inconsistency in inter-plate incubation times. The plates must be restacked so that the plate that started incubating first is read first.

4. The plates are moved to another stacker, reversing their order.

Reader

Stacker 1 Stacker 2 Stacker 3

VPrep

1

23

456

Reader


VPrep

2

1

3

45

6

Reader


VPrep

6

54

321


5. The remaining plates are restacked so that the plate that started incubating first lies on the bottom.

6. The plates are moved, one at a time, to a plate reader, and then to different rack for storage. In this example, the final rack is the same as the starting rack. The plates are moved from the rack to the reader after the time interval specified in the Protocol Task Parameters toolbar.

The actual incubation continues as the robot moves the plate to the reader and the reader prepares to take measurements.

7. When the run is complete all plates are in the final rack ready for removal from the BioCel.

Reader


VPrep

4

32

1

5

6

Reader


VPrep

1

23

456

Reader


VPrep

2

1

3

45

6


150

Procedure To set Restack task parameters:

1. In the process window, click the Restack icon.

2. In the Protocol Task Parameters toolbar either:

Select the empty stackers that you want to use for the task, and click Add.

Click Add dynamically-assigned stacker.

With the second option, the scheduler automatically assigns stackers during a run, and there must be at least two stackers available for this operation. VWorks pools racks that contain plates that use the same plate instance. For example, if a protocol specifies source plates entering the system for VStack 1 and VStack 2, VWorks will automatically begin downstacking from VStack 2 once VStack 1 is empty. You can consult the VWorks log toolbar to see the assignments made during the run.

3. In the Store up to text box, type a number equal to the number of plates you intend to incubate.

4. In the Incubate plate for text box, type the time interval, between when a plate enters the first restack stacker and leaves the second restack stacker.

This value is important because it can affect the timing of the incubation. For example, if the time taken to move all plates to the first restack stacker is greater than the time specified for the incubation, the first plate cannot be restacked and moved to the next task in time. This problem can be resolved by moving plates to two stackers before they are restacked.

Reader


VPrep

6

54

321


Setting Seal Task ParametersSeal Task Defined The Seal task seals a plate using a PlateLoc®.

If you are using more than one type of plate or seal and require different sealing temperatures, we recommend that you use a separate PlateLoc for each temperature. This will avoid time delays as the PlateLoc heats and cools between different plate or seal types.

!! IMPORTANT !! Do not use the same PlateLoc at more than one temperature in the same protocol.

When you open a protocol containing one or more Seal tasks, PlateLocs will immediately start adjusting to the temperatures defined in the task parameters.

Procedure To set Seal task parameters:

1. In the process window, click to select the Seal task icon.

2. In the Protocol Task Parameters toolbar, enter a seal time and seal temperature.

When you enter a seal temperature, the PlateLoc will immediately start adjusting to that temperature.

3. Select the PlateLoc to use for the sealing operation from the Select PlateLoc to use list box.

If you have more than one PlateLoc on the BioCel, make sure that you select the module with the correct sealing temperature and sealing time for the plate.


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Setting Stacker Task ParametersStacker Task Defined

The Stacker task moves plates in to or out of VStack® racks.

The process of moving a plate out of a rack is called downstacking. The process of moving a plate to a rack is called upstacking.

Plates may be returned to the same or a different VStack.

A single task can upstack to, or downstack from, more than one rack. For example, in a downstacking task, when all of the plates are removed from one rack the robot will pick plates from a second rack. The two racks are referred to as pooled downstackers.

Procedure To set Stacker task parameters:

1. In the process window, click to select the Stacker task icon.

2. In the list of available VStacks in the Protocol Task Parameters toolbar, select a VStack that you want to downstack from, or upstack to, and click Add.

To select more than one VStack, you can SHIFT-click or CTRL-click before clicking Add.

An asterisk next to a VStack in the list means that the VStack is currently assigned to a task that uses the same labware.

3. If you want to remove a VStack from your list of available VStack modules, select it and click Remove.

4. If you have added more than one VStack, you can change the order in which they are used:

a. Select a VStack.

b. Click Use earlier to promote the VStack or Use later to demote it.

5. To specify a time interval that determines when plates are made available to the system, select the Release a new plate check box and type in an interval time.

You could use this feature to avoid a plate processing bottleneck that results in plates having different incubation times. Consider a simplified example process in which plates are downstacked, incubated for 5 minutes, dispensed into, and then upstacked. When the protocol begins, the first plates are sequentially moved to platepads for incubation. The process of moving them only takes a few seconds so they are incubated simultaneously with slightly staggered incubation start times. Because the dispense task takes


longer than the time taken to move the plates to platepads, it is the limiting step and creates a processing bottleneck.

If the dispense task takes 2 minutes, plates that are ready for the pipetting step would have to wait. In this example, the first plate would incubate for approximately 5 minutes, the second plate for approximately 7 minutes, the third plate for approximately 9 minutes, and so on. To avoid these different incubation times, you could downstack one plate every 2 minutes. The plates are then incubated sequentially and not simultaneously.

6. If you want to dynamically assign upstacking VStacks, click Add dynamically-assigned stacker.

This option is only available for upstacking tasks.

With dynamic assignment you do not have to specifically assign every VStack that will receive plates because assignments are made automatically. All plates from the same downstacking VStack are moved to the same upstacking VStack.

When VStacks are dynamically assigned, the text “TBD,” meaning To Be Determined, is added to the Stacker task icon.

You can determine which VStacks contain which plates at the end of the run by consulting the run log or the VStack displays.


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Setting StoreX Task ParametersStoreX Task Defined The StoreX task performs three different actions, depending on its

position in the process:

!! IMPORTANT !! Do not move a StoreX task once you have added it to a process because its function (load, unload or incubate) will not change as you intend. If you want to move a StoreX task in a process, delete the task and drag a new task to its final destination.

Relationship with Linker Files

StoreX load and unload tasks have no protocol task parameters to configure, but to use them you must set up a linker file instead.

To learn how to set up a load or unload StoreX task, you also need to read the following topics:

❑ “Inventory Management Overview” on page 231

❑ “Inventory Manager Views and Filters” on page 234


❑ “Working with Linker Files” on page 238

Transfer Station A transfer station is used to pass plates from a StoreX incubator to the BioCel robot. Transfer stations must be properly configured before running a protocol containing a StoreX task.

For more information about configuring a transfer station, see “About Setting Up a StoreX Transfer Station” on page 230.

Position of Task in Process

Action

First Unload.

Moves one or more plates from a StoreX incubator to the BioCel.

Last Load.

Moves one or more plates from the BioCel to a StoreX incubator for long term storage.

Between a Stacker or StoreX task that moves plates in to the system and a task that moves plates out of the system

Incubate.

Moves one or more plates from the BioCel to a StoreX incubator and incubates it for a specified time before being removed by another task.


Procedure StoreX load and unload tasks have no protocol task parameters to set up. However, the StoreX incubate task does.

To set StoreX incubate task parameters:

1. In the Protocol Task Parameters toolbar, select the incubator that you want to incubate the plates in from the list box.

2. In the Incubation time text box, enter the time that you want to incubate for.

About StoreX Bar Code Reading

If your StoreX includes a west-side bar code reader, whenever a plate is unloaded, its bar code is read. The reading is compared to the value in the inventory management system to make sure that the bar code is the one expected.

If there is a mismatch, an error dialog box will open giving you a choice of three actions:

Action Meaning

Abort The run will end.

Retry Use the value listed in the database for this plate.

Ignore Overwrite the value in the database with the value that was read.


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Setting Teleshake Task ParametersTeleshake Task Defined

The Teleshake task moves a plate to a Teleshake plate shaker and shakes it for a specified time, in a specified direction, and at a specified speed.

When to Use Use this procedure when creating a protocol.

To see how this procedure fits into the overall process of performing a run, see “Overview of Performing a Run” on page 80.


Procedure To set Teleshake parameters:

1. In the process window, click the Teleshake task icon.

2. In the RPM text box of the Protocol Task Parameters toolbar, enter a number to indicate the relative speed of the shaking.

3. In the Direction text box, enter the direction in which to shake the plate.

Directions are specified using the points of the compass and can be in a circular motion, for example NWSE (north, west, south, east), or in a back-and-forth motion, for example, NS.

4. In the Duration text box, enter the time to shake the plate for.


Setting User Message Task ParametersUser Message Task Defined

The Administrator or Technician who creates a protocol can add User Message tasks to provide reminders to the operator. The reminders are in the form of messages that appear on the screen at the appropriate time and pause the protocol until acknowledged by the operator.

User message tasks could, for example, be used to remind the operator to empty the waste container, fill a reservoir, or remove plates.

!! IMPORTANT !! Remember to remove all user messages from protocols that you intend to run unattended.

Example of Use User messages are often given their own process. In the example shown below, the protocol has four user messages that remind the operator to perform final run-preparation tasks. The User Message tasks are performed before any plates are downstacked.

The intended sequencing of the User Message tasks is ensured by the addition of Signal tasks to the other processes in the protocol. For more information about adding signal tasks, see “Specifying Task Order Across Processes” on page 162.

When to Use To see how this procedure fits in to the overall process of performing a run, see “Overview of Performing a Run” on page 80.

Procedure For general information about creating a protocol and the steps required before performing this procedure, see “Creating a Protocol: Workflow” on page 110.

To set User Message task parameters:

1. In the process window, click the User Message icon.

2. In the Protocol Task Parameters toolbar, select one of the following Message will appear options:

Option Description

First plate of the series only Displays the message the first time it is encountered for that process during the run.


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3. If you want to trigger an alarm when the task executes, select the Sound alarm checkbox.

When the alarm is triggered a user interface message box opens, a sound is generated, and the lights on the posts of the BioCel flash.

4. If you want a notification email to be sent when the task executes, select the Email notification check box.

This feature requires that the BioCel is set up to send email notifications. For more information, see “Setting Up Email” on page 6 and “Notification of Errors by Pager or Email” on page 103.

5. Type the message that you want to display:

a. Type the message title in the top text box.

b. Type the message body in the bottom text box.

Every x plates Displays the message the first time it is encountered for that process during the run, and then every x number of times it is encountered for that process during the run.

As an example, if the value of x is 3, the first plate in the process will trigger the message, the next two plates will not trigger the message, and the fourth plate will trigger the message.

Last plate of the series only Displays the message the last time it is encountered for that process during the run.

Option Description


Setting Vacuum Task ParametersVacuum Task Defined

The Vacuum task requires a vacuum plate and vacuum pump to be fitted on the BioCel. The task is used to perform a vacuum filtration with filter plates.

!! IMPORTANT !! Do not confuse this type of task with the Delid/Relid task, which is used to remove lids from plates.

For information, see “Setting Delid/Relid Task Parameters” on page 135.



Procedure To set Vacuum task parameters:

1. In the process window, click the Vacuum task icon.

2. In the Protocol Task Parameters toolbar:

a. In the Amount of time to draw vacuum text box, enter the length of time that you want the vacuum to pull.

b. In the Post-vacuum delay text box, enter the time that you want to elapse between the time the vacuum pump stops and when the plate is available to be picked up by the robot.

The delay is the time that elapses before the robot will pick up the plate, allowing the vacuum under the plate to dissipate. If this value is too small the robot may not pick up the plate correctly.


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Setting Waitfor Task and Signal Task ParametersIntroduction The Waitfor task works with a Signal task to specify the order across

processes in which tasks are performed. You must first set the Waitfor task and then set the Signal task.

For more information about how to use Waitfor tasks and Signal tasks, see “Specifying Task Order Across Processes” on page 162.

When to Use To see how these procedures fit into the overall process of performing a run, see “Overview of Performing a Run” on page 80.


Setting Waitfor Task Parameters

To set Waitfor task parameters:

1. In the process window, click the Waitfor task icon.

2. In the Protocol Task Parameters toolbar, type a name for the task.

Setting Signal Task Parameters

To set Signal task parameters:

1. In the process window, click the Signal task icon.

2. In the Available waitfors text box of the Protocol Task Parameters toolbar, select the Waitfor task that you want to reference.

3. Click Add.

The task moves to the lower box.


Setting Zeiss Task ParametersZeiss Task Defined The Zeiss task moves a plate to a Zeiss Multimode plate reader, and

instructs the reader to perform a particular assay.

When to Use Use this procedure when creating a protocol.

To see how this procedure fits into the overall process of performing a run, see “Overview of Performing a Run” on page 80.


Procedure To set Zeiss task parameters:

1. Make sure that an assay has been created using Zeiss software on the dedicated computer.

2. In the process window, click the Zeiss task icon.

3. In the Assay text box of the Protocol Task Parameters toolbar, type the name of the assay to run.

The name must exactly match the name of the assay file, including the file name extension. It is not case sensitive.

4. From the Bar code to send list box, select the side of the plate with the bar code that you want to be listed in the reader output data.


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Specifying Task Order Across ProcessesIntroduction If you are running more than one process in a protocol, you may want to

specify that a particular task in one process is performed before a particular task in another process. You do this when creating a protocol by using the combination of a Waitfor task and a Signal task. The two tasks work together.

Example In this example, the Administrator or Technician creating the protocol wants to make sure that a bar code is applied to plate 1 before plate 2.

The operator creates the protocol shown in the following diagram.

The order in which plate 1 and plate 2 are incubated is selected by the scheduler program. Without the Waitfor and Signal tasks, this would also be the case for the barcoding operation. However, in this protocol, the Waitfor task, called “Label Me Second”, is included for Plate 2, and this causes the process to wait until it receives an instruction to continue. Meanwhile, the bar code is applied to Plate 1.

After the bar code has been applied to Plate 1, the Signal task called “Signal Label Me Second” releases the wait condition on Plate 2 and the bar code is applied.

For information about how to set up the Waitfor and Signal tasks, see “Creating a Protocol: Workflow” on page 110.

Waitfor task Signal task

This chapter is intended for people with Technician or Administrator privileges. It gives the procedures for configuring the parameters for individual pipette tasks in a protocol. Before reading this chapter you should be familiar with the concepts presented in the chapter “Creating a Protocol: Advanced Topics” on page 193.

Procedures for configuring tasks are given in “Setting Task Parameters” on page 125.

Setting Pipette Task Parameters 7

Chapter 7: Setting Pipette Task ParametersBioCel User Guide

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Configuring a Pipette Process: ExampleIntroduction This topic gives an example of how to configure a protocol that performs

a simple pipetting operation.

The Goal The goal of the pipetting operation in this example is to pipette 20 µL of 1X TE buffer from a reservoir on a particular VPrep® into a Costar 96-well plate.

Creating a Protocol The first step is to create a new protocol by setting up a plate instance for the plate you want to pipette into.

Following the procedure in “Setting Up a Plate Instance” on page 112 you name the plate instance “Plate A” and select the “Costar 96-well plate” plate type.

Downstacking a Plate

The next step is to follow the procedure in “Setting Stacker Task Parameters” on page 152 to add a Stacker task that downstacks a plate from an appropriate stacker.

165Chapter 7: Setting Pipette Task ParametersBioCel User Guide

Adding a Pipette Process Task

Next, you follow the procedure in “Adding and Configuring a Pipette Process Task” on page 169 to add a Pipette Process task.

Because there can be a number of Pipette Process tasks in a protocol, this particular pipetting operation is identified by the name selected from the list box in the Pipette Task Parameters toolbar. In this simple case there is only one name to select, which is “Process1.”

Selecting a VPrep In this example, there are two VPrep pipettors already installed on the BioCel® so you need to associate the one you want to use with the pipette process.

You do this in the pipette process editor. In the following example, the task will use VPrep1. VPrep2 remains available but is not used for this task.

Configuring the VPrep Shelf

You want to aspirate 20 µL of 1X TE buffer from a reservoir. This means that you have to configure a shelf of the VPrep to hold the reservoir that will contain the buffer. You decide to use a 384 V11 Reservoir (manual fill) 21.5 deep plate type for the reservoir.

We know that the VPrep itself has already been configured in VWorks™ as a device because you were able to select it in the previous step. We can also see it listed as a device in the device manager. To open the device manager you click the Device Manager tab.


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Each shelf that you want to use on the VPrep must also be configured as a device. The shelves are already set up as devices, but you need to make sure that shelf 1, where you want to place the buffer reservoir, is configured correctly. Again looking at the device manager you see that there are two shelves configured as reagent shelves, which can hold reservoirs.

On selecting reservoir 1 you see that it is assigned to shelf 1 of VPrep 2, which is what you want. However, the labware associated with the shelf is the wrong type.

If you leave it as V11 MicroWash 384, the pipette tips may crash into the reservoir because the task will be performed on the assumption that the tips are moving into a 384 V11 Reservoir (manual fill) 21.5 deep reservoir.

So, you change the Labware association to 384 V11 Reservoir (manual fill) 21.5 deep.

Note: To save the changes in the device manager you need to have Administrator login privileges.

Note that when you associate a type of labware with the VPrep shelf, you are also associating all of the parameters for that type of labware stored in the labware database. The VPrep references the labware database parameters so that the pipette tips move to the right depth, position, and so on, as they enter the reservoir.

After configuring a VPrep shelf, compile the current protocol to check for errors.


Adding an Aspirate Pipette Task

The next step is to add an Aspirate pipette task.

Following the procedure in “Setting Aspirate Pipette Task Parameters” on page 173, you add the Aspirate pipette task.

Associating the Task with a Liquid Class

In the Pipette Task Parameters toolbar of the Aspirate pipette task you need to tell the system what class of liquid it is aspirating. The system then uses the parameters stored in the liquid library database for that class, during the aspiration operation.

In this case you select the class 1XTE.

You can see the parameters used for the class by clicking the Edit button, which opens the liquid library editor. For more information about the liquid library editor, see the Database and Security User Guide

Associating the Task with the VPrep Shelf

In the Pipette Task Parameters toolbar of the Aspirate pipette task you need to tell the system what type of labware to aspirate from.

In this case there are two choices. If you select Plate A, the Costar 96-well plate you downstacked will be moved to the VPrep and the volume aspirated from it. Instead, you select reservoir1, which is the name of the device that holds the buffer reservoir.

Finally, you specify that we want to aspirate 20 µL.

The modified task is shown in the following diagram:


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Adding a Dispense Task

To complete the pipetting operation we have to add a dispense task and set the parameters using the procedure in “Setting Dispense Pipette Task Parameters” on page 180.

The dispense task is dragged into the pipette process pane.

The task correctly defaults to dispense into Plate A, but the dispense volume is incorrect and there is no associated liquid class. After editing the task parameters, the task is shown in the following diagram:

The protocol is now complete.


Adding and Configuring a Pipette Process TaskAdding a Pipette Process Task

The first step in creating a pipette process is to add a Pipette Process task to the protocol editor. A Pipette Process task is added in the same way as any other task. See “Adding and Deleting Tasks and Pipette Tasks” on page 117 for more information.

Setting Pipette Process Parameters

When you add the Pipette Process task a new pipette process is started in the pipette process editor. The pipette process is identified by its pipette process link icon.

For more information about what this link icon represents, see “About Tasks, Processes and Protocols” on page 42.

Because you can have more than one pipette process in a protocol, you must link the Pipette Process task to the pipette process by setting the Pipette Process parameters.

To set the Pipette Process parameters:

1. Select the Pipette Process task in the protocol editor.

2. In the Pipette Task Parameters toolbar, select the pipette process that you want to use for this pipetting task.

3. If the pipette process is for a replicate pipetting series, so that the same plate can be used over and over again, select the Use single instance of plates check box.

If the plate is a tip box, when this option is selected, the tips will be picked up and the tip box will be moved from the VPrep. At the end of the pipetting series, the tip box will be returned to the VPrep and the tips replaced in it.


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Associating the Link Icon

Because you can have more than one VPrep on a BioCel, you must link each pipette process link icon with one or more VPrep pipettors that you want the pipette task to be able to use. You do this by setting the parameter for the pipette process link icon.

To link a Pipette Process task to a pipette process:

1. In the pipette process editor, select the pipette process link icon.

2. In the Available pipettors list of the Pipette Task Parameters toolbar, select one or more pipettors to link to and click Add.

The selected pipettors move to the lower box and become available for the pipette task to use.


Configuring a VPrep Shelf As a DeviceIntroduction When you set parameters for some pipette tasks, you have to select the

type of labware or device used in the task. The following screenshot shows both a plate and a device in the list box of an Aspirate pipette task.

The plate in the list box refers to Plate A in the associated process.

With Plate A selected, the robot will move the plate to the VPrep and liquid will be aspirated from it.

The device in the list box refers to a reagent shelf on the associated VPrep. With shelf 1 selected, the VPrep head will move to shelf 1 and the VPrep will aspirate from whatever type of labware sits on the shelf.

Before you can run the protocol, you have to associate a type of labware with the VPrep shelf. You do this in the device manager.

When to Use This Procedure

Use this procedure when creating a protocol that uses a type of reservoir on the VPrep that is not currently set up.

Procedure All shelves on your VPrep were set up as devices at the factory. This procedure shows you how to modify the existing settings for a shelf.

To configure a VPrep reagent shelf as a device:

1. Click the Device Manager tab.

2. Select a reagent shelf in the Device List.

3. Make sure that:

The Parent device is the VPrep you intend to use.

The Shelf number is the shelf you intend to use (reagent shelves have odd numbers, with shelf 1 being at the top).


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If these are not correct, select another reagent shelf in the Device List.

4. Optionally, change the Device Name to one that describes the type of liquid being used by typing over the existing name.

5. Select the type of labware that will contain the reagent from the Labware list box.

6. Click the blank column to the right of Allowed/prohibited labware.

7. Click the ellipsis button.

The Labware Classes dialog box opens.

8. Make sure that the labware you intend to use on this VPrep shelf is in the Labware classes allowed to use this device column and not in the prohibited column.

For more information about the labware editor and how to use this dialog box, see the Database and Security User Guide.

9. Save the device file.

For more information, see “Working With Device Files” on page 221.


Setting Aspirate Pipette Task ParametersAspirate Pipette Task Defined

An Aspirate pipette task is used with a VPrep to draw up liquid from a plate or reservoir.

Setting Aspirate Pipette Task Parameters

Having associated a VPrep shelf with the labware type that you will aspirate from, you can now set the Aspirate pipette task parameters.

To set Aspirate pipette task parameters:

1. Add an Aspirate pipette task icon to the pipette process editor window.

2. If you have defined a liquid class for the liquid you intend to aspirate, select it from the Liquid class list box at the bottom of the Pipette Task Parameters toolbar.

For more information about defining liquid classes, see the Database and Security User Guide.

3. Complete the following fields:

Field Description

Aspirate volume The volume of liquid to be drawn up into each pipette tip.

Aspirate velocity The rate at which to draw up liquid.

If you selected a liquid class, this value is entered automatically from the liquid library editor and cannot be edited here.

Aspirate acceleration The rate of increase in velocity before the maximum aspirate velocity is reached.


Distance from well bottom The distance between the bottom of the pipette tips and the bottoms of the plate wells or MicroWash tray chimneys.

If you are using dynamic tip retraction this value sets the lowest point to which the tips will travel.


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4. If the VPrep head has fewer tips than the plate has wells, select a quadrant configuration from the Quadrant(s) diagram to indicate which well quadrant of the plate you want to aspirate from.

To select a quadrant, click a representative well. Two possible examples are shown below.

5. In the Plate to Aspirate from list box, select the type of labware or device to aspirate from, as described in “Configuring a VPrep Shelf As a Device” on page 171.

6. If you do not want to record this dispense in the transfer log, clear the Record in transfer log check box.

You might do this, for example, if you are running a casual test protocol.

For more information about the transfer log, see “Working with the Log Toolbar” on page 104.

Tip retract distance The distance that the tips should move downwards per unit volume of liquid being aspirated.

This value allows the tips to move downwards during aspiration to maintain a certain height below the surface of the liquid.

You will need to determine an appropriate value by trial-and-error for each type of plate you use.

You might want this value to be the same as the Tip Retract Distance for the Dispense pipette task.

Pre-aspirate volume The volume of air to be drawn up before the pipette tips enter the liquid.

Post-aspirate volume The volume of air to be drawn up after the liquid is drawn up.

Field Description


Setting Change Instance Pipette Task ParametersIntroduction The Change Instance pipette task is used in combination with a pipette

loop to perform replicate dispense operations from a mother plate into a series of daughter plates.

Part of an example protocol, which contains a mother plate and the first of 10 daughter plates, is shown below.

An example pipette process for the mother plate is shown below.

Note: This example has been simplified for the purposes of explanation.

When the protocol runs, 100 µ1 from each well of the mother plate are aspirated and 10 µ1 are dispensed into the first daughter plate (Daughter Plate 1). When the Change Instance task is reached, Daughter Plate 2 is moved into the system and 10 µ1 are dispensed into it from the mother plate. This loop repeats until all 10 daughter plates have been dispensed into.

Procedure To set change instance pipette task parameters:

1. Set up a protocol and pipette processes following the example shown above.

2. In the Pipette Task Parameters toolbar, from the list box, select the first daughter plate for the plate instance to change instance on.


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3. If you are using a script in the protocol that involves task skipping, check the Spawn control check box to force the BioCel to only bring in the next plate when the Change Instance task is reached.

The script may otherwise override this flow.


Setting Change Tips Pipette Task ParametersChange Tips Pipette Task Defined

The Change Tips pipette task uses the robot to apply or remove VPrep pipette tips.

Pairs of Change Tips pipette tasks are usually used together. For example, if the protocol starts with tips already on the VPrep, the first Change Tips pipette task would remove the tips and the second Change Tips pipette task would install new tips.

Change Tips pipette tasks are always used as part of a whole process created for the sole purpose of changing tips, an example of which is described in this topic.

Requirements To be able to change tips automatically on the BioCel you need a:

❑ Lid removal device for tipbox lids.

For more information, see “Lid-Removal Devices” on page 31.

❑ Tipbox shelf configured on your VPrep.

Configuration of VPrep shelves is performed through the device manager and should be performed by Velocity11® personnel. For more information, see “Working With Device Files” on page 221.

❑ Tipbox, containing tips, that is in a robot-accessible position, typically in a VStack®.

Also, if you are removing tips first, you will need an empty tipbox on the tipbox shelf of the VPrep you intend to use for the operation.

Overall Process The overall process of changing tips on a VPrep is:

1. Create a process for the tipbox, such as in the following example.

If your tipbox has a lid, you will need to check the Plates have lids check box in the plate instance and add Delid/Relid tasks to remove the lid before the pipette process.

2. Create a pipette process to change tips, such as in the following simple example.


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Creating the Process For the Tipbox

Before you can add a Change Tips pipette task, you must create a process for the tipbox that will contain the tips.

Creating a process for the tipbox:

1. Click the Protocol Editor tab.

2. Click Add.

A plate definition icon appears in the protocol editor window.

3. If the Protocol Task Parameters toolbar is not showing, select View > Toolbars > Protocol Task Parameters.

4. In the Protocol Task Parameters toolbar:

a. Type a name for the plate in the Plate Name text box.

b. In the Plate type list box, select the tipbox that has already been configured for use on the shelf of the VPrep that you intend to use.

Configuration of VPrep shelves is performed through the device manager. For more information, see “Configuring a VPrep Shelf As a Device” on page 171.

When you select a tipbox, Stacker, Pipette process and Waste tasks are automatically added.

c. In the Simultaneous Plates text box, type the maximum number of plates of this type that you want to be available to the system at one time.

For advice on how to set the the number of simultaneous plates, see “Setting the Number of Simultaneous Plates” on page 116.

d. If the tipboxes have lids, select the Plates have lids check box.

If the check box is unavailable, make sure that the selected plate type is set to allow the use of a lid in the labware editor. For more information about the labware editor, see the Database and Security User Guide.

!! IMPORTANT !! If this option is not selected and the tipbox has a lid, the VPrep head will crash into the tipbox lid and return a z-axis position error that will require a recovery procedure.

e. Leave the Plates enter the system sealed check box clear.

f. If the tipboxes have a bar code on the south side, select the first Incoming plates have a bar code... check box.

g. In the Bar Code Control group box, select one or more of the options if you want bar codes on the tipboxes to be read and compared with a bar code input file during a run.


h. If the tipboxes have a bar code on the west side, select the second Incoming plates have a bar code... check box.

For more information about bar code input files, see “Setting Apply Label Task Parameters” on page 127.

5. Set the Stacker task parameters.

6. Set the pipette process task parameters.

7. If you only intend to add tips during this process, delete the Transfer plate to trash task.

8. Add any other tasks that you want to for the tipbox.

You could, for example, add an Apply label task to place a bar code on the tipbox.

Creating the Pipette Process

After you have created a process for the tipbox, you can create a pipette process for the Change Tips pipette task.

To create a pipette process for changing tips:

1. Click the Pipette Process Editor tab.

2. Drag a Change Tips pipette task to the pipette process window.

3. In the Pipette Task Parameters toolbar, select either:

4. From the list box, select the name of the tipbox that you assigned in the topic “Creating the Process For the Tipbox” on page 178.

5. Add other pipette tasks, including a second Change Tips pipette task, as required.

Option With This Option, During the Protocol...

❑ Press On New Tips

❑ Tips off

Puts tips on to a VPrep head.

Removes tips from a VPrep head.

For more information, see “Setting Change Tips Pipette Task Parameters” on page 177.


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Setting Dispense Pipette Task ParametersDispense Pipette Task Defined

A Dispense pipette task is used with a VPrep to dispense liquid into a plate.

Dispense Value Limits

You cannot dispense more volume than you aspirated.

If you enter a total dispense volume that is greater than the total aspirate volume you will get an error message when you compile the protocol. More specifically, the Aspirate Volume + Pre-Aspirate Volume + Post-Aspirate Volume must be greater than, or equal to, the Dispense Volume + Blowout Volume + Post Dispense Volume.

Procedure Having associated a VPrep shelf with the labware type that you will aspirate from, you can now set the Dispense pipette task parameters.

To set Dispense pipette task parameters:

1. In the pipette process window, click the Dispense pipette task icon.

2. If you have defined a liquid class for the liquid you intend to dispense, select it from the Liquid class list box at the bottom of the Pipette Task Parameters toolbar.


3. Either:

Type the volume that you want to move out of each pipette tip in the Dispense Volume text box.

Select the Empty tips check box.

You may need to drag the toolbar to widen it so you can see the check box. Select this option if you want to empty the tips rather than deliver a specific volume of liquid.

4. Complete the remaining fields:

Field Description

Dispense velocity The rate at which to dispense the liquid.


Dispense acceleration The rate of increase in velocity before the Dispense Velocity is reached.



5. If the VPrep head has fewer tips than the plate has wells, select a quadrant configuration from the Quadrant(s) diagram to indicate which well quadrant of the plate you want to dispense to.


6. If you want the tips to touch one or more sides of the plate wells:

a. Select the Enable tip touch check box.

b. Type a value for the tip touch rise height.

This is the height that the tips should move upwards before touching the side of the wells.

c. Type a value for the Tip touch horiz distance.

When the value for this parameter is zero, the tips will move horizontally one well radius. The well radius is defined in the labware database for the type of plate you are using. If you want

Distance from well bottom The distance between the bottom of the pipette tips and the bottoms of the plate wells or MicroWash tray chimneys.


Retract distance The distance that the tips should move upwards per unit volume of liquid being dispensed.

This value allows the tips to move upwards during dispensing to maintain a certain height above the surface of the liquid.


You might want this value to be the same as the Tip Retract Distance for the Aspirate pipette task.

Blowout volume The volume of air to blow out when the tips are in the liquid.

This is typically the same as the pre-aspirate volume.

Post-dispense volume The volume of air to blow out when the tips are out of the liquid.

Field Description


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the tips to touch harder, increase this value. If you want the tips to touch more lightly, enter a negative value.

For more information about using the labware editor to add or modify labware definitions, see the Database and Security User Guide.

d. In the Number of sides to touch text box, type a value for number of sides of the wells that you want the tips to touch.

7. In the Plate to dispense to list box, select the plate or device to dispense to, as described in “Configuring a VPrep Shelf As a Device” on page 171.

8. If you do not want to record this dispense in the transfer log, clear the Record in transfer log check box.

You might do this, for example, if you are running a casual test protocol.


Setting Dry Tips Pipette Task ParametersDry Tips Pipette Task Defined

The Dry Tips pipette task is used with a tip dryer on a VPrep with a fixed-tip head to dry the pipette tips.

There are two phases to drying:

❑ Initial.

Rapidly raises the temperature from ambient to a temperature suitable for drying.

❑ Final.

Maintains a suitable drying temperature.

The goal when setting Dry Tips pipette task parameters is to raise the temperature quickly for a short time and then apply less heat to dry the tips.

Procedure Use this procedure when creating a protocol.

To set Dry Tips pipette task parameters:


Field Description

Initial heat Percentage of the maximum heat

Initial heat time Time for which to apply the initial heat

Final heat Percentage of the maximum heat

Final heat time Time for which to apply the final heat, starting when the initial heat time ends


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Setting Loop Pipette Task ParametersLoop Task Defined The loop pipette task allows you to repeat a set of tasks within a process.

Procedure This procedure is illustrated with an example in which an aspirate/dispense pair of tasks is looped four times.

To set loop pipette task parameters:

1. Open the Pipette Process Editor to display the process in which you want to add the loop pipette task.

An example is shown below.

2. In the pipette process window, click to select the Loop pipette task icon and drag it into the process in front of the first task that you want to be in the loop.

A Loop pipette task icon and End of loop pipette task icon are added to the process.

3. Drag the End of loop pipette task icon to the other side of the last task you want to be in the loop.

4. Select the Loop task pipette icon and in the Pipette Task Parameters toolbar, enter the number of times you want the tasks inside the loop to run.


Setting Mix Pipette Task ParametersMix Pipette Task Defined

A Mix pipette task is used with a VPrep to mix reagents by aspirating and then dispensing.

\

Procedure Having associated a VPrep shelf with the labware type that you will aspirate from, you can now set the Mix pipette task parameters.

To set Mix pipette task parameters:

1. In the pipette process window, click to select the Mix pipette task icon.

2. If you have defined a liquid class for the liquid you intend to mix, select it from the Liquid class list box at the bottom of the Pipette Task Parameters toolbar.



Field Description

Mixing volume The volume of liquid to be aspirated and dispensed to each plate well.

Number of mixing cycles The number of aspirate/dispense operations.

Aspirate velocity The rate at which to draw up liquid.


Aspirate acceleration The rate of increase in velocity before the maximum aspirate velocity is reached.






Distance from well bottom

The distance between the bottom of the pipette tips and the bottoms of the plate wells or MicroWash tray chimneys.



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4. If the VPrep head has fewer tips than the plate has wells, select a quadrant configuration from the Quadrant(s) diagram to indicate which well quadrant of the plate you want to mix in.


5. If you want the tips to touch one or more sides of the plate wells:


b. Type a value for the tip touch rise height.


c. Type a value for the tip touch horizontal distance.

When the value for this parameter is zero, the tips will move horizontally one well radius. The well radius is defined in the labware database for the type of plate you are using. If you want the tips to touch harder, increase this value. If you want the tips to touch more lightly, enter a negative value.


d. In the Number of sides to touch text box, type a value for the number of sides of the wells that you want the tips to touch.

Retract distance The distance that the tips should move upwards or downwards per unit volume of liquid being dispensed or aspirated.

This value allows the tips to move upwards or downwards during dispensing or aspirating to maintain a certain height below or above the surface of the liquid.


Pre-aspirate volume The volume of air to be drawn up before the pipette tips enter the liquid, and before mixing begins.

Last-cycle blowoutf volume

The volume of air to blow out when the tips are in the liquid once the mixing is complete.


Field Description


6. In the Plate to mix list box, select the type of labware or device to mix in, as described in “Configuring a VPrep Shelf As a Device” on page 171.


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Setting Pump Reagent Pipette Task ParametersPump Reagent Task Defined

The Pump Reagent pipette task is used on a VPrep to pump liquid into an installed autofilling reservoir. Reservoirs are typically filled with washing buffer or water and drained through the gravity drain.

!! IMPORTANT !! If you run an empty reservoir step and a fill reservoir step in the same protocol, check the protocol to make sure that it will not lead to an overflow.

Weigh Shelf Calibration

If you are using an autofilling reservoir, you should also calibrate the reservoir on the WeighShelf. The calibration sets 100% as the weight of a full reservoir and 0% as the weight of an empty reservoir.

For more information about calibrating a reservoir on a WeighShelf, see the VPrep User Guide.

Procedure To fill a VPrep reservoir:

1. In the pipette process window, click the Pump Reagent icon.

2. In the Pipette Task Parameters toolbar, select Fill reservoir.

The Fill reservoir and Empty reservoir values determine whether the pumps will fill or empty the reservoir.

To empty the reservoir you must complete the Autofill Configuration information on the Shelves tab of the VPrep Diagnostics software. For more information, see the VPrep User Guide.

3. In the list box, select the shelf on which the reservoir is located.

4. In the for text box, type the the pumping duration.

This is the time in seconds that the pumps pump.

5. In the at text box, type the percentage of maximum pumping rate.

This, combined with the pumping duration, determines the volume of fluid moved.

6. In the every text box, type a number that controls how frequently the liquid is pumped.

7. For example, if you type 3, the pump will run every third time the task runs.

8. If you are using a WeighShelf, in the Min level text box, enter the minimum percentage of liquid that you want the reservoir to contain.

A typical value is 45%.

9. If you are using a WeighShelf, in the Max level text box, enter the maximum percentage of liquid that you want the reservoir to contain.

A typical value is 60%.


Setting Wash Tips Pipette Task ParametersWash Tips Pipette Task Defined

A Wash Tips pipette task is used with a VPrep to wash pipette tips. It is typically used with a MicroWash tray.

If you are using a MicroWash tray, this task can also be used to wash the MicroWash tray manifold.

For more information about MicroWash trays, see the VPrep User Guide.

Washing Pipette Tips Having associated a VPrep shelf with the labware type that you will wash at, you can now set the Wash Tips pipette task parameters.

To wash pipette tips:

1. If you have defined a liquid class for the liquid you intend to use for washing, select it from the Liquid class list box at the bottom of the Pipette Task Parameters toolbar.

For more information about creating liquid classes, see the Database and Security User Guide.

2. Either:

Type the volume that you want to move out of each pipette tip in the Dispense Volume text box.

Select the Empty tips check box.

You may need to drag the toolbar to widen it so you can see the check box. Select this option if you want to empty the tips rather than deliver a specific volume of liquid.


Field Description

Wash Volume The volume of liquid to be aspirated and dispensed to each plate well.

Number of wash cycles The number of aspirate/dispense operations.

Aspirate velocity The rate at which to draw up the liquid.


Aspirate acceleration The rate of increase in velocity before the Aspirate Velocity is reached.





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4. If the VPrep head has fewer tips than the plate has wells, select a quadrant configuration from the Quadrant(s) diagram to indicate which well quadrant of the plate you want to mix in.




Distance from well bottom



Retract Distance The distance that the tips should move upwards or downwards per unit volume of liquid being dispensed or aspirated.


You will need to determine an appropriate value by trial-and-error.

Pre-aspirate volume The volume of air to be drawn up before the pipette tips enter the liquid, and before mixing begins.

Last-cycle blowout volume

The volume of air to blow out when the tips are in the liquid once the mixing is complete.


Inflow pump The relative rate of liquid flow into the MicroWash tray manifold.

This value should be high enough for the washing liquid to just bubble over the tops of the chimneys.

Outflow pump The relative rate of liquid flow out of the MicroWash tray manifold.

This value should be higher than that of the inflow pump to prevent an overflow.

Field Description


5. If you are using a MicroWash tray and want to dispense the wash liquid to waste instead of dispensing it back into the reservoir of washing liquid:

a. Select the Dispense to waste at height of check box.

The tips will dispense outside the MicroWash tray chimneys.

b. Type a value into the Dispense to waste at height of text box .

This is the height, in millimeters, above the MicroWash chimneys at which the tips will dispense. Used in combination with the dispense to waste property. Enter a negative number to ensure that the tips are below the tops for the chimneys.

6. If you want the tips to touch the outside tops of the chimneys to remove drops from the tips:


b. Enter a value for the Tip touch rise height.


c. Type a value for the Tip touch horiz dist.



7. In the Plate to wash list box, select the type of labware or device to wash, as described in “Configuring a VPrep Shelf As a Device” on page 171.

You may need to lower the log toolbar to see this parameter.


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Washing the MicroWash Tray Manifold

To wash the MicroWash tray manifold:

1. Create a process that contains only a pipette process.

2. Add a Wash Tips pipette task to the pipette process.

3. Enter the following values for the task:

4. Run the process.

Field Value

Wash volume 0

Number of wash cycles 0

Inflow pump Variable

Outflow pump Equal to or greater than inflow pump. The pump is required because draining by gravity may be insufficient.

This chapter is intended for people with Technician or Administrator privileges. It provides the background information necessary to set up certain tasks.

Before reading this chapter you should be familiar with the concepts presented in the following chapters:

❑ “Creating a Protocol: Basics” on page 109



Note: The chapter is not a tutorial on writing protocols — it provides the basic reference information you will need to write protocols.

Creating a Protocol: Advanced Topics 8

Chapter 8: Creating a Protocol: Advanced TopicsBioCel User Guide

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Setting Up VWorks Plug-InsWhat is a Plug-In? A plug-in is a program file that works in collaboration with a software

application to extend the capability of the application. Plug-ins are often developed by third-party organizations.

You have probably downloaded plug-ins to use with your Web browser so you can watch streaming video, search with particular search engines, download newsfeeds, and so on, all from within your browser.

Plug-ins used with Velocity11® applications are Dynamic Link Library (DLL) files. You can either use plug-ins created by Velocity11, or create your own custom plug-ins.

How a VWorks Plug-In Works

APIVWorks™ includes an API (Application Programming Interface) that allows specific program values to be passed to it from an external application, specifically a VWorks plug-in. In turn, the plug-in is able to query a file, database or third-party application to obtain information that it needs.

Data ProcessingBecause the plug-in is a software program itself, it is able to analyze the information it receives, process it, and output values that depend on the received information. In other words, the values that the plug-in outputs do not have to be the same as the values it receives from the query. This is explained by the following diagram.

As a simple example, if the plug-in queries a text file and a bar code field value of trial621 is returned, the plug-in could process this and output a value of trial621_may06_2004_10:24.

Text File

LIMS

Database

VWorks

APIValues passed

to protocol

Plugin DLL

Processing

195Chapter 8: Creating a Protocol: Advanced TopicsBioCel User Guide

Velocity11 FileReader plug-in

Velocity11 has created a plug-in for VWorks, called FileReader.dll. This plug-in specifies the content of bar code fields printed with a VCode®.

For more information, see “About the FileReader Plug-In” on page 196.

Custom Plug-Ins If you want to develop your own plug-in, you will need to obtain the Software Developer’s Kit (SDK) from Velocity11. The kit contains sample plug-ins, a tester application and documentation.

Process Overview The following table gives an overview of the process of using a VWorks plug-in.

Step Topic

1. Obtain the files that the plug-in needs to use:

❑ The <filename>.dll (plug-in file)

❑ Any library files referenced by the plug-in

❑ Any text files referenced by the plug-in

2. If the plug-in will be referencing a LIMS (Laboratory Information Management System) database, make sure that the database is prepared for use and connected on the network that the BioCel® is on.

3. If necessary, install and register the associated library files.

See directions for the individual plug-in for more information.

4. Install and register the plug-in file.

See directions for the individual plug-in for more information.

5. Set up VWorks to use the plug-in.

See “About the FileReader Plug-In” on page 196 for more information.


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About the FileReader Plug-InIntroduction Velocity11 has created a plug-in for VWorks, called FileReader.dll.

Plug-In Function The FileReader plug-in is used to specify the content of bar code fields printed with a VCode.

Defining Bar Code Field Content

The Apply label task provides several ways to define the contents of the bar code fields printed on a series of plates during a run. For a list of the different ways, see “Setting Apply Label Task Parameters” on page 127. However, without a plug-in, for each label in a given run, the Apply label task cannot apply:

❑ Two different bar code input files for two different fields

❑ Two different bar code data inputs for two different fields

❑ Two different increments for two fields

❑ Numeric increments for one field and alphanumeric increments for another different field

In the following screenshot, Field2 and Field3 use the same bar code input file for the data in the fields. However, this function is limited because there is no way to input two different pieces of data on the same label from one file.

The FileReader plug-in allows VWorks to input the data in the bar code fields from a text file. Functionally, the text file is similar to a bar code


data file (see “Using Bar Code Data Files” on page 228) except that it includes data for all fields in a bar code instead of just one field. This allows two fields on the same label to contain different data in the same run, without using prefixes and suffixes.

A screenshot of a FileReader plug-in text file is shown below. This example is a tab-delimited text file, but a comma-separated text file could also be used.

Note how the order of the columns references the order of the tabs in the Apply label task Protocol Task Parameters toolbar.

The six columns of a particular side correspond to the six fields in the protocol task parameters.

The column “South3” is the column that contains the root data that will be printed on the south side of the plate in field 3. Each row of the table represents a different cycle in the run. The first row contains the root data that will be printed during the first run cycle, and so on.

The following screenshots show how the same plug-in is used in a total of four fields, on two sides of the plate.

Using these parameters, data from the above plug-in file would print the following labels:


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Repeating Columns

A text file with data for bar codes on only one side of the plate is sufficient to print the same labels on other sides of the plate. To understand this, consider the columns that can contain input data for one side of the plate as a six-column set. If there is only one set in the file, and it has six or fewer data-containing columns, the set is repeated for the other sides of the plate where you have selected “Use this label” from the list box.

Sending Print Commands to a VCodeBefore a bar code label is printed, VWorks queries the plug-in DLL and obtains the content of the fields to print on the bar code label.

Using Prefixes and SuffixesYou can use prefixes and suffixes in a bar code field that also uses a plug-in, just as you can with bar code input files and bar code data files. An example field with a prefix is shown in the following screenshot.

Field Printed Labels in Run Cycle 1

South, Field 2 r1c2

South, Field 3 r1c3

West, Field 1 r1c7

West, Field 3 r1c9


Setting up the FileReader Plug-inAbout Setting Up the Plug-In

For an overview of the process of setting up a plug-in, see “Setting Up VWorks Plug-Ins” on page 194.

To set up the plug-in in VWorks in preparation for a run, you need to:

❑ Set up the plate instance protocol task parameters (see “Setting Up a Plate Instance” on page 112)

❑ Set up the Apply label task protocol task parameters (see “Setting Apply Label Task Parameters” on page 127)

Procedures To install and register the plug-in file:

1. Navigate to C:\WINDOWS\system32.

2. Look for the plug-in file named FileReaderDLL.dll.

3. If the file is not already there you will need to install and register it with the operating system:

a. Copy the file into this directory.

b. Right-click the file and click Open With.

The Open With dialog box opens.

c. Make sure that the selected program is Microsoft® Register Server.

d. Click OK.

The file is now registered with the operating system.


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e. Click OK to close the dialog box.

To install and register the plug-in file:

1. Navigate to C:\VWorks Workspace.

2. If there is no directory named “plugins”, create one.

3. Add the <plug-in>.dll file into the plug-ins directory.

4. Right-click the file and click Open With.

A Caution dialog box opens.

5. Click Open With.

6. A Windows dialog box opens.

7. Select Select the program from a list and click OK.

The Open With dialog box opens.

8. Make sure that the selected program is Microsoft Register Server.

If this program is not in the list, browse to C:\WINDOWS\System32 and select the program regsvr32.exe.


9. Click OK.

The ActiveX file is now registered with the operating system.


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Using JavaScript in VWorksAbout JavaScript JavaScript is a general-purpose programming language that requires an

interpreter to run its programs.

You are probably most familiar with JavaScript where it is used to create dynamic effects in Web pages. This form of JavaScript is made up of a core language with the addition of Web browser-specific language, and is processed by the JavaScript interpreter that is built into modern browsers. The core JavaScript language provides programming capabilities for any application that includes a JavaScript interpreter. VWorks is an example of such an application—it uses a JavaScript 1.5 interpreter.

JavaScript Resources

There are many JavaScript resources available online and in print. If you want to learn more about JavaScript for use in VWorks, look for resources that cover the core JavaScript language separately from the browser, client-side language and Document Object Model.

Web ReferencesYou can find useful information at:

http://www.mozilla.org/js/

Print Reference

A good print reference is JavaScript: The Definitive Guide, Fourth Edition, published by O’Reilly.

JavaScript in VWorks In VWorks, JavaScript programs (scripts) can be used to change the parameters of a protocol task immediately before it is scheduled. This extends the capability of VWorks because the parameters can be changed dynamically during a run, based on:

❑ Information passed from an external source, such as a database

❑ The number of times the protocol has cycled

❑ Feedback on changing conditions during the run

Examples of Use Some specific examples of how you can use JavaScript are:

❑ To print the parameters of a task to the VWorks log

❑ To run a command line that launches an external application, such as a batch file or database updating program

❑ To simplify protocol writing, for example, by incrementing pipetting volumes each cycle of a protocol to perform a dilution series

Where Scripts are Written

Scripts are written directly into the text box of the Advanced Settings tabs of tasks that support them. You have the option of typing a statement that references an external script file using the "open()" function, or typing the entire script into the script text box.

http://www.mozilla.org/js


The following screenshot shows a short script that prints the parameters of a task to the log toolbar, just before the task runs.

About VWorks-Defined Functions and Objects

The VWorks interpreter supports the JavaScript 1.5 core functions and objects. Velocity11 has also defined its own functions and objects that can be used in VWorks scripts.

VWorks-Defined Global Functions

The following VWorks-defined functions are available globally, meaning that they are not restricted to a particular object or programming context.

VWorks-Defined Objects

The VWorks JavaScript interpreter provides two objects that can be accessed by a script. They are the plate object and task object.

Function Description

print() Prints time-stamped messages to the VWorks log.

Parameter: Text string

Example: print(plate.name)

open() Opens a file.

Parameter: Text string

Example: open(c:\vworks workspace\vworks3\text.txt)

run() Runs a program as though it is being called from a command line.

Parameters:

❑ Text string. Required. Allows you to initiate a command that you could otherwise enter into the Windows® Run dialog box, such as notepad text.txt (opens a file named text.txt in Windows Notepad).

❑ Boolean True/False. Optional. Default is False. If True, VWorks waits for the function to complete before continuing (blocking).


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Plate Object The plate object provides access to properties of the plate that the current task is operating upon.

PropertiesThe plate object has the following properties:

Methods

The plate object has the following methods, available on those systems with the volume-tracking database option.

Property Data Type Description

plate.name String Name of the plate.

plate.instance Integer Plate instance number.

plate.labware String Name of the labware type.

plate.barcode Array Array of four strings corresponding to south=0, west=1, north=2, east=3.

Example:

plate.barcode [“One”, “Two”, “Three”, “Four”]

where each of the numbers is a bar code number.

plate.volume Array of arrays

An array of floating point numbers, the number of which in the array depends on the number of wells in the labware (96, 384, or 1536). arranged in row, column format.

This property is only enabled on BioCel systems that have the volume-tracking database option.

Method Comments

plate.setUserData(string key, string value)

Stores ‘value’ under the key ‘key’ in a database record associated with this plate

plate.getUserData(string key) Returns the ‘value’ stored earlier using plate.setUserData


Task Object The task object is a VWorks-defined generic object that refers to the currently executing task. It allows the properties of the task to be accessed using a standard syntax. Depending on which task is executing, a different set of properties may be available.

PropertiesThe task object provides a comprehensive set of properties that can be read/write, or read-only. These properties specifically affect the behavior of the task that is about to be executed by the VWorks Scheduler.

For example, the Aspirate task has a property called “volume”. To store this property in a variable you would write:

x = task.volume

To set the volume property of the Aspirate task to the value stored in the variable 'x', you would write:

task.volume = x

In this example, the run-time interpreter determines through the context that 'task.' refers to the currently executing Aspirate task.

Attempting to access properties that are inappropriate for the current task will result in a scripting syntax error, but will not halt the execution of your protocol.

For lists of the properties for each available task in VWorks 13.x, see “The JavaScript Task Object and Properties” on page 208.

Methods

The task object has the following methods:

Method Comments

task.skip() Skips execution of the current task. Use this function to conditionally execute a task, such as in this example which skips the task if the simulator is not running:

if (!isSimulatorRunning())

task.skip()

task.pause() Pauses the protocol and opens a dialog box that asks you whether you want to continue or abort the run.

Use this function if you need to pause the protocol to, for example, replenish the fluid in a static reservoir. You could use the print() function to add a note to the log toolbar describing the action to take when the BioCel® has paused.

task.isSimulatorRunning() Returns true if this is a simulated run.

Has no arguments.


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None of the task object methods accept any parameters.

These are generic methods that are the same regardless of the task that is executing them. The properties of these methods are specific to the current task.

About Variables The default behavior of VWorks JavaScript is that the values of all variables are cleared (set to undefined) before the next protocol is run.

You have the option to change this so that the value of a variable assigned in a script is held in memory until VWorks is closed. This means that if you assign the value to a variable in one protocol, the same value will be used in the next protocol with the same variable. This is the reset script context feature.

To clear the reset variables default option:


The Protocol Options dialog box opens.

2. In the Rules group box, clear the Reset script context before protocol executes check box.

Quadrant Representation

In JavaScript, an array is a built-in object that stores a collection of like values, called elements. Each element is accessed by an index value that is enclosed in square brackets. Index values can be non-negative integers or strings.

The following example script declares an array with three elements:

var vehicle_type = new Array(3);

vehicle_type[0] = “car”;

vehicle_type[1] = “truck”;

vehicle_type[2] = “van”;

Because a plate is already an array of wells, locations on plates (quadrants) are represented in Velocity11 JavaScript as an array of arrays. for example, the quadrant property of the task object for one task is represented as:

[[1,1]]

In this representation, the first number refers to the plate row and the second number refers to the plate column. These numbers can be represented by variables in a script, as shown in the following statement.

task.repeat() Schedules the task to be repeated (VWorks version 12+).

Method Comments


task.quadrants = [[disp_row,disp_column]]

For two quadrants, the representation would be:

[[1,1],[1,2]]

Cautions When you run a script that dynamically changes the values of task properties, there is a risk that a value will be set that causes a problem. We therefore recommend that before using a script, you run the simulator with each set of values that will be set by the script. Running scripts cannot cause robot crashes, because scripts cannot modify teachpoints. However, an incorrect task.tipOffset property (Distance from well bottom parameter) on a VPrep® could cause the pipette tips to crash into the bottom of the wells resulting in loss of sample and damage to plates.

In addition, be aware that when a protocol is being compiled, it uses the values displayed in the Protocol Task Parameters toolbar screen and not the values that will be set by any scripts. This means that there may be errors in the protocol that are not detected during compilation. The values that appear in the Task Parameter toolbar do not change to reflect the effect of any script.

Also, scripts do not check pipetting volumes before the run begins, so you must make sure that the pipetting steps make logical sense. For example, you will not be alerted beforehand if a script will attempt to aspirate 1 mL from a plate well that can only hold 0.5 mL.

Example Scripts Example 1

This script prints the word “hello” to the log toolbar and log.txt file.

print(“hello”);

Example 2

This one-line script opens an external file that could contain another script. The new script is run immediately.

open(“C:\scripts\script1.txt”)

Example 3This script prints a list of the properties for the task to the log toolbar. It is an essential part of determining the names of properties when creating JavaScripts.

for(x in task) {

print(“task” + x + “=” + task[x];

}

Script-Writing Service

Velocity11 offers a custom script-writing service for VWorks and other applications. Please contact us for more information.


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The JavaScript Task Object and PropertiesIntroduction The VWorks JavaScript interpreter includes a task object that is defined

by Velocity11.

Task Properties Properties Available to All TasksThe following properties can be used for any task.

Aspirate Task

The JavaScript Aspirate task properties are listed below, along with the data type of the property, the names of the corresponding aspirate properties in the Protocol Task Parameters toolbar, and a reference to more information.

Property Data Type Description

task.name String Name of the task, for example “Aspirate.”

task.description String Description of the task that is given under the icon in the protocol editor.

For example, a downstack task that has the script print(task.description) will send the following text to the protocol log:

Downstack from stacker2

Property Data Type Task Parameter Comments

task.plateName String Plate name The name of the plate.

Read only.

task.acceleration Float Aspirate acceleration The rate of increase in velocity before the maximum aspirate velocity is reached.

If you selected a liquid class, this value is entered automatically from the liquid library editor.

task.liquidClass String Liquid class list box The name of the liquid class.

See the Database and Security User Guide.

task.postAspirateVolume Float Post aspirate volume The volume of air to be drawn up after the liquid is drawn up.

task.preAspirateVolume Float Pre aspirate volume The volume of air to be drawn up before the pipette tips enter the liquid.


Change Tips Task

These properties are the same as the properties described for the Change Tips task “Setting Change Tips Pipette Task Parameters” on page 177.

task.quadrants Array of pairs of integers

Quadrant selection diagram

A quadrant is an evenly spaced array of locations that is addressable by the tips on a pipette head. A 96-well head can dispense into a 96-well plate, four quadrants of a 384-well plate, and 16 quadrants of a 1536-well plate. A 384-well head can dispense into a 384-well plate or the four quadrants of a 1536-well plate.

task.retract Float Tip retract distance The distance that the tips should move downwards per unit volume of liquid being aspirated.

This value allows the tips to move downwards during aspiration to maintain a certain height below the surface of the liquid.


You might want this value to be the same as the Tip Retract Distance for the Dispense pipette task.

task.tipOffset (Distance from well bottom)

Float Distance from well bottom



task.velocity Float Aspirate velocity The rate at which to draw up liquid.


task.volume Float Aspirate volume The volume of liquid to be drawn up into each pipette tip.



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Dispense Task

These properties are the same as the properties described for the Dispense task “Setting Dispense Pipette Task Parameters” on page 180.



task.action Integer ❑ Press On New Tips (integer = 1)

❑ Tips off (integer = 2)

Puts tips on to a VPrep head or removes tips from a VPrep head.

For more information, see “Setting Change Tips Pipette Task Parameters” on page 177.

Property Data Type Task Parameters Comments


task.acceleration Float Dispense acceleration The rate of increase in velocity before the Dispense Velocity is reached.


task.blowoutVolume Float Blowout volume The volume of air to blow out when the tips are in the liquid.


task.liquidClass String Liquid class (list box) The name of the liquid class.


task.postDispenseVolume Float Post dispense volume The volume of air to blow out when the tips are out of the liquid.


Quadrants (diagram) A quadrant is an evenly spaced array of locations that is addressable by the tips on a pipette head. A 96-well head can dispense into a 96-well plate, four quadrants of a 384-well plate, and 16 quadrants of a 1536-well plate. A 384-well head can dispense into a 384-well plate or the four quadrants of a 1536-well plate.


task.retract Float Retract distance The distance that the tips should move upwards per unit volume of liquid being dispensed.

This value allows the tips to move upwards during dispensing to maintain a certain height above the surface of the liquid.


You might want this value to be the same as the Tip Retract Distance for the Aspirate pipette task.

task.tipOffset Float Distance from well bottom



task.tipTouch Boolean Enable tip touching Whether you want the tips to touch the sides of the plate wells or not.

task.tipTouchHorizontalDistance

Float Tip touch horizontal distance


task.tiptouchRiseHeight Float Tip touch rise height The height that the tips should move upwards before touching the side of the wells.

task.tipTouchSides Integer Number of sides to touch

The number of sides of the wells that you want the tips to touch.



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Dry Tips Task

These properties are the same as the properties described for the Dry Tips task “Setting Dry Tips Pipette Task Parameters” on page 183.

Mix Task

These properties are the same as the properties described for the Mix task “Setting Mix Pipette Task Parameters” on page 185.

task.velocity Float Dispense velocity The rate at which to dispense the liquid.


task.volume Float Dispense volume The volume of liquid to be moved out of each pipette tip.




task.dryTime Integer Initial heat time Time for which to apply the initial heat

task.heatPercent Integer Initial heat Percentage of the maximum heat

task.finalDryTime Integer Final heat time Time for which to apply the final heat, starting when the initial heat time ends

task.finalHeatPercent integer Final heat Percentage of the maximum heat



task.aspirateAcceleration Float Aspirate acceleration The rate of increase in velocity before the maximum aspirate velocity is reached.



task.aspirateVelocity Float Aspirate velocity The rate at which to draw up liquid.


task.blowoff Float Last cycle blowout volume

The volume of air to blow out when the tips are in the liquid.


task.cycles Integer Number of mixing cycles

The number of aspirate/dispense operations.

task.dispenseAcceleration Float Dispense acceleration The rate of increase in velocity before the Dispense Velocity is reached.


task.dispenseVelocity Float Dispense velocity The rate at which to dispense the liquid.




task.preAspirateAirGap Float Pre-aspirate volume The volume of air to be drawn up before the pipette tips enter the liquid.





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task.retract Float Retract distance The distance that the tips should move upwards or downwards per unit volume of liquid being dispensed or aspirated.






task.tipTouch Boolean Enable tip touching Whether you want the tips to touch the sides of the plate wells or not.

task.tipTouchHorizontalDistance

Float Tip touch horiz. dist When the value for this parameter is zero, the tips will move horizontally one well radius. The well radius is defined in the labware database for the type of plate you are using. If you want the tips to touch harder, increase this value. If you want the tips to touch more lightly, enter a negative value.


task.tipTouchSides Integer Number of sides to touch

The number of sides of the wells that you want the tips to touch.

task.volume Float Mixing volume The volume of liquid to be aspirated and dispensed to each plate well.



Pump Reagent Task

These properties are the same as the properties described for the Pump Reagent task “Setting Pump Reagent Pipette Task Parameters” on page 188.

Wash Tips Task

These properties are the same as the properties described for the Wash Tips task “Setting Wash Tips Pipette Task Parameters” on page 189.


task.action Integer ❑ Fill reservoir (value = 0)

❑ Empty reservoir (value = 1)

The Fill reservoir and Empty reservoir values determine whether the pumps will fill or empty the reservoir.

To empty the reservoir you must complete the Autofill Configuration information on the Shelves tab of the VPrep Diagnostics software. For more information, see the VPrep User Guide.

task.howOften Integer Every The number that controls how frequently the liquid is pumped.

For example, if you type 3, the pump will run every third time the task runs.

task.maxLevel Integer Max level The maximum percentage of liquid that you want the reservoir to contain.

task.minLevel Integer Min level The minimum percentage of liquid that you want the reservoir to contain.


task.shelf String (unnamed list box) The shelf on which the reservoir is located.

task.speedPercent Integer at The percentage of maximum pumping rate.

task.time Integer for The time in seconds that the pumps pump.


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task.aspirateVelocity Float Aspirate velocity The rate at which to draw up liquid.


task.aspirateAcceleration Float Aspirate acceleration The rate of increase in velocity before the maximum aspirate velocity is reached.


task.blowoff Float Last cycle blowout volume

The volume of air to blow out when the tips are in the liquid.


task.cycles Integer Number of wash cycles The number of aspirate/dispense operations.

task.dispenseAcceleration Float Dispense acceleration The rate of increase in velocity before the Dispense Velocity is reached.


task.dispenseToWaste Boolean Dispense to waste at height of (check box)

The tips will dispense outside the MicroWash tray chimneys.

task.dispenseVelocity Float Dispense velocity The rate at which to dispense the liquid.



task.heightAboveWaste Float Dispense to waste at height of (text box)

The height, in millimeters, above the MicroWash chimneys at which the tips will dispense. Used in combination with the dispense to waste property. Enter a negative number to ensure that the tips are below the tops for the chimneys.

task.inFlowPercent Integer Inflow pump The relative rate of liquid flow into the MicroWash tray manifold. This value should be high enough for the washing liquid to just bubble over the tops of the chimneys.



task.outFlowPercent Integer Outflow pump The relative rate of liquid flow out of the MicroWash tray manifold. This value is typically zero because the fluid is drained by gravity.

task.preAspirateAirGap Float Pre-aspirate volume The volume of air to be drawn up before the pipette tips enter the liquid.





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task.retract Float Retract distance The distance that the tips should move upwards or downwards per unit volume of liquid being dispensed or aspirated.






task.tipTouch Boolean Enable tip touch Whether you want the tips to touch the sides of the plate wells or not.

task.tipTouchHorizontalDistance Float Tip touch horiz. dist. When the value for this parameter is zero, the tips will move horizontally one well radius. The well radius is defined in the labware database for the type of plate you are using. If you want the tips to touch harder, increase this value. If you want the tips to touch more lightly, enter a negative value.


task.volume Float Wash volume The volume of liquid to be drawn up into each pipette tip.



Understanding the Configuration Settings in a Pipette TaskAbout This Topic Dozens of separate pieces of data are required by VWorks to complete a

single pipetting task. These range from the velocity at which to aspirate a liquid to the height at which the gripper should approach a plate that is sitting on a platepad. These data are the configuration settings. With the right privileges, you can modify and add configuration settings to fine-tune and extend the capabilities of your BioCel.

How you can modify configuration settings is discussed in other topics. This topic uses the example of an Aspirate pipette task to provide the conceptual background you need to understand:

❑ The relationships between the device manager, labware editor, liquid library editor, task parameters and protocol file

❑ What information is stored in a protocol

❑ Why you perform certain steps when creating protocols

❑ How to resolve protocol errors

Before reading this topic, it may help to read “Configuring a Pipette Process: Example” on page 164. This topic presents the same information from a different perspective.

Information Flow Diagram

The following diagram explains how information flows from the various data stores in VWorks into a single Aspirate pipette task that is stored as part of a protocol file.

Four main kinds of information are associated with a pipette task in a protocol file. These are:

❑ General task properties set in the Pipette Task Parameters toolbar

❑ Device information

❑ Labware information

❑ Liquid properties information

This information is included in the pipette task through a cascade of associations.

The association between the liquid type and the pipette task is made directly be selecting a liquid class for the pipette task.

When a protocol is saved, the names of the device file, plate types, and liquid classes are saved with it so that the information in the device manager, labware database and liquid library database can be referenced during a run.


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More Information For more information about the device manager, see “Introduction” on page 171.

For more information about the liquid library editor, see “Setting Labware and Liquid Parameters” on page 255.

Editor

Liquid Library

Device

Manager

Data stored includes:•

• Device type (such as Pipettor reagent shelf)• Parent device (such as VPrep1)• Robot approach height• Labware classes allowed to be used on this device •

Data stored includes:• Aspirate Parameters• Dispense parameters• Equation editor

Device name

Liquid class

Plate to...

Toolbar

Task

Parameters

Labware Editor

Data stored includes:• Plate dimensions• Gripper offsets• Maximum robot speed• General description of labware• Assignment of labware class (such as TipBoxes and TallPlates)

[Click Manage Devices tab to open.]

[Click Diagnostics, then Labware Editor to open.]

[Click Edit in Task Parameterstoolbar to open.]

[Click a pipette task to open.]

Flow of data

Legend

Plate type

Pipette Task

File

Protocol


Working With Device FilesDevice Defined A device is an item on the BioCel that has an entry in the device

manager. A device can be either a module or a location on the BioCel that can hold a piece of labware.

Examples of devices are:

❑ VPrep shelf 5

❑ VPrep

❑ QFill

❑ Plate pad 3

❑ Hotel - 15

Device Configuration Every device on your BioCel was correctly configured at the factory. However, administrators will need to reconfigure the device settings for VPrep shelves when changing the type of reservoir contained on a shelf.

For information about configuring VPrep shelves, see “Configuring a VPrep Shelf As a Device” on page 171.

Device File The data entered into the device manager can be saved as a device file and loaded at a later time. Like protocol files, device files are XML files that can be edited in an XML editor or text editor.

Device File Location Device files have the file name format: <file name>.dev and are stored in the folder location that you specify when saving the file.

Saving a Device File After you make changes in the device manager you must save the changes for them to be available the next time the protocol is opened.

To save a device file:

1. Make sure you are logged in as Administrator.

2. If you want to save the file in the current location select File > Device File > Save As.

3. If you want to save the file in a different location:

a. Select File > Device File > Save Device File As.

b. Navigate to the folder in which you want to save the file.

c. Click Save.

The path of the device file specified in the protocol file and Protocol Options dialog box is changed to reflect the different location.


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Loading a Device File

When you open a protocol file the device file is automatically referenced so you do not need to load it. If you want to load a new device file for your current protocol you can use the following procedures.

To load a device file: method 1:

1. In Windows, navigate to the device file.

2. Double-click the file.

VWorks is launched and the device file is loaded.


1. Select File > Device File > Open.

2. Navigate to the folder that contains the file to load.

3. Click Open.

If you load a device file using the following method, the device file will be saved with the protocol when you save the protocol.



2. In the Protocol Options tab of the dialog box, click the device file ellipsis button.

3. Navigate to the folder that contains the file to load.

4. Click Open.

Note: The file path displayed in the Protocol Options dialog box is updated if you save a protocol to a different folder.


About Bar Code Reading and TrackingIntroduction This topic gives an overview of the bar code reading and tracking

abilities of the BioCel.

Bar Code Readers and Printers

Every BioCel has a bar code reader built into its robotic arm that reads bar codes on the south side of a plate. If the “Incoming plates have bar codes on south...” check box is selected (see “Setting Up a Plate Instance” on page 112), every time a plate with a south-side bar code is picked up, the bar code reader reads the bar code.

Customized BioCel systems can have additional readers that read bar codes on other sides of the plate. These may be installed on VPrep shelves or platepads. Every time a plate is moved to one of these devices the bar code is read.

If your BioCel has a VCode, your BioCel has the additional ability to print and apply bar code labels. If the VCode includes an optional reader, your BioCel can read bar code labels on any side of the plate.

Third-party devices, such as the Liconic StoreX incubator may also have a built-in bar code reader.

Note: To read a bar code at a platepad bar code reader or VCode, use the Place Plate task.

About Bar Code Tracking

VWorks tracks the bar codes of all plates in the system that have bar codes applied either:

❑ On the BioCel

❑ Before entering the BioCel, but which were read as they entered the system

VWorks associates each bar code with a plate location so it is aware of where each plate is at all times. If during a run a bar code is read that does not match the bar code associated with that location, a mismatch error is reported. These bar code associations are held in memory and lost when the computer is turned off.

If your BioCel includes incubators to store and incubate plates, bar codes are additionally tracked using the inventory management system. Unlike the simple bar code associations described above, which are stored temporarily, the inventory management associations are permanently stored in a database.


Planning to add bar code labels to a plate

“Using Bar Code Input Files” on page 225

Adding a Bar Code task to a protocol

“Setting Apply Label Task Parameters” on page 127


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Using a platepad bar code reader “Setting Place Plate Task Parameters” on page 145

Bar code mismatch errors “Resolving BioCel Bar Code Reader Errors” on page 315

Inventory management system “Inventory Management Overview” on page 231

For more information about... See...


Using Bar Code Input FilesBar Code Fields When adding a VCode task to a protocol you set protocol task

parameters that specify the content of bar code fields. There are several ways to provide VWorks with bar code data. One way is to import it from bar code input files.

Bar Code Field Example

An example of the content of a bar code field is:

NAW1001

For detailed information about bar code fields and formats, see the VCode User Guide.

Bar Code Input Files File Name and LocationBar code input files are text files with the naming convention (<file name>.bar). They are stored in the location specified in the general VWorks options. For more information, see “Setting General Options” on page 48.

When to Use

You can use bar code input files to:

❑ Verify the bar codes on incoming plates, which are plates that are downstacked into the system.

This function is set in the parameters for the plate instance of the incoming plates:

❑ Specify each field of a bar code that is printed on a plate while on the BioCel.

How They Are CreatedBar code input files are typically generated by a LIMS (Laboratory Information Management System), although you can create them manually and save them in the specified folder location.


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File Structure

Bar code input files contain lists of bar code fields, or parts of fields, that are grouped together in series. In the following example there are two series:

❑ Set1

❑ Set2

Each series could be used to label a different side of the same plate, or label plates during different runs.

Viewing a Bar Code File in VWorks

You can view the bar code file that is currently associated with VWorks from within VWorks.

To view the associated bar code input file:

1. Select Tools > Show Bar Code File.

This opens a view of the bar code data file.


2. Click a tab to show a different series of data.

3. To close the window, click the close box.

Updating a Bar Code Input File

We do not recommend doing this, but if you change a bar code input file while a protocol is running, you must reload the file for the change to be registered.

To reload a bar code input file:

1. Select Tools > Reload Bar Code File.


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Using Bar Code Data FilesIntroduction This topic describes how to create and use bar code data files in

collaboration with bar code input files.

Bar Code Data Files File Format and LocationBar code data files are tab-delimited text files with the name <file name>.dat. They are stored in a location specified in the general VWorks options. For more information, see “Setting General Options” on page 48.

How They Work

A bar code data file acts as a lookup table that specifies what bar code fields to print on other sides of a plate. The typical sequence of events is as follows:

1. A plate with a south-side bar code is downstacked into the system.

2. The robot picks up the plate, reads the bar code, and verifies it against a bar code input file.

3. The robot moves the plate to a VCode.

4. The bar code that was read is used as a key to look up the bar code fields to print on the other sides of the plate, using the bar code data file as the lookup table.

5. The VCode prints bar codes on the other sides of the plate.

Bar code data files can also be used with incoming plates that have west-side bar codes. In this case, the bar code must be read at the VCode or platepad and not by the robot’s bar code reader.

!! IMPORTANT !! Bar code data files cannot currently be used with incoming bar codes on the north or east sides.

Bar code data files can still be used if the downstacked plate has no bar code, provided that incoming bar code verification is turned off. The plate could be moved to the VCode and labelled on its south or west side. That label could then be read and used with a bar code data file to specific the labels to be printed on the other sides of the plate.

For more information about bar code input files, see “Using Bar Code Input Files” on page 225.

Where They are Specified

The use of bar code data files is specified when configuring protocol task parameters for an Apply label task.

For more information, see “Setting Apply Label Task Parameters” on page 127.


File Structure An example of a bar code data file is shown below. The columns are separated by tabs.

!! IMPORTANT !! The columns must be in the order north, east, south and west, from left to right.


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About Setting Up a StoreX Transfer StationSet Up Transfer station platepads are set up at the factory. This topic explains

how they are set up in case you need to make changes.

If your transfer station has two platepads one platepad must be set to be the input platepad and the other must be set to be the output platepad.

The input and output platepads are separate devices which are selected in the StoreX device properties, as shown in the following diagram.


Inventory Management OverviewIntroduction This topic explains some of the concepts that are important to

understand when working with the inventory management database and StoreX tasks.

Also Read Before starting to create protocols that use StoreX tasks, you should also understand the information in:

❑ “Setting StoreX Task Parameters” on page 154



❑ “Resolving Inventory Management Problems” on page 318

Bar Code Tracking and Inventory Management

Plates are tracked on a BioCel using south-side bar codes. Every time the robot picks up a plate the bar code is read and compared with the plate that is expected.

This system accurately tracks plates through a protocol, but it is limited because the plate locations are stored in memory and are lost on exiting VWorks. The inventory management system increases the ability of the BioCel to track plates because plate tracking information is permanently stored in a database on the computer’s hard drive. This added function is only useful on BioCel platforms that allow for long-term plate storage in incubators. Inventory management is therefore only used with StoreX tasks.

Database Function The inventory management database maintains a list of plates in every incubator.

The information contained about plates in the database includes the:

❑ Cassette and slot location

❑ Plate name

❑ Labware type

❑ West-side bar code (if an optional incubator bar code reader is used)

A representation of the database is displayed in the Inventory Management dialog box. An example view is shown below.


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The list of plates in the system is updated every time a plate is moved robotically in to or out of an incubator so that at all times, the list is current.

From the inventory manager you can:

About Manually Moving Plates

It is important to note that, unless your incubator has a bar code reader, the plates in the incubator are not physically sensed so the database is unaware of plates that are manually added, removed, or moved by an operator. To keep the database synchronized with the incubator, always load and unload the incubator robotically. If you want to load and unload the incubator manually, you will need to either:

❑ Run the simulator each time to make the database match the incubator.

When correctly set up, the simulated run will change the plates listed in the database without actually moving plates.

❑ Create new plates using the plate linker dialog box (see “Adding StoreX Plates Manually” on page 250).

Terminology When describing the movement of plates, it is important to use terms correctly. The terms load and unload are used from the incubator’s perspective. The terms input plates and output plates are from the BioCel robot’s perspective.

Procedure See...

Delete plates from the database “Deleting Labware” on page 249

Add or change the type of labware associated with a plate

“Using Inventory Labware Selection” on page 249

Inventory the plates in an incubator

“Reinventorying the Plate Management System” on page 252

Term Definition

Unload The act of moving a plate from an incubator into the BioCel system.

Load The act of moving a plate from the BioCel system into an incubator.


Database Backup The inventory management database can be backed up onto another computer using a software utility. If you want to do this, contact the Velocity11 Service Center for more information.

System Plates that are processed by the current protocol are considered to be in the BioCel system.

For example:

❑ A plate on a platepad is in the system.

❑ A plate in a plate hotel is in the system.

❑ A plate being incubated in an incubator is in the system.

❑ A plate half-way up a stacker is not in the system, unless it will be moved during the current protocol.

❑ A plate being stored in an incubator is not in the system unless it will be moved during the current protocol.

Input plates Plates that are taken out of the incubator during a protocol.

Output plates Plates that are put in to an incubator during processing.

Term Definition


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Inventory Manager Views and FiltersInventory Manager Views

There are three ways to view the plates in the Inventory Management dialog box.

To set the view:

1. Navigate to Tools > Inventory Management.

The Inventory Management dialog box opens.

2. From the Select view type list box, select one of the following options.

Filtering Displayed Plates

You may have many plate records stored in the database. To simplify your view of the database, you can filter the records that are displayed.

To filter the plate records:

1. Right-click on the database list and select Show where.

2. Select from the available filtering options.

View Description

View by plate Displays every plate in the inventory.

This is the most frequently used view.

View by location Displays both plates and slots.

View unassigned plates Displays plates that were orphaned during previous runs. This means plates that are on the BioCel but not in an incubator.

Unassigned plates do not appear in linker groups so cannot be used.


To show all plate records:

1. Right-click on the database list and select Show all.

About Linker Groups and FilesIntroduction Before starting to create protocols that use StoreX tasks, you should

understand the information in this topic and read “Inventory Management Overview” on page 231.

Linker Groups A subset of plates listed in the database inventory can be associated together to form a plate linker group, which defines the plates that will be moved out of an incubator during an unload task.

Similarly, a subset of slots can be associated together to form a slot linker group, which defines the slots that will be filled by plates during a load task.

Note: This applies when plates are downstacked and added to an empty incubator, or when they are unloaded from the incubator and then loaded back into the incubator.

The following screenshot shows a linker group.

Linker File A single protocol can contain more than one incubator load or unload task, and can therefore be associated with more than one linker group. The collection of linker groups for a single protocol are maintained in a linker file.

A linker file is created in, and represented visually by, the Plate Linker dialog box.


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Concept Summary Diagram

To summarize the relationship between linker groups and linker files, one protocol can only have one linker file, but one linker file can have many linker groups. This is illustrated in the following diagram:

One protocol can only be associated with one linker file at any one time. However, the same protocol can be used with different linker files at

Linker File

Protocol

Process B

Process A

Process C

Processes

Load task

linker group

Load task

linker group

Unload task

linker group

Unload task

linker group

Incubator Tasks


different times. This would be useful if you have a protocol that you want to reuse with different plates.

Note: You do not have to create all of the linker files using the same protocol, but the names of the processes used to create the linker files must be the same.

How Linker Files are Used

Linker files are used to define the group of plates that will be moved in to and out of an incubator during:

❑ A single protocol run that is manually started.

For more information, see “About Linker Groups and Files” on page 235.

❑ A run that is scheduled in advance using a runset.

For example, a runset may run three protocols, the first using linker file A, the second using linker file B and the third using linker file C.

For more information, see “About Starting Runs Automatically” on page 87.

Group Membership A single plate can be a member of more than one linker group.

XML Format The list of plates in a linker group are stored as an XML file with the file name extension .vlk, in a location selected by your BioCel administrator. During BioCel set up at the factory, linker files are stored in a folder at the following location:

C:\VWorks Workspace\Linker files

Linker files should not be edited directly because of the possibility of introducing errors. Always create and edit linker groups within the Plate Linker dialog box of VWorks. You can back up linker files though by copying them to another disk.


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Working with Linker FilesIntroduction Linker files work with StoreX tasks to move groups of plates in to and out

of StoreX incubators.

In addition to this topic, you should also read:

❑ “Setting StoreX Task Parameters” on page 154


Structure of This Topic

Because the concept of linker files can be difficult to understand, this topic uses a sequence of common protocol examples.

The examples illustrate how you can use a linker file to:

❑ Move a group of plates in to an incubator, using a single process.

This can be used for pre-run loading of an incubator.

❑ Move a group of plates out of an incubator, using a single process.

This can be used for post-run emptying of an incubator.

❑ Move a single plate from one position in an incubator to another position in the same incubator, using a single process.

❑ Perform a timed incubation, using a single process.

❑ Move plates in a multi-process protocol.

When to Create Linker Files

You do not have to save linker data as a file before using it for a protocol, however, if you do not save the file the linker information will be lost when you close VWorks.

You can create a linker file in advance of the time that you want to run the protocol, or you can create it as part of setting up the protocol to run.

You cannot create a linker group while a protocol is running.


Clearing the Current Linker File

Before creating a new linker file you will need to clear the linker groups displayed in the Plate Linker dialog box.

To clear the current linker file:

1. Navigate to File > Linker File > New.

2. Click OK in the VWorks dialog box that asks you if you want to delete the current linker group.

The linker file groups are cleared.

Pre-Run Loading To load an empty incubator with plates before a run, create a separate protocol such as that shown in the following example:

In this procedure you will select a group of incubator slots (slot linker group) that you want to move the plates in to after they have been downstacked.

To load plates before a run:

1. Add a plate instance for the plates you want to load.

For more information, see “Setting Up a Plate Instance” on page 112.

2. Add a stacker task for the VStack® that contains the plates.

3. Drag a StoreX task into the process to create the last task, which becomes a load task.

4. Set the stacker parameters.




7. Select the Output Plates tab.

The name of the process that includes the load task (the only option as there is only one process) is selected by default.


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8. Click the first slot that you want to be in the group, then hold down the SHIFT key and click the last slot that you want to be in the group.


9. Click Add selected plates.

10. The slot linker group is added to the list of Plates currently in the selected group.


11. Click OK to close the Plate Linker dialog box.

12. Start the run.

The plates will be downstacked and moved to the incubator. For instructions for starting a run, see “Starting a Run from VWorks” on page 83.

Emptying an Incubator

In this example, the protocol unloads all of the plates from an incubator and moves them to a VStack. This is the best way to unload an incubator because it also removes the plate associations from the database.

In this procedure you will select a group of plates (plate linker group). For comparison, in the previous example a group of slots was selected.

To empty an incubator:

1. Add a plate instance for the plates you want to unload.

For more information, see “Setting Up a Plate Instance” on page 112.

2. Drag a StoreX task into the process to create the first task, which becomes an unload task.

3. Drag a stacker task into the process to provide somewhere for the plates to go.

4. Set the stacker parameters.


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The Input Plates tab and the name of the process that includes the unload task (the only option as there is only one process) are selected by default.

7. Click the first plate that you want to be in the group, then hold down the SHIFT key and click the last plate that you want to be in the group.





9. Click OK to close the Plate Linker dialog box.

10. Start the run.


Moving a Plate This example illustrates how you can move a single plate from one place in an incubator to another place in the same incubator. This procedure is more complex than the previous two procedures because it involves two StoreX tasks in the same process.

To move a plate:

1. Create a process that has a load and an unload task, as shown in the following example.




The Input Plates tab and the name of the process are selected by defaults.


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4. In the Plate inventory list, click the plate that you want to move and click Add selected plates.

The plate is moved to the selected Plates currently in selected group list.

5. Select the Output Plates tab.

6. The name of the “test protocol” process is selected by default.

7. In the Plate inventory list, select the slot that you want to move the plate to.

You can identify a slot because it has no plate associated with it.


The slot is added to the list of Plates currently in the selected group.

9. Start the run.


Note: If you want to return the plate to the same location in the incubator, click Add selected plates & return to original locations in step 4 and jump to step 9.

Performing a Multi-Process Incubation

In this example, the BioCel has two incubators, one set at 4 degrees Celsius and the other set at 37 degrees Celsius. The incubator devices were named after their temperatures to make it easier to set up the protocol.

The protocol has two processes. The first moves a group of plates from 37 degrees to 4 degrees, and the second moves a group of plates in the reverse direction.


To perform a multi-process incubation:

1. Create the protocol shown above.




4. Click the Input Plates tab.

5. Set up the first process:

a. Click to select the process named multiprocess1.

b. Select the plates in the 37-degrees incubator that you want to move.


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Naming the device after the temperature makes it easy to select the right plates.

c. Click Add selected plates.

The plates are moved to the Plates currently in the selected group list.

d. Click the Output tab.

The process named multiprocess1 is selected by default.

e. In the Plate inventory list, select the slots in the 4-degrees incubator that you want to move the plates in to.

f. Click Add selected plates.


6. Set up the second process:

a. Click the Input Plates tab.

b. Click to select the process named multiprocess2.

c. Select the plates in the 4-degrees incubator that you want to move.


e. Click the Output tab.

f. Select the process named multiprocess2.


g. In the Plate inventory list, select the slots in the 37-degrees incubator that you want to move the plates in to.

h. Click Add selected plates.


7. Start the run.

Using Bar Code Input Files with Linker FilesIntroduction You can use bar code input files to specify which plates should be in a

linker group. If you previously used a bar code input file to label a collection of plates, which are now stored in an incubator, you can conveniently re-use the file to create the linker file.

For general information about bar code input files, see “Using Bar Code Input Files” on page 225.

Procedure !! IMPORTANT !! All plates with bar codes listed in the selected bar code input file series must be present in the incubator for this method to be successful.

To use a bar code input file to create a linker file:




3. Click the Browse button for the Import bar code file and navigate to the .bar file that you want to use.

4. From the Bar code group list box, select the series that you want to use.

In the following example of a bar code input file, the options would be Set1 and Set2.


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5. Click Import.

The plates labelled with the bar codes listed in the series will be used to create a group and will appear in the Plates currently in the selected group list.

6. Specify a labware type for each plate....

The easiest way to do this is to use the Labware selection list. For more information, see “Using Inventory Labware Selection” on page 249.


Using Inventory Labware SelectionIntroduction Depending on how you use the inventory management system, you may

find that some of the plates listed in the Inventory Management dialog box either do not have a specified labware type or have an incorrect labware type. You can correct this using the inventory labware correction function.

Adding or Changing Labware

To add or change a labware type for a group of plates:

1. In the Inventory Management dialog box, click in the Labware column of the first plate in the group you want to select.

2. SHIFT-click the last plate in the group you want to select.

3. While SHIFT-click the last plate again in the Labware column.

4. From the dialog box, select the labware type.

5. Click anywhere in the list.

The labware type will be changed for all selected plates.

Deleting Labware You can delete one of more plates from the database.

To delete a plate from the database:

1. In the Inventory Management dialog box, click in the Labware column of the first plate in the group you want to select.

2. SHIFT-click the last plate in the group you want to select.

3. Click Delete selected plates.


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Adding StoreX Plates ManuallyIntroduction You may not always want to unload and load an incubator using the

robot and VStack module. To manually load plates, you have two options:

❑ Load the plates by hand and then use a protocol with the simulator to simulate the movement of plates into the incubator.

For more information, see “Checking a Protocol” on page 122.

❑ Load the plates by hand and then use the Create new plates feature of the Plate Linker dialog box.

This feature is described in this topic.

Procedure To add a cassette of StoreX plates manually:

1. Remove a cassette from the incubator, and unload any plates that it contains.

2. Fill the cassette with plates and load the cassette back in to the incubator.




5. In the Default name for new plates text box, type a name that you would like to appear in front of every plate name.

6. In the Plate inventory, click and then SHIFT-click to select every slot in the cassette.


7. Click Create new plates.

The plates are given a name, listed in the plate name column. The given plate name is prepended to the each plate name, followed by a number.


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8. Click OK.

9. Navigate to Tools > Inventory Management and review the inventory in the Inventory Management dialog box.

10. Specify the plate types for the plates, following the directions in “Using Inventory Labware Selection” on page 249.

Reinventorying the Plate Management Sys-temAbout Reinventorying

The accuracy of the database can be checked by performing an inventory of the database.

The incubator’s bar code reader checks all selected slots for the presence of a bar-coded plate and reads the bar codes. The results are checked against the BioCel database.

Reinventorying Logic If a plate is found in a slot that, according to the database, should not have a plate, a plate record is added to the database for that slot, including the plate’s bar code. If that bar code is already associated with another slot in the database, the previous association is deleted. In doing this, the system assumes that the plate has been manually moved.

!! IMPORTANT !! For reinventorying to be successful, each plate must have a unique bar code.

If the database has a record for a plate in a particular slot, but the inventory finds no plate in that slot, the association between that slot and the plate is deleted and the plate entry is cleared from the database. However, the data in the system associated with the plate is not deleted. If in the future, if the plate is returned to the system the data can be reassociated with it.

This chapter is for people with Administrator login privileges. It covers how to administer user accounts, edit labware definitions and collect plate reader data. It also covers how to use the safety interlock override.

Other chapters that are intended for administrators are:

❑ “Creating a Protocol: Basics” on page 109

❑ “Creating a Protocol: Advanced Topics” on page 193



Administrator Procedures 9

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Creating a User AccountIntroduction Administrators create accounts to enforce privileges for different levels

of users.

For more information about privileges, see the Database and Security User Guide.

Procedure To create a user account:

1. Select Tools > Manage Users.

2. In the User Editor dialog box, click Add.

3. In the User Name text box, type a name for the user.

4. From the Access Level list box, select the privilege that you want to assign to the user.

5. Assign a password:

a. Click Change Password.

b. Enter a password in the New text box.

c. Re-type the password in the Confirm New text box.

d. Click OK.

6. Click OK.

!! IMPORTANT !! If you do not assign a password, a blank password will automatically be assigned. This means that anybody can log in to VWorks™.

255Chapter 9: Administrator ProceduresBioCel User Guide

Setting Labware and Liquid ParametersIntroduction The BioCel® software includes a:

❑ Labware database

❑ Liquid library database

These databases are maintained in the Windows® registry and are accessed using the labware editor and the liquid library editor.

The databases on your BioCel already contain most of the information you need. If you want to use new types of labware or new liquids, or want to optimize settings that are already defined in the databases, you will need to work with the labware editor or liquid library editor. This topic explains how to open the labware editor and liquid library editor.

Labware Editor The labware editor is used to define the detailed dimensions of microplates, tipboxes, pin tools, and so on. These dimensions are needed by the robot and VPrep® for accurate plate manipulation.

To open the labware editor from VWorks:


2. In the Device List, select Labware from the Built-in Devices.

3. Click Device Diagnostics.

The labware editor opens.

Liquid Library Editor The liquid library editor is used to set parameters that affect pipetting accuracy and precision.

To open the liquid library editor from VWorks:


2. In the Device List, select Liquids from the Built-in Devices.


The liquid library editor opens.


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More Information For more information about using the labware editor and liquid library editor, see “Understanding the Configuration Settings in a Pipette Task” on page 219 and the Database and Security User Guide.

Ultramark Plate Reader Data FileIntroduction The Ultramark plate reader measures the absorbance of samples in

microplate wells and stores the measurement data in a comma separated file on the controlling computer.

This topic explains how to define where the plate reader data files are stored.

Data File Folder To set the data file output folder:


2. In the VWorks Options dialog box, click the Log Options tab.

3. Click the Reader output file ellipsis button.

4. Navigate to the folder in which you want to store the data file.

5. Enter a file name, but leave off the extension.

6. Click Save and make sure that the correct file path is displayed.

7. Click OK.

257Chapter 9: Administrator ProceduresBioCel User Guide

Network CardsIntroduction You may need to provide some of the information in this topic to your

network administrator for your BioCel to be connected to your organization’s network.

Your BioCel has two network cards. The network connections for these cards are named WAN and LAN.

Network Connections

Note: Depending on how you have personalized your operating system, you may need to use a slightly different procedure from the one below.

To see the network connections in Windows:

1. In Windows, from the Start menu select Settings > Control Panel.

2. Double-click the Network and Dial Up Connections icon.

The Network and Dial-up Connections window opens.

LAN Network Card

The LAN network card is used for communication between the computer and modules that use Ethernet communication cable. This network is considered to be the local area network.

The LAN network card has a fixed IP address, which is 192.168.0.1.

WAN Network Card

The WAN network card is for networking with your organization’s network. The settings for this card should be configured by your network administrator in the same way that any PC would be configured to make it available to your network.

The WAN network card has an IP address that is dynamically assigned by your domain name server when you start your BioCel’s computer.


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Network IP Addresses

To see the IP addresses of the two network cards:

1. In VWorks, click the Device Manager tab.

2. Select a VStack® from the Device List.


4. In the Discovered BioNet Devices dialog box, click the drop-down arrow for the Select the Ethernet adapter to use... list box.

!! IMPORTANT !! Make sure that you do not change the selected IP address when you do this. VStacks should be always be connected to the LAN network with the 192.168.0.1 IP address.

This chapter explains how to use diagnostics software to control the robot and third-party modules.

Using Diagnostics Software 10

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About Diagnostics SoftwareBackground The robot, and every module used with the BioCel®, can be controlled

independently of VWorks™ using diagnostics software. Diagnostics software communicates directly with modules using simple commands.

It is used for:

❑ Troubleshooting

❑ Setting teachpoints

❑ Performing manual operations outside a protocol

For example, if an error occurs during a run that leaves a plate where it should not be and the VStack® stage out of its home position, you can use Robot Diagnostics to move the plate and VStack Diagnostics to return the VStack stage to its home position.

Opening Diagnostics Software

Note: VWorks is transitioning to a new user interface design. If the following procedure does not open the device’s diagnostics software, click the Diagnostics button in the control toolbar of the main page and select the relevant device.

To open a diagnostics software program:

1. In VWorks, click the Device Manager tab.

2. In the Device List, expand the general name of the device whose diagnostics you want to open.

3. Click to select the particular device that you want to communicate with.


The diagnostics dialog box opens.

261Chapter 10: Using Diagnostics SoftwareBioCel User Guide

Where to Find Diagnostics Instructions

Most modules manufactured by Velocity11® include diagnostics software that is specific for the module. You can find instructions for using this software in the relevant user guide.

Diagnostics software for third-party modules has been developed by Velocity11, and you can find instructions for this software in this chapter of the guide. This chapter also includes robot and Bio I/O Diagnostics, which are specific to the BioCel.

For more information, see:

❑ “Using AliQuot Diagnostics Software” on page 262

❑ “Using Bio-Tek Diagnostics Software” on page 266

❑ “About Bio I/O Diagnostics Software” on page 270

❑ “Using the Echo 550” on page 270

❑ “Using Envision Diagnostics Software” on page 272

❑ “Using iSeries Diagnostics Software” on page 275

❑ “Using Lid Hotel Diagnostics” on page 278

❑ “Using Multidrop Diagnostics Software” on page 279

❑ “Using Nanodrop Diagnostics” on page 282

❑ “Using QFill Diagnostics” on page 286

❑ “Using Robot Diagnostics Software” on page 288


❑ “Using Teleshake Diagnostics Software” on page 306


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Using AliQuot Diagnostics SoftwareIntroduction The aliQuot is a low volume liquid dispenser for the delivery of reagents,

reaction mixes, cells, beads, chemical solutions and liquids into 96-, 384- and 1536-well microplates.

You can use AliQuot Diagnostics software to manage device profiles, set basic options and perform a test fill.

For general information about the aliQuot, see the Genetix aliQuot user documents.

About AliQuot and QFill2 Software

When you first open the AliQuot Diagnostics software, the title bar reads QFill2. This is because the same underlying code is used to operate the aliQuot and QFill2 modules. You have to choose to display the aliQuot functions in the user interface.

To display the aliQuot-specific functions:

1. Select the AliQuot mode check box.

The title bar reads AliQuot Diagnostics and an AliQuot tab is displayed.

Note: The BioCel supports the operation of the QFill2 from this diagnostics software dialog box, However, VWorks version 13 does not use the ActiveX that underlies this dialog box to support the QFill2 during protocols. See “Using QFill Diagnostics” on page 286 for how to use the QFill2 with VWorks.

Filtration System Velocity11 can add a vacuum system to allow the aliQuot to draw the samples in a filtration plate through the well filters and into a collection plate.

You have to choose to display the filtration-specific functions in the user interface.

To display the filtration-specific functions:

1. Select the Enable filtration check box.

The Filtration tab is displayed.


Managing Profiles A profile defines the communication settings between the BioCel computer and the aliQuot and as well as some other basic settings.

Changes to other settings can be made in the AliQuot Diagnostics software, but these are not saved in a profile and are therefore lost when you exit VWorks.

A profile was already created for your aliQuot at the factory, but if you want to use a different profile, you will need to create the profile and then select it in the device manager.

The following settings are saved in an aliQuot profile:

For more information about these settings, see the information later in this topic.

To get a new profile you can either create one from the beginning, or save an existing profile and edit the settings that you want to change.

Setting Comments

AliQuot mode Whether the AliQuot mode check box is selected or not on the Control tab

AliQuot purge on or off Whether Auto purge on or off is selected on the AliQuot tab

AliQuot purge time The Purge time entered when AliQuot purge is on.

The Purge time is the duration of the purge operation.

AliQuot purge interval The Purge interval entered when AliQuot purge is on.

The Purge interval is the time between purges.

COM port The computer’s serial port that the AliQuot is connected to

Filtration port Defines the Bio I/O port used to provide vacuum sensor information for an optional filtration station. You should not need to change this number.


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To create a new profile:

1. In the Profiles group box of the Control tab, click New.

2. Enter a name for the profile in the Create New Profile dialog box.

3. Click OK.

A new profile is saved with the default profile settings.

To save and modify an existing profile:

1. In the Profile list box of the Control tab, select an existing profile on which you want to base your new profile.

2. Click Save As.

3. In the Save Profile As dialog box, replace the name with a new one and click OK.

4. Edit the profile settings and click Apply.

Performing a Manual Operation: Overview

The general process for performing a manual operation on the aliQuot for is:

1. Select or create a profile that has the basic settings you require for the operation.

2. Define other settings not stored in the profile.

3. Perform a fill test.

Setting Up the aliQuot

To set up an aliQuot for a manual operation:

1. Select or create a profile that has the settings you require, according to the following table:

Setting Diagnostics Page

Comments

AliQuot mode Control The AliQuot check box must be selected in the profile.

AliQuot purge on or off

AliQuot Select On if you want to periodically push fluid through the lines. This can remove blockages in the line.

AliQuot purge time AliQuot Enter the duration of the purge operation.

AliQuot purge interval AliQuot Enter the time between purges.

COM port Control This is the number of the serial port to which the aliQuot is connected. If you have more than one aliQuot on your system, you must select the port for the module that you want to communicate with.


2. If required, in the Timeout text box, enter a different time that the computer will wait for a response from the aliQuot to say that the fill operation is complete.

The default value is 60 seconds.

3. If you want to use vacuum filtration:

a. On the Control page, select Enable filtration.

The Filtration tab appears.

b. In the Start Filtration group box, select When fill starts to start the filtration at the same time that the dispense begins, or After fill completes to start the filtration when the dispense ends.

c. If you want a delay between the time the start filtration signal is sent to the aliQuot and the beginning of the vacuum pull, enter a value for Filtration delay.

d. In the Filtration time text box, enter a duration for the vacuum pull.

e. If you want a delay between the end of the filtration and when the end of the operation is reported, enter a value for Post Filtration delay.

Performing a Fill Test

Once you have set up the aliQuot, you can perform a fill test.

To perform a fill test:

1. In the Fill Test group box, click in the text box and type the volume of liquid to dispense into each well of the plate.

2. Click Fill.

The plate is filled.

Filtration port Filtration This is the Bio I/O port used to communicate with the optional aliQuot filtration unit. If you have more than one aliQuot using filtration, you will need to select the number that corresponds to the filtration unit with which you want to communicate.

Setting Diagnostics Page

Comments


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Using Bio-Tek Diagnostics SoftwareIntroduction This topic explains how to manipulate a Bio-Tek ELx405 automated

microplate washer, using Bio-Tek Diagnostics software.

We strongly recommend that you read the Bio-Tek ELx405 Washer Operator’s Guide before using the ELx405 on the BioCel. You can also refer to the less-detailed online help, which can be accessed from the Bio-Tek Diagnostics software.

About Bio-Tek Diagnostics Software

The Bio-Tek ELx405 can be controlled through the built-in keypad. In addition, Velocity11 has developed a user interface, which is the Bio-Tek Diagnostics software, to allow BioCel users to operate an ELx405 using the BioCel computer.

!! IMPORTANT !! If you use the ELx405 to create a program, you will not be able to access it through Bio-Tek Diagnostics. If you create a program through the Bio-Tek Diagnostics you will not be able to access it through the keypad.

About Linked Programs

You cannot create linked programs using the Bio-Tek Diagnostics software. Instead, you can add two or more consecutive Bio-Tek Washer tasks to a protocol.

Setting Parameters To set Bio-Tek Diagnostics parameters:

1. Select the name of the Bio-Tek program that you want to run from the Select program to run list box.

Note: If you need to create a program, select Show programs and follow the directions in the remaining sections of this topic for how to set up the program.

2. Select the name of the washer to use from the Select washer to use list box.

Setting Basic Properties

To set the basic properties:

1. In the Protocol Task Parameters toolbar, click Show Programs to open the Bio-Tek Diagnostics software.

2. From the Program list box of the Bio-Tek Diagnostics software, select a program.

3. From the Select washer to use list box, select the model of ELx405 that you have.

!! IMPORTANT !! If you select the wrong model, VWorks will freeze when you run the program through either Bio-Tek Diagnostics or a VWorks protocol.

4. From the Plate type list box, select the type of plate.


5. From the Program type list box, select the type of program to run.

For more information about types of programs, see the Bio-Tek ELx405 Washer Operator’s Guide.

6. From the Buffer valve list box, select the valve corresponding to the reagent that you want to use.

Creating a Program You can create a program, which is a named collection of parameter settings, from the Bio-Tek Diagnostics software.

To create a program:

1. Click New.

2. Type a name for the program in the New Program dialog box.

3. Click OK.

4. Complete the parameter settings, as required, in the Bio-Tek Diagnostics dialog box.

Refer to the parameter tables below and the parameters described in the Bio-Tek ELx405 Washer Operator’s Guide.

5. Click Save.

Running a Program You can run any program that was created using Bio-Tek Diagnostics software.

!! IMPORTANT !! Before running a program, make sure that the Bio-Tek Washer display does not read “UNDER EXTERNAL CONTROL.” If it does, VWorks will freeze when you run the program and you will have to end the application from the Microsoft®

Windows® Task Manager.

To run a program:

1. Select the program from the Program list box.

2. Click Run.

Resetting the Bio-Tek Washer

Resetting the Bio-Tek washer performs a software reset of the washer, which has the same effect as switching the power off and on. You might use this feature to recover from a suspected communication problem with the module.

To reset the Bio-Tek washer:

1. Click Reset.


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2. Wait for the beep before using the washer.

Accessing Online Help

To open the Bio-Tek washer’s online help:

1. Click HELP ME!

2. If the Help file does not open, navigate to the folder C:\VWorks Workspace\bin\BioTek and select the file 405ocx.hlp.

Running a Standard Program

The Bio-Tek Washer includes a number of standard programs, for uses such as measuring the accuracy and precision of dispense volumes.

!! IMPORTANT !! Before running a program, make sure that the Bio-Tek Washer display does not read “UNDER EXTERNAL CONTROL.” If it does, VWorks will freeze when you run the program and you will have to end the application from the Microsoft Windows Task Manager.

To run a standard program:

1. Select the program from the Standard program list box.

2. Click Run.

Parameters Tables Some of the parameter names used in the Bio-Tek Diagnostics software are slightly different to the names given in the Bio-Tek ELx405 Washer Operator’s Guide and online help. The names that are different are listed in the following tables to help you when looking up information.

Aspirate Parameters

Velocity11 Bio-Tek Diagnostics Label

Bio-Tek Parameter

Horizontal position Horizontal Aspr Pos

Horizontal y-position Horizontal Y Aspr Pos

Crosswise aspirate options Crosswise On

Crosswise aspirate height Crosswise Height

Crosswise horizontal position Crosswise Horiz Pos

Crosswise horizontal y-position Crosswise Horiz Y Pos

Final aspirate delay Final Aspr Delay


Dispense Parameters

More Information For general information about diagnostics software, see “About Diagnostics Software” on page 260.

For important information about setting up a Bio-Tek ELx405, see “Bio-Tek Washer Set Up” on page 73.

For more information about adding a Bio-Tek Washer task when creating a protocol, see “Setting Bio-Tek Washer Task Parameters” on page 133.

Velocity11 Bio-Tek Diagnostics Label

Bio-Tek Parameter

Prime before dispense Prime Before Start

Dispense volume per well Dispense Volume

Horizontal position Horizontal Disp Pos

Horizontal y-position Horiz Y Disp Pos

Bottom wash volume Bottom Disp Volume

Bottom wash flow rate Bottom Flow Rate

Bottom wash height Bottom Disp Height

Bottom wash horizontal position Bottom Horiz Pos

Bottom wash horizontal y-position Bottom Horiz Y Pos


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About Bio I/O Diagnostics SoftwareAbout the Bio I/O Diagnostics Software

The Bio I/O Diagnostics software is used by Velocity11 personnel for troubleshooting communication problems. You should not need to use the Bio I/O Diagnostics software.

Using the Echo 550Introduction The Echo 550 transfers drops of liquid between microplates for

compound reformatting applications.

Creating a Profile A profile stores settings that are used to facilitate a connection to an Echo 550. A profile was created for your Echo 550 at the factory, but if you want to add another Echo 550, you will need to create a profile for it.

To create a profile:

1. In the device manager, select the echo device.

2. Click Device Diagnostics to open the diagnostics software.

3. Click the Profiles tab.

4. Click Create.

5. In the New Profile dialog box, enter a name for the profile and click OK.


Note: The name of the Host Address should be IP address of the Echo 550 computer.

The name appears in the Profile Control list box.

Performing a Manual Transfer

You can perform a manual Echo550 transfer through the diagnostics software.

To perform a manual transfer:

1. In the device manager, select the echo device.

2. Click Device Diagnostics to open the diagnostics software.

The diagnostics software opens to the Diagnostics page.

3. Place a source plate into the Echo550:

a. Select an Echo550 plate definition from the Source plate definition list box.

b. Click Extend source stage.

c. Place a plate on the stage that matches the selected definition.

d. Click Retract source stage.

4. Place a destination plate into the Echo550:

a. Select an Echo550 plate definition from the Destination plate definition list box.

b. Click Extend destination stage.

c. Place a plate on the stage that matches the selected definition.

d. Click Retract destination stage.

5. Select an existing protocol from the Transfer protocol list box.


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6. Optionally, select one or both of the following options:

7. Click Execute transfer protocol.

Using Envision Diagnostics SoftwareIntroduction The Envision Diagnostics software is used to:

❑ Manually connect to a PerkinElmer Envision plate reader

❑ Move plates into and out of the reader

❑ Run Envision protocols on the reader

Creating a Profile A profile stores settings that are used to facilitate a connection to an Envision. The names of current profiles are displayed in the list box.

Typically, one profile is created for a single Envision. Your BioCel is likely to only have one profile, so you will probably never need to change it or create a new one.

You could set up a different profile for every user account on the computer, but typically the computer will only have one user account.

Option Comments

High-speed transfer The stage “scans” across the plate and does not stop moving.

The alternative is for it to stop at each well.

Fast survey A survey is performed before a run, in which a sample of wells are analyzed.




2. Click New profile.

3. In the New Envision Profile dialog box, type the name for the profile and click OK.

The name appears in the Current Envision Profile list box.

4. Select the name of the Envision profile that you want to edit or modify in the Current Envision Profile list box.


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5. Enter the name of the computer that controls the Envision into the Server name text box.

6. In the Authentication Information group box, enter the username, name of the domain that the server is on, and the password for the user account on the Envision’s computer that you want to use.

7. Click Save profile.

Controlling the Envision

The Envision is controlled from the Control page of the diagnostics software.

To manually load and unload plates:

1. Click the Control tab.

2. In the Current Envision Profile group box, select the profile you want to use.

3. Click Open profile.

4. Click Load plate or Unload plate.

The plate is loaded into the Envision or unloaded from the Envision.

Envision protocols are created on the Envision’s own computer. After creation, the name of the protocol appears in the Envision Functions list box of the diagnostics software.

For information about switching between computers on the BioCel monitor, see “Module Computers” on page 27.


To run an Envision protocol:

1. Click the Control tab.

2. In the Current Envision Profile group box, select the profile you want to use.

3. Click Open profile.

4. From the Envision Functions list box, select the protocol that you want to run.

5. Click Run protocol.

If there is a plate on the plate stage it is loaded. The protocol runs.

Using iSeries Diagnostics SoftwareAbout This Topic This topic explains how to use the iSeries Diagnostics software. Read this

if your BioCel is equipped with environmental control options.

About Environmental Control

The environmental control capability of your BioCel is fully configured by Velocity11 before delivery and you should not need to make any configuration changes. You may occasionally want to interact with the iSeries Diagnostics software to monitor environmental conditions, make minor changes and troubleshoot communication problems with the iSeries controllers.

You will not need to use all of the features of the iSeries Diagnostics software. Those procedures that are relevant to you are given in this topic and in “Resolving Environmental Control Problems” on page 317.

How Environmental Control Works

An iSeries controller is a small box with a digital display, located behind a side door.

In the most general sense, an iSeries controller is used to maintain a particular environmental condition by providing feedback control for a sensor/effector pair.

A sensor provides a voltage or current input to an iSeries controller. The iSeries controller compares that voltage or current with the setpoint defined for a controller output. If the voltage or current is higher or lower than the setpoint by a particular margin the output device state toggles on or off, which creates a change in the environment.

In the case of temperature control, the sensor is a thermocouple and the effector is a heating element.

In the case of humidity control, the sensor is a hygroscope and the effector is a humidifier.

!! IMPORTANT !! Although it is possible to change environmental control settings directly using the iSeries controllers, we recommend that you do not do this. Attempting to make changes


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when VWorks is communicating with the iSeries controllers may corrupt data.

About iSeries Profiles

Each type of control has its own iSeries controller. For example, one controller may be used to control and display the table temperature and another to control and display the air temperature. Each controller is given its own profile in the iSeries Diagnostics software.

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Naming an iSeries Controller

You may want to create a casual name for each iSeries controller.

To name an iSeries controller:


2. From the Profile name list box, select the profile that you want to name.

3. In the Output Parameters group box, type the name in the Output 1 friendly name text box.

Note: Currently, only Output 1 is used by the BioCel.

Viewing the Current Reading

You can view the current iSeries controller reading.

To view the current iSeries controller reading:

1. Click the Status tab.

2. View the display in the Status group box.

Note: The user-defined units label that is located above the display refers to measuring units, such as relative humidity percentage, that provide a voltage input using the iSeries Process mode. For more information about modes, see the iSeries documentation.

Changing the Setpoint

To change the setpoint value:

1. Click the Status tab.

2. In the 1 or 2 text box, as appropriate, edit the setpoint value.


Changing the Display Color

To change the color of the iSeries display:


2. In the Display Parameters group box, select a color option for the Normal Display color.

Note: Changing the display color settings for Alarm 1 and Alarm 2 will have no effect on your system.

Changing the Number of Displayed Decimal Places

You can change the number of decimal places shown on the display. Depending on the input type, some options are inactive.

To change the number of displayed decimal places:


2. In the Display Parameters group box, select an option for Decimal places.

Changing the Temperature Units

You can monitor and display temperature in degrees Celsius or degrees Farenheit.

To change the temperature units:


2. Select a profile that measures temperature using a thermocouple from the Profile name list box.

3. In the Input Parameters group box, select either F or C, for Farenheit or Celsius.

4. Change the setpoint to reflect the new temperature units.

For more information, see “Changing the Setpoint” on page 276.



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Using Lid Hotel DiagnosticsIntroduction The Lid Hotel† diagnostics software provides a way to identify which

positions contain lids and to set a profile for the device. †Concept developed by Novartis Pharma AG, NIBR/DT/IAT, Basel, Switzerland.

About Lid Hotel Profiles

As the profile for your lid hotel was set during manufacture, you will not need to use the features on the Profile tab.

Viewing Full Lid Hotel Positions

To view full lid hotel positions:

1. Open the Lid Hotel Diagnostics software.

The Diagnostics page shows an array of lights. The lights turn on green for positions that contain lids.


Using Multidrop Diagnostics SoftwareAbout This Topic This topic explains how to manipulate a Thermo Labsystems Multidrop

microplate dispenser independently of VWorks, using Multidrop Diagnostics software.

Multidrop Diagnostics Dialog Box

In stand-alone mode, the Multidrop microplate dispenser is operated using the buttons and switch on its control panel.

Velocity11 has developed Multidrop Diagnostics software to allow BioCel users to operate the instrument using the BioCel computer.

The software uses a single dialog box.


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Defining Terms The Multidrop has priming and purging functions that can be controlled through the Multidrop diagnostics.

PrimingPriming moves liquid through the dispensing system into waste to make sure that there is no air in the lines.

PurgingPurging moves liquid back into the liquid cassettes.

Basic Setup Before you can manipulate a Multidrop, make sure that it is correctly initialized.

To initialize a Multidrop:

1. In the Profile Settings group box, select the Multidrop to communicate with from the list box.

The value in the Com port changes to match the Multidrop you selected.

2. If you want to prime the fluid lines when you initialize the Multidrop, select the Prime checkbox and enter the volume of liquid you want to prime with.

3. Click Initialize.

Creating and Deleting Devices

You do not need to use the New, Save, or Delete buttons in the Profile Settings group box. These are for Velocity11 use only.

Filling a Plate Refer to the Multidrop User Manual for information about preparing to fill a plate.

To fill a plate:

1. In the Dispense Program group box, select the number of wells in the plate.

2. If you want to prime the Multidrop, enter the volume of liquid to prime with in the Prime volume text box.

3. In the Dispense volume text box, enter the volume of liquid that you want to dispense into each well.

4. To shake the plate after the dispense, enter a value into the Shake time text box.

5. To purge the lines after the dispense, select the Purge x times when complete check box, and enter the number of times to purge.

If you want to return all liquid, the value of x may need to be greater than one.

6. To dispense into all wells, make sure that the Entire plate option is selected.

7. To only dispense into some of the wells:


a. Select the Selected columns option.

b. Click Clear All.

c. In the number matrix, click the numbers corresponding to the columns to dispense into.

In the following example liquid will be dispensed into columns 2, 4, 6 and 8 of a 384-well plate.

8. Click Dispense.

Non-Dispense Operations

You can perform basic non-dispense operations using the buttons in the Multidrop Commands group box.

To purge the liquid lines:

1. Enter a value in the Times to purge text box and click Purge.

If you want to return all liquid, the value of x may need to be greater than one.

To prime the liquid lines:

1. Enter a value in the Prime volume text box and click Prime.

To shake the plate:

1. Enter a value in the Shake time text box and click Shake.

More Information For general information, see “About Diagnostics Software” on page 260.

For brief information about setting up a Multidrop, see “Multidrop Set Up” on page 74.

For detailed information about the Multidrop, refer to the Multidrop 384 User Manual.


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Using Nanodrop DiagnosticsIntroduction The Nanodrop is an 8-channel pipettor that dispenses 0.1–40 µL of liquid

into each well.

For detailed information about the Nanodrop, see the Nanodrop User Manual.

How the Software Works

You can use Nanodrop Diagnostics software to:

❑ Create a Nanodrop profile that initiates the communication with the computer

❑ Perform an individual operation, such as dispense or wash, using the parameters set in a Quick Run Method, and referencing a calibration file for increased accuracy

Software Pages The Nanodrop Diagnostics has two pages.

Actions Page


Profiles Page

About Nanodrop Profiles

A profile is one or more settings that are remembered after you exit VWorks. In the case of the Nanodrop, the only setting stored in a profile is the COM port, which identifies the serial port to be used for communication between the module and the computer.

You need to have one profile for every Nanodrop on your BioCel, as illustrated in the following screenshot of a system that has two Nanodrop pipettors.

All profiles should have been set up at the factory so you should not need to create a new one unless you are adding another Nanodrop to your system.

If you have more than one Nanodrop on your BioCel you will need to select the profile for the one you want to communicate with.


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To select a Nanodrop profile:

1. In the Actions tab, select the profile from the Profile list box.

2. Click Connect.

To Create a Profile You only need to create a new profile if you are adding a Nanodrop to your BioCel.

To create a Nanodrop profile:


2. Click Add.

3. In the Profile Details dialog box, type a name for the profile.

4. Select an available communications port from the Serial port list box.

5. Click OK.

Calibration Files Calibration files contain the results of gravimetric calibration tests and are used to adjust the volume delivery process to make sure that volumes delivered are accurate.

Calibration files are initially provided by Innovadyne, but you can perform your own calibrations, the results of which are stored in a file. Calibrations are performed through Innovadyne’s Nanodrop software and the files can only be selected through the Velocity11 Nanodrop Diagnostics software.

QRM Files QRM (Quick Run Method) files store collections of Nanodrop settings. QRM files are created through Innovadyne’s Nanodrop software and are selected through the Velocity11 Nanodrop Diagnostics software.

Examples of settings stored in QRM files are:

❑ Dispense volume

❑ Syringe volume

❑ Tip clean (enabled or disabled)

❑ Aspirating air gap rate

❑ Whether or not to wash


Running an Individual Operation

You can use Nanodrop Diagnostics software to perform the following actions.

The actions use the settings in the selected QRM file, and any calibration corrections from the selected calibration file.

To perform an individual operation:

1. From the Files group box, of the Actions page select a QRM file and calibration file.

2. Click the button corresponding to the required action.

3. If you want to stop the action, click Abort.

Action Meaning

Prime Priming clears air bubbles from the syringe path tubing. Prime the Nanodrop if it has been left idle for more than two hours.

Dispense Delivers liquid into the plate wells.

Wash Cleans the insides and outsides of the tips. The operation is performed with the tips immersed in the wash station.

Rinse Cleans the insides of the tips. The operation is performed above the wash station in the park position.

Purge Purging clears air bubbles from the pressure path and syringe path. Purging is often performed after priming to make sure that the valves contain no air.


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Using QFill DiagnosticsAbout This Topic This topic explains how to manipulate a Genetix QFill2 independently of

VWorks, using QFill Diagnostics software.

QFill Diagnostics Dialog Box

In stand-alone mode, a QFill2 is operated using a built-in keypad. Velocity11 has developed QFill Diagnostics software to allow BioCel users to operate a QFill2 using the BioCel computer.

The software uses a single dialog box.

Basic Setup Before you can manipulate a QFill2, you must make sure that it is correctly identified.

To make sure that the QFill2 is identified:

1. Check that the QFill Number is correct for the module that you want to communicate with.

This number identifies a specific QFill2 when there is more than one on the BioCel. You can find out the number of a QFill2 by referring to the label on the module, by trial-and-error, or by looking at the Device Number in the device manager.

2. Check that the Comm Port number matches the serial port number for the module that you want to communicate with.

You can find out the Comm Port number from the label on the serial port cable near where it plugs into the QFill2. The number is also the same as the Input number in the device manager.

The Comm Port number should be added automatically when you select the QFill number after it has been defined for the first time, and you should not need to change it.

Creating and Deleting Devices

You should not need to use the Create New QFill or Delete QFill buttons. These are for Velocity11 use only.


Dispensing Into a Plate

Refer to the QFill2 user manual for information about preparing to fill a plate.

To dispense into a plate:

1. Make sure that there is a plate on the QFill stage.

2. Make sure that the reagent bottle has sufficient liquid in it for the dispense.

3. Set the dispense volume:

a. In the Volume Setup group box, type the QFill volume into the text box.

b. Click Update Volume.

c. Click OK.

The volume you last entered is saved until the next time a protocol is run, which will override this value.

4. In the Filling Test group box, click Start.

5. Monitor the success of the fill by looking at the Success and Fail indicators.

The Success and Fail indicators provide feedback from a sensor that measures pressure in the dispensing bottle. The Fail indicator light is illuminated if the:

QFill2 is not turned on

QFill2 has a disconnected communication cable

Bottle fails to pressurize

About the Filtration Port

The Filtration Port defines the Bio I/O port used to provide vacuum sensor information for an optional filtration station on the QFill2. You should not need to change this number.


For brief information about setting up a QFill2, see “QFill2 and AliQuot Set Up” on page 74.

For detailed information about the QFill2, refer to the QFill2 user manual.


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Using Robot Diagnostics SoftwareAbout This Topic This topic explains how to move the robot using Robot Diagnostics

software.

For general information about diagnostics software, and to learn how to open diagnostics software, see “About Diagnostics Software” on page 260.

!! DAMAGE HAZARD !! Before you use Robot Diagnostics software to move the robot, make sure that there is nothing on the table that the robot can crash into. Move the robot slowly.

Robot Axes The robot has three axes of movement:

Setting Robot Speed To set the speed of robot movement:

1. In the Robot Speed group box, select Slow, Medium, or Fast.

Note: We do not recommend using the Fast setting for manual control.

Moving the Robot by Hand

Robot movement is controlled by motor servos. You can move the robot by hand in the plane of the robot arm, but you cannot change its height.

To move the robot by hand:

1. In the Servo control group box, select R & T servos off.

Axis Description

r Radial.

The horizontal distance, in millimeters, between the back of the robot’s gripper in the home position and the back of the robot’s gripper in the current position.

t (theta)

Angle.

The angle, in degrees, between the center point of the robot’s gripper in the home position and the center point of the robot’s gripper in the current position.

z Height.

The vertical distance, in millimeters, between the center point of the robot gripper at the home position and the center point of the robot gripper at the current position.


2. Holding the end effector, which is the last segment of the arm, slowly move the arm to where you want it, in the horizontal plane of motion.

3. Select R & T servos on to return control to VWorks.

Jogging the Robot You can move the robot in increments, in either the z-axis, r-axis, or t-axis. The process of moving in increments is called jogging.

!! DAMAGE HAZARD !! Before you jog the robot, make sure that there is nothing on the table that the robot can crash into. Move the robot slowly and keep the jog increment small until you are certain that there is no obstruction.

To jog the robot:

1. If you intend to pick up a plate, in the Jog Settings group box, either:

Select a type of labware from the list box, in which case the appropriate value is automatically entered into the Gripper offset text box.

Enter the value directly into the Gripper offset text box.

2. In the Jog settings group box, check, and possibly change, the following settings:


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3. In the Position Control group box, click one of the following buttons:

The readout displays the current coordinates of the robot in relation to the home position.

Moving the Gripper You can open and close the robot’s gripper in a single movement.

To open or close the robot’s gripper:

1. In the Position Control group box, click Open gripper or Close gripper.

Setting Comments

Gripper offset The height above the teachpoint, which is typically 2–3 mm.

You will rarely need to change this value from the values automatically entered for the plate type. However, you can type a value into the Gripper offset text box if you need to.

Jog increment The distance or angle to move the robot at each jog.

Button Moves the robot...

Down Down, decreasing the z-axis value

Up Up, increasing the z-axis value

In In towards the center of the robot’s radius, decreasing the r-axis value

Out Out from the center of the robot’s radius, increasing the r-axis value

CW Clockwise, decreasing the t-axis value

CCW Counterclockwise, increasing the t-axis value


Homing and Resting the Robot

Homing and resting the robot both move the robot to the home position, but there are some important differences between these two actions.

HomingEach axis of the robot has a sensor that is triggered when the robot is in a specific position. This position defines the home position for that axis.

When the robot is homed, it moves the r-axis, followed by the t-axis and then the z-axis until the sensors on each axis are in the triggered position. This home position serves as a positional reference for all other points, with z, r, t coordinates of 0, 0, 0.

You should home the robot after a high speed crash. The robot homes automatically when you start VWorks.

Resting

When the robot is moved to the rest position, it takes the shortest path to the z, r, t coordinates of 0, 0, 0. Provided the home coordinates have not changed, this position is the same as the home position.

Resting the robot is faster than homing the robot because all axes move simultaneously and the arm moves faster because it is not using the sensors.

You may choose to move the robot to the rest position to quickly move it out of the way when you are working on the table.

To home or rest the robot:

1. Click Home or Move to rest position.

Checking Communication Time

The Position Control group box displays the time interval between the receipt of positional coordinates from the robot. This refresh time should be less than 45 milliseconds. If it is consistently greater than this, contact the Velocity11 Service Center.

Reading a Plate’s Bar Code

You can use diagnostics software to read a plate’s bar code for troubleshooting purposes.

To read a plate’s bar code:

1. Place the plate with the bar code on a platepad.

2. Select the device from which to pick up the plate in the Position 1 list box.

3. In the Position 2 list box, select Nowhere.


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4. For Position 1, enter a value for the approach height.

The approach height is the height to raise the robot gripper above the teachpoint when the robot moves the plate horizontally towards or away from the place plate position.

Make this value large enough to avoid catching the plate on a lip, or other protuberance, as it is moved from a position, but not so high that the robot hits a shelf or other object above the position.

This value is device-dependent. For most devices a value of 8–10 mm will work. Start with a value of 6 mm for picking a tipbox from a VPrep shelf when making these settings.

!! IMPORTANT !! If approach heights are set incorrectly, it could result in a robot crash.

5. Click Pick & Place 1->2.

The robot moves to Position 1 and picks up the plate.

6. In the Bar Code Testing group box, click Read bar code.

The bar code is read and displayed in the Bar Code Testing group box.

:

Ignoring Robot Errors

You have the option of ignoring robot errors when using Robot Diagnostics. You may do this, for example, when you want to simulate the movement of plates without using plates, which would otherwise give a plate sensor error.

This setting only affects the use of Robot Diagnostics. It does not affect VWorks error settings.

To ignore errors when using Robot Diagnostics:

1. Select Ignore errors.

For more information about robot errors, see “Resolving Robot Errors” on page 311.


Checking the Plate Sensor

The plate sensor in the robot gripper may need to be recalibrated if it is not sensing a plate when there is a plate in the gripper.

The plate sensor indicator in the Robot Diagnostics is used by Velocity11 service staff to help in the recalibration. You can also use it to check the function of the plate sensor.

To check the plate sensor:

1. Move the robot to a position that has a plate.

For more information, see “Moving the Robot to a Teachpoint” on page 293.

2. Close the gripper.

3. Look at the Plate present indicator.

If the indicator is on, the plate sensor is registering a plate in the gripper.

4. Open the gripper.

Moving the Robot to a Teachpoint

You can move the robot directly to any teachpoint when there is no plate in the gripper.

To move the robot to a teachpoint:

1. From the Position 1 or Position 2 list box, select the teachpoint to move to.

2. Click Move to point for either Position 1 or Position 2, as appropriate.

!! DAMAGE HAZARD !! When you use the Move to point function, the robot does not use the Approach height. Instead, it moves to the point using the most direct path. If there is a plate in the gripper, the plate may contact a lip on the device, causing a robot crash. Also, if there is a plate at the position and the robot grippers are closed, there will be a robot crash.


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Moving a Plate Between Teachpoints

You can move the robot from one teachpoint to another, and then back again. If the first teachpoint has a plate, the robot will pick it up and move it to the second teachpoint.

To move a plate between teachpoints:

1. Select one teachpoint from the Position 1 list box.

2. Select the other teachpoint from the Position 2 list box.

3. To move a plate from:

Position 1 to Position 2, click Pick & Place 1->2

Position 2 to Position 1, click Pick & Place 2->1

Locating the Teachpoint File

You may need to locate the robot teachpoint file so you can send it to us for troubleshooting purposes.

To locate the teachpoint file:

1. View the path to the file at the bottom of the Robot Diagnostics dialog box.

Changing Robot Profile Settings

Robot-specific settings are grouped into a profile. BioCel platforms with more than one robot use more than one profile. You should rarely, if ever, need to change the robot profile on your BioCel.

!! IMPORTANT !! If you change the robot profile and later click Save & Exit, the values are changed in VWorks, which will affect protocols that you run afterwards.

To change robot Profile Settings:

1. Type the new value into the text box for the parameter you want to change, using the following table as a guide.

Parameter Description

Robot COM port The communications port to which the robot is connected.


BCR COM port The communications port to which the robot’s bar code reader is connected.

Gripper open delay Interval between the time the gripper starts to open and the time the robot starts to depart from a plate.

If this value is set too low, the gripper may not have completely released the plate before the robot moves, causing the plate to be dragged.

Gripper close delay Interval between the time the robot reaches the teachpoint and the time the gripper starts to close.

If this value is set too low, the plate is held too high in the gripper.

Retry pushdown Pushdown is a robot action used with filtration stations, vacuum platepads and vacuum shelves on VPrep pipettors.

The purpose of the action is to flatten a plate on the stage. It is used with thin plates that tend to warp. If, during operation, the vacuum seal indicator indicates the absence of a seal, the robot will push down on the plate in an attempt to create a seal.

The value for this parameter the distance pushed down in millimeters.



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Fine-Tuning Robot TeachpointsAbout Teachpoints Teachpoints are axis position coordinates needed by:

❑ The robot, to be able to accurately pick up and move plates to and from devices

❑ VPrep heads, to be able to accurately position pipette tips into plate wells

❑ VSpin™ centrifuges, to be able to accurately position the buckets in relation to the door

❑ VStack stackers, to be able to accurately position the plate stage during operation

Teachpoint coordinates are relative to the robot’s or module’s home position. They are set up by Velocity11 before shipping and verified at your site on installation. However, you may occasionally need to fine-tune teachpoints.

For information about module teachpoints, see the relevant user manual. This topic covers only robot teachpoints.

About Robot Teachpoints

Teachpoints are initially set at the factory using a custom teachpoint plate calibration tool. Each teachpoint is then fine-tuned as necessary. You should not need to create new teachpoints, but you may occasionally need to fine-tune existing teachpoints.

The Effect of Inaccurate Teachpoints

This section uses the example of a teachpoint that is inaccurate in the r-dimension to illustrate the implications of inaccurate teachpoints in general.

The first diagram shows where the gripper picks up a plate on a platepad when the r-teachpoint is set accurately. Notice that the r-teachpoint (optimal teachpoint) is aligned with the inside surface of the gripper back.


In the next diagram the r-value of the teachpoint is too small. The back of the robot gripper stops at the actual teachpoint, and the plate is held too far back in the gripper. Row M on the plate is aligned with the space between the gripper pad instead of row L.

The next diagram shows what happens when this plate is delivered to a platepad that has an optimal teachpoint. The inside surface of the gripper back stops at the optimal teachpoint, delivering the plate too far forward. The plate does not sit correctly in the platepad.

Optimal teachpoint

Back of plate

A

B

C

D

E

F

G

H

I

J

K

L

M

N

O

P

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A

B

C

D

E

F

G

H

I

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00

01

5

Optimal teachpoint

Back of plate

Actual teachpoint


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The ability to tolerate a deviation from the optimal teachpoint depends on the tolerance in the geometry of the device that receives the plate.

It is less important for the absolute value of the teachpoint for a plate position to be optimal than it is for the teachpoints of the position at which a plate is picked up and the position to which the plate is delivered to be work together. To explain further, if the teachpoint at the pick position is 1 mm less than the optimum r-value and the teachpoint at the place position is 1 mm less than the optimum, the end result is that the plate is placed accurately at the position. Also, if the teachpoint of the picking position has an r-value that is low by 1 mm and the teachpoint of the placing position has an r-value that is high by 1 mm, the combined effect is that the plate is placed 2 mm forward of where should be.

These concepts explain that accurate placement of a plate is a property of both the picking position’s teachpoint and the placing position’s teachpoint. Therefore when you are fine-tuning a teachpoint, always consider the teachpoint of the position that a plate is collected from.

When teachpoints are initially set at the factory, they are defined as described in the following table.

Optimal teachpoint

Where back of plate should be

Distance plate is too far forward

A

B

C

D

E

F

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01

5

Axis Teachpoint position is set when the...

r Bumper of the plate calibration tool touches the back of the gripper

t Plate is centered in the gripper

z Bottom of the gripper is just above the bottom of the plate skirt, although in some cases, this needs to be adjusted because of specific plate geometry


Fine-Tuning a Robot Teachpoint

The process of fine-tuning robot teachpoints is empirical. You make small, incremental adjustments until a plate can be accurately picked up and placed at a position.

!! IMPORTANT !! To help standardize the process, it is imperative to select one platepad to use as a reference picking position for all teachpoints.

Teachpoints are manipulated through the Robot Diagnostics software. You should be familiar with the features of this software before working with teachpoints. For more information, see “Using Robot Diagnostics Software” on page 288.

To fine-tune a robot teachpoint (part one):

1. Examine the teachpoint coordinates for other devices that you know should be aligned in one or more axes with the device whose teachpoint you are working on.

For example, all stackers sitting directly on the table and mounted in equivalent hole patterns should have very similar z- and r-values. This may give you a clue about whether the teachpoint is inaccurate and in which direction.

2. If this is the first time that your BioCel has had its teachpoints fine-tuned, select a platepad to use as your picking reference position.

If you have fine-tuned teachpoints before, make sure you use the same platepad for the picking reference position.

3. Click Diagnostics.

4. Click Robot.

This opens the Robot Diagnostics window.

5. In the Position 1 list box, select the reference platepad.

6. In the Position 2 list box, select the device whose teachpoint you want to fine-tune.

7. Check the values for the approach heights.

The approach height is the height to raise the robot gripper above the teachpoint when the robot moves the plate horizontally towards or away from the place plate position.

Make this value large enough to avoid catching the plate on a lip, or other protuberance, as it is moved from a position, but not so high that it hits a shelf or other object above the position.

This value is device-dependent. For most devices a value of 8–10 mm will work. Start with a value of 6 mm for picking a tipbox from a VPrep® shelf when making these settings.

!! IMPORTANT !! If approach heights are set incorrectly, it could result in a robot crash.

To fine-tune a robot teachpoint (part two):

1. Set the Robot Speed to Slow.

2. Click Pick & Place 2>1.


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3. Carefully watch how the robot places the plate and listen to the sounds it makes.

If the plate catches the lip of the plate position, because the r- or t-value is incorrect, it can make a double-click sound. If the z-value is incorrect the plate will make a dropping sound or a crunching sound, depending on whether the value is too high or low.

4. When you have established the direction and approximate magnitude of the inaccuracy, set the jog increment.

5. Click Move to Point for Position 2.

6. Click the appropriate jog button to move the gripper, and click Teach point here for Position 2.

This temporarily applies the new teachpoint setting. If you click Cancel the new setting will not be saved.

7. Using the Pick & Place function, move the back plate to the reference position, repeat the move to the place position, and look to see if the accuracy has improved.

8. Continue with this iterative process until the plate is placed correctly.

9. Click OK to save the new teachpoint.


Using StoreX Diagnostics SoftwareIntroduction Before using the StoreX Diagnostics software, you should be familiar

with Liconic Instruments’ Operating Manual for StoreX, which explains the StoreX features, specifications, provision of gases, and maintenance and safety guidelines,

The same StoreX Diagnostics software is used for all models of StoreX. This means that some software features may not be applicable to your model.

Re-Initializing the StoreX

If you bump your StoreX the carousels may move out of their registered position. If this happens you will need to reinitialize communication with the StoreX.

To reinitialize communication with the StoreX:


2. In the Current profile list box, make sure that the StoreX that you want to communicate with is selected.

3. Click Use this profile.

I/O and Climate Control Procedures

The I/O and Climate Control page is used to:

❑ Set environmental conditions

❑ Rotate a Cassette to access a particular slot from the glass door

❑ View the StoreX sensor readings

❑ Manually manipulate the gate and transfer station (swap station)


302

To set the StoreX environmental conditions:

1. Enter a value into one of the Setpoint text boxes.

The value represents the point that the StoreX will try to maintain during operation. For example, if the setpoint for the current temperature is 40, the StoreX will regulate its internal temperature so that it remains at 40 degrees Celsius.

2. Click Set.

For information about setting an alarm to be triggered if the actual measurement varies from the set point, see “Adding an Alarm” on page 65.

Setting Automatic Update of Climate Data

You can set the diagnostics software to allow the climate control data to be constantly updated. This setting does not apply when a protocol is running.

To allow automatic updating of climate data:

1. Select the Auto-update sensor values check box.


Plates Procedures The Plates page is used to transfer plates between the incubator and StoreX transfer station.

!! IMPORTANT !! If you load or unload a plate from a StoreX, the change will not be recorded in the database.

To transfer the plate to and from a StoreX:

1. From the list boxes, select the cassette and slot that you want to transfer the plate to or from.

2. If your StoreX transfer station is equipped with a bar code reader and you want to read the bar code after moving a plate to the transfer station, select Read bar code after unloading.

3. Click Unload plate or Load plate.

Profiles Procedures A profile stores a collection of properties that apply to a particular StoreX. You should only need to change a profile if you change the configuration or model of a StoreX. If you change the value of a property you must save the change before closing.


304


1. Click Create new profile.

2. Click Yes or No in the Update current profile? dialog box depending on whether you have made changes to the currently selected profile or not.

3. In the list box, replace the text New profile #<number> text with the name you want to give the profile.

4. Change any values in the StoreX Parameters group box using the following table as a guide:


This device uses The serial port of the BioCel computer to which the StoreX is attached.

BCR on The serial port of the BioCel computer to which an optional bar code reader is attached.

Number of carousel levels Different models of StoreX have different numbers of carousel levels. This is where you specify how many carousel levels your model has.

Cassettes per level The number of cassettes in one carousel. A cassette is a vertical stack of slots that can be removed and replaced.

Slots per cassette on lower level A slot is a position that contains a plate. This value specifies how many plates the lower cassette can hold.


5. Click Rename profile to save the new profile.

The name of the button changes to Update profile.

To select a profile to use:

1. From the Current profile list box, select the profile and click Use this profile.

To edit a profile:

1. From the Current profile list box, select the profile.

2. Edit the StoreX Parameters.

3. Click Update profile.

If the StoreX is bumped it can move out of registration and should therefore be re-homed.

To re-home the StoreX:


2. Click Use this profile.

About the Macros and Teachpoints Pages

The Macro and Teachpoint pages are for Velocity11 use only.

Macros provide a way for service technicians to program the firmware. Incubator teachpoints are set up during manufacture and should not need to be adjusted.

Slots per cassette on upper level

A slot is a position that contains a plate. This value specifies how many plates the upper cassette can hold.

Load/unload timeout An error is generated when the StoreX does not load or unload a plate by this time period after the command was sent.

A default value is set for this parameter, but because different incubators have different response times, this value is editable.

Lower level slot spacing Spacing between the bottom of one plate and the bottom of the next one in the stack.

This value is constant for an incubator and should not be changed.



306

Using Teleshake Diagnostics SoftwareAbout This Topic This topic explains how to manipulate a Teleshake independently of

VWorks, using Teleshake Diagnostics software.

For general information about diagnostics software, see “About Diagnostics Software” on page 260.

Procedure To operate a Teleshake:

1. If you have more than one Teleshake on your BioCel, select the number of the one you want to operate in the Select device to work with group box.

2. Click OK.

This chapter tells you how to keep your BioCel® in good working order and what to do when you encounter a problem.

Maintenance and Troubleshooting 11

Chapter 11: Maintenance and TroubleshootingBioCel User Guide

308

Routine MaintenanceBioCel Maintenance The BioCel does not require a lot of routine maintenance.

In general, practice good housekeeping by cleaning up spills and following the procedures described in “Performing Post-Run Clean-Up” on page 106.

Once a month, check that the:

❑ Robot gripper pads are not torn, cracked or otherwise worn

❑ Overhead doors remain at the correct height

❑ Liquid handling tubing is not torn, cracked or discolored

❑ Air filter is clean

❑ Main air pressure reads 90–100 psi (0.62–0.69 MPa)

❑ Table top is free of debris, such as pieces of chipped plates and microtubes

Checking the Air Filter for Replacement

If the house air supplied to the BioCel is clean, the air filter should rarely need to be changed.

For a diagram showing the location of the air filter, see “Air Panel” on page 19.

To check the air filter for replacement:

1. Open the air panel door by inserting a large flat-bladed screwdriver into the keyhole and turning clockwise.

2. Look through the window at the front of the air filter container.

If there are any oil droplets on the bottom of the filter, or if there is general dirt, the filter should be changed. Contact the Velocity11®

Service Center for instructions.

Module Maintenance For information about routine maintenance of the individual modules, see the relevant module documentation.

Replacing Fluorescent Tube Lights

The interior of the BioCel has standard type fluorescent tube lights that occasionally need to be replaced. We recommend that two people work together to replace a light.

To replace a fluorescent tube light:

1. If your BioCel has a light switch, turn off the lights.

2. Either shut down the BioCel or, at the power strip, unplug the power cord that goes to the light.

3. With one person working at each end of the light, remove the light cover.

4. Remove the lamp.

309Chapter 11: Maintenance and TroubleshootingBioCel User Guide

5. Install a new, identical lamp.

6. Replace the cover.

About Error HandlingCauses of Errors The BioCel is a complex instrument that requires the interaction of

hundreds of parameters, configurations, and operator setup tasks for a protocol to run successfully. Errors on the BioCel have many causes, including poor protocol writing, incorrect operator setup, variation in plates, hardware failure and software failure.

It is important to understand that error handling is a normal part of operating the BioCel and that errors usually do not mean that the BioCel has malfunctioned. Most errors are a result of operator error.


310

Compilation Warnings and ErrorsCompilation Warnings

Compilation warnings are displayed in the VWorks™ log toolbar, listing the task that caused the warning.

Warnings are generated, for example, when:

❑ Pipette tips are on the VPrep® head at the start of the protocol so a tips-off task is run before a tips-on task

❑ No label is printed during a VCode® task

Compilation Errors Compilation errors are listed in the VWorks™ log toolbar. If you are logged in with Operator, User or Guest privileges, you will be unable to continue with the protocol. If you are logged in with Administrator privileges, the dialog box will allow you to run the protocol despite the errors.

Errors are generated, for example, when:

❑ Operating parameters are out of range, denoted by red text in fields of the Task Parameters toolbar

❑ A task asks a VPrep to pipette from a plate that does not exist in the system

❑ Volumes in pipette steps do not match, such as when a dispense volume is greater than a previous aspirate volume

❑ A specific VStack® has not been assigned to a Stacker task

❑ A Signal task has no associated Waitfor task

Resolving Device ErrorsDevice Initialization Errors

When you start VWorks, if there is a device initialization error, make sure that the device is turned on and that the communications cable is connected properly. If that does not solve the problem, contact the Velocity11 Service Center.


Resolving Robot ErrorsAbout Robot Errors Robot errors are among the most common errors that occur during a

run.

Types of Robot Error There are four types of robot error.

Door Interlock Error Recovery

A door interlock error occurs when an overhead door is opened during a run.

To recover from a door interlock error:

1. Make sure that the system is in a valid state for the protocol. In other words, make sure that you have not made changes that will cause a further error, such as moving a plate to a position that should not have a plate, or cause samples to be switched around, such as moving a plate from one VStack to another.

2. Close the overhead door that was opened.

3. In the Robot Error dialog box, select Retry, or Ignore & Continue, leaving device in current state, depending on the current state of the robot.

If you are an administrator you can use the interlock override to continue the run with the overhead doors open.

For more information about using the interlock override, see “Overriding the Safety Interlock” on page 314.

Emergency Stop Error Recovery

Emergency stop errors are generally more difficult to recover from than other types of error and should be handled by an administrator.

With an emergency stop error, power is cut to modules and devices (see “Power System” on page 20 for exceptions), and VWorks loses information about the state that the modules and devices are in. This prevents VWorks from continuing the protocol.

!! IMPORTANT !! You cannot continue the current protocol run after an emergency stop has been activated.

Error Type Error Message

❑ Door interlock

❑ Emergency stop

While placing at <location> robot emergency stop or door interlock detected

Plate sensor Failed to sense plate when picking from <location>

Servo While placing at <location> a servo error has occurred


312

After an emergency stop button is pushed, all device motion stops and error messages are generated in the error log as the scheduler attempts to continue with the protocol.

To recover from an emergency stop:

1. Clean up any spills or debris if necessary.

2. Twist the activated emergency stop button in a clockwise direction.

The spring-loaded button pops out.

3. Close any open doors.

4. Push the reset button on the power panel.

A stop dialog box opens in addition to the Robot Error dialog box that is already open.

For more information about the power panel, see “Power Panel” on page 17.

5. Activate the interlock override.

For more information about overriding the interlock, see “Overriding the Safety Interlock” on page 314.

6. If the protocol includes a pipette task, in the VPrep EStop detected dialog box, click Retry.

7. If there is a plate in the gripper, move it back to the pickup location:

a. Establish the location that the plate was picked from.

b. In the Robot Error dialog box, click Diagnostics.

c. Gently hold the plate in your fingers, or ask another operator to do the same.

d. Click Open Gripper to release the plate to your hand.

8. Close all overhead doors.

9. Remove the interlock override key.

10. Push the reset button on the power panel.

11. Click Abort Process in the stop dialog box.

This closes VWorks. When you restart VWorks, communication with the modules and devices that lost power is re-established.

s

0000

6


Plate Sensor Error Recovery

Before you can recover from a plate sensor error, you must establish the cause of the error.

To recover from a plate sensor error:

1. If there is no plate in the gripper, establish whether the plate was:

Knocked out of the gripper.

In this case establish what knocked the plate out of the gripper and contact Velocity11.

Missing from the location that the robot attempted to pick it up from.

In this case, place the correct plate in the location and click Retry in the Robot Error dialog box.

Not picked up.

In this case, there may be a problem with either the labware definition for the plate or a teachpoint. Check the teachpoint at the position where it failed to pick up the plate, and also the teachpoint at the previous position. For information about checking teachpoints, see “Fine-Tuning Robot Teachpoints” on page 296. If there does not seem to be a teachpoint error, contact Velocity11.

2. If the plate is held in the gripper but is not seated correctly, establish whether the plate was positioned correctly at the pickup location.

If the plate was not positioned correctly at the pickup location, reposition the plate and click Retry in the Robot Error dialog box.

If the plate was positioned correctly at the pickup location, there may be a problem with the approach or departure height. Alternatively, there may be a problem with the labware definition for the plate, a teachpoint, or the plate sensor. In this case, you should contact Velocity11.

Servo Error Recovery The robot’s motion is controlled by a servo system that cuts power to the robot if it encounters resistance to movement that is slightly higher than that expected from just the inertia of a plate. When the power is cut, a servo error is generated.

The great majority of servo errors occur when the plate being carried crashes into another plate sitting on a device. Rarely, a servo error will occur if a plate crashes into another object, such as a VPrep module shelf.

To recover from a servo error:

1. If the error was not caused by a plate crash the problem is probably an inaccurate teachpoint, in which case contact Velocity11 for assistance.

2. If the error was caused by a plate crash:


314

a. In the Robot Error dialog box, click Diagnostics.

b. In the Diagnostics dialog box, click Home.

Do not click Move to rest because this moves the robot to the home position too quickly.

c. Click the OK to close the Robot dialog box.

d. Make sure that the plates are still usable and in the positions they would be in if the robot move had not failed.

e. In the Robot Error dialog box, click Ignore & Continue, leaving device in current state.

s

Overriding the Safety InterlockProcedure This procedure should only be performed by an Administrator.

To continue a run using the interlock override:

1. Insert the override key into the interlock key hole on the power panel and turn it clockwise to the zero position.

2. In the Robot Error dialog box, select Retry.

!! INJURY HAZARD !! Only fully trained BioCel Administrators should have access to, and use of, the safety interlock key. Use the override only when you know how the robot and VPrep modules will move during the protocol, when the robot speed is slow, and when you have taken measures to keep away from the areas in which the robot and VPrep modules will be moving.

For more information about the interlock override, see “Opening an Overhead Door During a Run” on page 97.


Resolving BioCel Bar Code Reader ErrorsIntroduction The information in this topic refers to errors generated by the following

platform bar code readers:

❑ Robot bar code reader

❑ Optional VPrep shelf bar code readers

❑ Optional platepad bar code readers

For information about resolving VCode bar code errors, see “VCode Errors” on page 316.

Types of Bar Code Misread Errors

There are two types of bar code misread error.

Bar Code Error Option

The result of a bar code misread error depends on the “Halt on bar code misreads” error option that you select. For more information about this option, see “Setting Error Options” on page 51.

If the option is selected:

❑ The protocol pauses.

❑ An error is generated in the log.txt file and VPrep module log file.

❑ A dialog box opens, allowing you to enter the correct bar code.

If the option is not selected:

❑ An error is generated in the log.txt file and VPrep module log file.

❑ The protocol continues without pausing so there are no recovery steps.

Bar Code No-Read Errors

When a bar code cannot be read, and the “Halt on bar code misreads” error option is selected, an error message is generated stating “Could not read <side> bar code on plate at <device>.”

Error Type Description

Bar code no-read A bar code reader is unable to read a bar code when it picks up a plate.

For more information, see “Bar Code No-Read Errors” on page 315.

Bar code mismatch The bar code of the plate that is picked up does not match the bar code that VWorks expects in that position.

For more information, see “Bar Code Mismatch Errors” on page 316.


316

Bar Code Mismatch Errors

When the plate that is picked up does not match the bar code that VWorks expects in that position an error message is generated stating “Scanned <side> bar code: <scanned bar code> does not agree with expected: <expected bar code> for plate at <location>.”

Recovering From Bar Code Errors

To recover from a bar code error:

1. Enter the correct bar code in the text box of the Bar code confirmation dialog box.

2. Click OK.

The run continues.

VCode ErrorsAbout VCode Errors VCode errors, which include bar code errors, are generated by VCode

modules and displayed in VWorks. An example VCode error is shown below.

For more information about resolving VCode® errors, see the VCode User Guide.


Resolving Environmental Control ProblemsIntroduction Refer to this topic if your BioCel is equipped with environmental control

options and there is a problem.

iSeries Controller Panel

The main iSeries controller panel has three digital readouts, three fuses, and three circuit breakers.

Replacing an iSeries Fuse

If the lights go out on an iSeries digital display, you will need to replace the fuse.

To replace an iSeries fuse:

1. Unscrew the fuse located to the left of the digital readout.

2. Screw in a new, identical fuse.

Resetting an Environmental Control Circuit Breaker

Three circuit breakers are located to the left of the iSeries digital readouts. If one of these breakers trips, it cuts power to either the:

❑ Table heating elements

❑ Air heating elements in the box suspended from the ceiling of the BioCel

❑ Humidifier

If the BioCel fails to maintain a temperature or humidity setting, reset the circuit breaker for the respective power line first. Attempting to reset a circuit breaker when the BioCel is operating will not cause a problem.

To reset an iSeries circuit breaker:

1. Push in the circuit breaker button.

If a breaker trips frequently, contact Velocity11 Service Center for help.

Resetting a Controller

If there appears to be a communication problem with an iSeries controller, you can reset the controller. This has the same effect as unplugging the controller power cord and then plugging it back in, but it avoids turning off the power.

To reset an iSeries controller:

1. If it is not already selected, click the Status tab.

2. Click Reset.


318

Resolving Plate Placing ErrorsAbout Plate Placing Errors

If the robot does not place a plate accurately on a device, the problem could be with the:

❑ Teachpoint for either that device or for the previously scheduled device, including approach height.

In this case see “Using Robot Diagnostics Software” on page 288 for more information about fine-tuning teachpoints.

❑ Plate.

In this case, replace the plate with one that is not deformed.

Resolving Inventory Management ProblemsChecking the Database Settings

The database on your BioCel was set up at Velocity11® using a Windows Open Database Connectivity (ODBC) interface. You should not need to change how the database is set up, but if you encounter any inventory management problems, you may need to check the database settings.

To check the database settings:

1. In Windows, navigate to Start > Settings > Control Panel > Administative Tools > Data Sources (ODBC).

The ODBC Data Souces Administrator dialog box opens.

2. Click the System DSN tab.


3. Click Configure.

The MySQL ODBC <version> Driver dialog box opens showing the database settings.

The Data Source Name and Database Name fields must both contain “velocity11”.

Testing the Connection

To test the database connection:

1. Follow the procedure in “Checking the Database Settings” on page 318 to open the MySQL ODBC <version> Driver dialog box.

2. Click Test Data Source.

A dialog box like the following example will confirm a successful connection.


320

Resolving Lid Removal ProblemsSuction-based lid Remover Problems

If your BioCel has a suction-based lid remover, you may occasionally find that it does not function properly. If this happens, you will need to adjust the vacuum sensor that provides feedback on whether a lid is attached to the suction cups.

This adjustment requires you to turn the air on and off through the Bio I/O Diagnostics software while making incremental adjustments to the screw head that lies in the hole on the side of the station. To do this you have to remove the side panel.

For help with this procedure, contact the Velocity11 Service Center.

Lid Hotel Problems Preventing Problems

To prevent problems with a lid hotel, make sure that:

❑ The rollers are free of debris and dirt.

❑ The robot holds the plates below the lids.

❑ Bar code labels are not applied to the lids.

❑ Stacks of labels are not allowed to build up on the plates.

❑ The lids are free of sticky residue from labels.

Solving Problems

If you receive a lid detection error, try the following:

1. Check that the plate type in the protocol is correct for the plate.

2. Check that the lid type in the protocol is correct for the plate.

3. Make sure that the sensors are working:

a. Open the lid hotel diagnostic software.

b. Move your hand in front of each sensor, one at a time, and look for a response in the diagnostics lights.

For more information, see “Using Lid Hotel Diagnostics” on page 278.

4. Check the lid hotel teachpoints to make sure that they are correct.

If you need help with this, contact the Velocity11 Service Center.

321IndexBioCel User Guide

IndexNote: You can also use the online help to search for information. You can download the latest version from the Support page of our website at www.velocity11.com.

Symbols.bar file format, 49.csv file format, 256.dat file format, 49, 58.pro file format, 45.vlk file format, 237

Numerics7900HT module, 28

Aaborting a run, 95AC power entry, 21accessories, 30ActiveX, registering, 199Administrator privilege, 110Advanced Settings tab, 202air

controlling flow, 23main supply, 16pressure, 81shutoff valve, 23switch, 23system, 23

air filter, 19checking, 308

air panelparts, 19

alarmadding, 65triggering, 158

alarm option, 51aliQuot

profile, 263setting up manual operation, 264test fill, 265

AliQuot diagnostics software, 262Aliquot task defined, 126API, 194Application Programming Interface. see API, 194Apply label task, 196

defined, 127, 223setting parameters, 127

approach height, 292, 293, 299aspirate acceleration, 185, 189Aspirate pipette task

adding, 167defined, 173setting parameters, 173

aspirate velocity, 185, 189

Bbar code

errors, 316field modifiers, 131format files, 127input file, 225inventory management, 231labelling requirements, 127log file, 132misread errors, 315misreads, 51printer, 223reading manually, 291tracking during a run, 223updating input file, 227viewing input file, 226

bar code data file, 228bar code errors

mismatch, 316no read, 315

bar code input file, 196, 225with linker file, 247

bar code log file, 56, 58bar code reader, 223

auxiliary, 30bar code reading

on a StoreX, 155barcodelog.txt, 56, 58Bio I/O

diagnostics software, 270BioCel

behind the side doors, 18, 20cleaning, 106components, 14definition, 14external features, 15overview, 14performing a run, 35, 79ready state, 39routine maintenance, 308shutting down, 107starting, 37

http://www.velocity11.com

IndexBioCel User Guide

322

Bio-Tek washer, 28diagnostics software, 266online help, 268setting up, 73

blowout volume, 181, 186, 190

Ccalibration file, Nanodrop, 284Centrifuge task

defined, 134setting parameters, 134

Change Instance process task, 175Change Tips pipette task

defined, 177requirements, 177

changing pipette tips, 177chimney. see MicroWash trayclean-room, 17, 21, 25clean-room filter, 25clean-room standards, 25climate control, 301command line VWorks launch, 86compilation errors, 310compilation warnings, 310compiling a protocol, 118, 122computer

disk space option, 52monitor damage hazard, 10networking. see networking

configuration settings, 219counterweight plate, 81

associating with a plate pad, 134manually loaded, 77robotically loaded, about, 77setting up robotic loading, 78

creating process for a tipbox, 178Cytomat, 28

Ddamage hazard

computer monitor, 10overhead door, 10

data files, 56database

BioCel, connecting to, 319inventory management, 233labware, 181, 186, 191, 211, 214, 218, 255liquid library, 255managing counterweights, 77third-party, 194

DC power supply, 21deadlock, 116device

configuring VPrep shelf, 171defined, 221initialization errors, 310lid removal, 31querying, 101

device file, 7, 221loading, 222saving, 221

device managerrelationship with other configurations, 219

diagnostics softwareabout, 260AliQuot, 262Bio I/O, 270Bio-Tek, 266Envision, 272iSeries, 275Lid Hotel, 278Multidrop, 279Nanodrop, 282opening, 260robot, 288StoreX, 301Teleshake, 306

dialog boxNumber of Cycles, 54, 84Protocol Options, 54

dispense acceleration, 180, 185, 190dispense limits, 180Dispense pipette task

adding, 168defined, 180setting parameters, 180

dispense velocity, 180, 185, 189dispense volume, 180, 189dispensing to waste, 190, 191distance from well bottom, 181DLL files, see Dynamic Link Library filesDry Tips pipette task


Dynamic Link Library files

EEcho 550

manual transfer, 271profile, 270

emailnotification, 158setting up, 6

email option, 51emergency stop, 22

button, 96


compared to interlock, 97recovering from, 312

emergency stop button, 95enable wires, 22environment output file, 56environment.txt, 56environmental control, 21, 82, 301

adding an alarm, 65how it works, 275monitoring, 99troubleshooting, 317

environmental enclosure, 30Envision Diagnostics, 272Envision task, setting, 138error handling, 309error message display. see Log toolbar.error options, 51errors

bar code reader, 315door interlock, 311emergency stop, 312plate placing, 318plate sensor, 313robot, 292servo, 313setting scheduler behavior options, 52VCode, 316

Ethernet cable, 16Ethernet hub, 22event messages. see log toolbar

Ffans

clean-room, 22, 25clean-room specifications, 26console, 25

filedevice, 7environment output, 56protocol, 7protocol log, 7reader output, 56, 58teachpoint, 294

FileReader plug-in, 195, 196filter for clean-room, 25filtration station, 24, 263, 287filtration using aliQuot, 262finding plates, 101folder for image file root, 56fuse, 21

Ggeneral options, setting, 48

gripper, 290gripper close delay, 295gripper offset, 290gripper open delay, 295

Hhazards. see safetyhotel. see plate hotel and lid hotelhumidity. see environmental control

Iimage file root folder, 56incubation timed with StoreX, 140incubation. see Incubate TaskInflowPump, 190, 217injury hazard

interlock override, 10side door, 9

interlockair shutoff valve, 19air system, 23compared to emergency stop, 97overriding, 314recovering from errors, 311safety, 10

interlock override, 82injury hazard, 10

inventory managementdatabase, 231, 233filters, 234overview, 231views, 234

IP addresses. see networkingiSeries

diagnostics software, 275replacing fuse, 317setpoint, 276

iSeries controller, 21monitoring, 102naming, 275profiles, 276resetting, 317

iSeries measuring units, 59

JJavaScript

about, 202cautions when using, 207examples, 207global functions, 203plate object, 204resources, 202task object, 205, 208


324

variables, 206VWorks, 202VWorks objects, 203

JavaScript scripts, 110, 111JavaScript script-writing service, 207JavaScript uses, 202jog increment, 290jogging. see robot

Kkeyboard shelf, adjusting, 27

Llabware database, 181, 186, 191, 211, 214, 218, 255labware editor

definition, 255opening, 255relationship with other configurations, 219

labware, changing in plate inventory, 249library files, 195Liconic incubator. see StoreXlid hotel, 30, 31, 278Lid Hotel diagnostics, 278lid remover, suction based, 31lid remover, suction-based, 30lights, maintenance, 308LIMS system, 195linker file

about, 235clearing current, 239with bar code input file, 247working with, 238

linker groupabout, 235file format, 237

linking a pipette process, 170liquid class, 180liquid library database, 255liquid library editor

definition, 255opening, 255relationship with other configurations, 219

log filebar code, 56, 58, 132measurements output, 59pipette, 57pipettor transfer, 56protocol, 56, 57, 64setting options for, 61types, 56

log file options, 60log files, searching, 105

log options, 60Log Options page, 56Log toolbar, 84, 104

adding a note, 105options for, 104

Log toolbar, message display, 60log.txt, 56log.txt file

about, 57adding a note to, 105

logging in, 41loop pipette task

setting, 184

Mmain panel, 23manifold

air distribution, 23see also MicroWash tray

measurements output log file, 59measurements.txt, 59MicroWash trayMicroWash tray, washing, 192Mix pipette task


mixing cycles, 185mixing volume, 185module shelf, 30modules

definition, 28list of, 28preparing for a run, 69

Multidrop diagnostics, 279Multidrop module, 28

setting up, 74Multidrop task

setting parameters, 141Multidrop, setting up, 74

NNanodrop diagnostics software, 282Nanodrop profiles, 283Nanodrop task, setting parameters, 143networking

cards, 257IP addresses, 257

Notepad, using, 57notes, adding about protocol, 118Number of Cycles dialog box, 54, 84

Ooperating system. see Windows


optionslog and data file, 60setting error, 51setting general, 48

overhead doordamage hazard, 10

overhead door, lifting, 95

Pparticle counter, 25Pierce task


pinch valve, 24pipette log file, 57pipette process

configuration settings, 219creating for changing pipette tips, 179defined, 44linking a pipette task to, 170setting parameters, 169

pipette process link icon, 43pipette process task

adding, 169adding example, 165defined, 43

pipette process task, adding, 165pipette task

defined, 44pipette tips

changing, 177, 179dryer, 183touching, 191washing, 189

pipetting operation, example, 164pipettor transfer log file, 56piplog.txt, 56, 57Place Plate task


platemoving in StoreX, 243plate sensor errors, 313see also counterweight plate

plate hotel, 30descriptionplacing and removing, 76

plate instancedefinition, 42setting parameters, 112versus task, 42

plate inventory, changing labware, 249plate object

JavaScript, 204plate placing errors, 318plate sensor, checking, 293PlateLoc, 28

see also Seal tasksetting up, 71

platepads, transfer station input and output, 230PlatePierce, 28

see also Pierce taskplates

finding, 101moving in StoreX, 232placing, 69reinventorying in StoreX, 252see also simultaneous plates

plug-in, 110custom, 195definition, 194FileReader, 195FileReader, about, 196how it works, 194process overview, 195registering ActiveX, 199setting up, 199

post-dispense volume, 181power panel, 17power supply, main, 16pre-aspirate volume, 190pre-emergency stop current, 21pre-run checks, performing, 81pre-UPS current, 21priming, 280printing a protocol, 68process, defined, 42protocol

adding notes about, 118compiling, 118, 122creating example, 164defined, 43file name, 45opening, 47overall process of creating, 110printing, 97saving, 118simulating, 122specifying order of tasks, 162understanding before a run, 68

protocol file, 7protocol file format, 45protocol log file, 7, 56, 57protocol log file, example, 64protocol notes, adding, 118Protocol Options dialog box, 54


326

Protocol Options rule, 54Protocol Task Parameters toolbar, 197Protocol Task Parameters toolbar and configura-tion, 219protocol, optimizing, 54pump

inflow, 190outflow, 190

Pump Reagent pipette taskdefined, 188

Pump Reagent task, setting parameterspurging, 280pushdown defined, 295

QQFill task


QFill2, 28setting up, 74

QRM file, Nanodrop, 284quadrant, 174, 181, 186, 190quadrant representation in JavaScript, 206querying devices, 101

Rreader output file, 56, 58Reader.dat file, 56refrigeration block, 30registry file, 7regulators, 19, 23Remp CSP task, 147reserve tank, 24reservoir filling, see VPrepreset button, 22Restack task

process overview, 147setting parameters, 150

resting the robot, 291retract distance, 181, 186, 190robot

axes, 288brakes, 22communication time, 291errors, 311homing, 291jogging, 289moving, 288preventing a crash, 48profile, 294recovering from servo errors, 313resting, 291speed, 288

runaborting, 95cleaning up after, 106defined, 44monitoring, 99monitoring progress, 101overview, 80scheduling, 87starting, 83stopping, 95what happens after, 84

runsetdefined, 87examples, 91filtering, 89opening, 90saving, 90stopping, 90working with, 88

runset file, 87

Ssafety

general hazards, 9interlock override, 10, 22

saving a protocol, 118scheduler behavior options, 52screen message options, 104scripts. see JavaScript, 202SDK. see Software Developer’s Kit, 195Seal task


servo errors, recovering from, 313setpoint value for iSeries, 276setting up email, 6shutting down, 107side door injury hazard, 9Signal task


simulating a protocol, 122simultaneous plates, 113, 116SpectraFluor, 28Stacker task


starting a run automatically, 87starting a run. see runstarting the BioCel, 37starting VWorks, 40status lights, 102stopping a run, 95


StoreXemptying, 241loading, 239moving plate in, 243multi-process incubation, 244reinventorying plates, 252setting up, 73timed incubation, 140transfer station, 31

StoreX Diagnostics, 301StoreX measuring units, 59StoreX task

and linker files, 154defined, 154

suction-based lid remover, 31system definition, 233

Ttask

adding, 117defined, 42deleting, 117specifying order in a protocol, 162types, 120User Message, 85

task objectJavaScript, 205

task parameter setting, 120Task Parameters toolbar. see Protocol Task Pa-rameters toolbarteachpoint file, 294teachpoints

fine tuning, 296inaccurate, 296moving a plate between, 294moving robot to, 293

Technician privilege, 110Teleshake, 28

setting up, 71Teleshake diagnostics, 306Teleshake task, 156temperature. see environmental controltip touch horizontal distance, 181, 186tip touch rise height, 181, 186tip touching, 181, 186tipbox, 178tips. see pipette tipstoolbar see individual toolbar namestoolbars, closing, 101training on the BioCel, 9transfer log, 182transfer station, 154

setting input and output, 230

StoreX, 31trash. see waste receptacletroubleshooting, files to send, 6turning on. see starting the BioCel

UUltra Multimode Reader module, 28Ultramark, 28

file format, 256setting the output folder, 256setting up, 72

uninterruptible power supply. see UPSUPS

connections, 21status, 100

user account, creating, 254User Message task, 85


UV lights, 21

Vvacuum filtration. see QFill2vacuum system, 24Vacuum task


vacuum, creating, 23VCode, 28

errors, 316setting up, 72

VersaScan, image file root folder, 59volume

blowout, 181, 186, 190dispense, 180, 189mixing, 185post-dispense, 181pre-aspirate, 190wash, 189

VPrep, 22, 28brakes, 22changing tips, 179reservoir, 188selecting, 165setting up, 74

VPrep pumps, 22VPrep shelf

configuring, 165configuring as device, 171

VSpin, 28counterweight. see counterweight platesee also Centrifuge tasksetting up, 72


328

VStack, 28setting up, 71

VWorksfinding the version number, 2logging in, 41starting, 40

WWaitfor task


Wash Tips pipette task, defined, 189wash volume, 189washing pipette tips, 189waste bottle, 24

waste receptacle, setting up, 70Weigh Pad, 30Windows

logging on, 39registry editor, 255

workflow overview, 36

XXML format, 45XML schema, 45

ZZeiss Multimode module, 27, 28, 161

setting up, 74Zeiss task, setting parameters, 161

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