Ion Chef Instrument Network Connection

For Research Use Only. Not for use in diagnostic procedures.

Ion Chef™ Instrument Network ConnectionUSER GUIDEPublication Number MAN0013444

Revision C.0

Manufacturer: Life Technologies Holdings Pte Ltd | Block 33 | Marsiling Industrial Estate Road 3 | #07-06, Singapore 739256

The information in this guide is subject to change without notice.

DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, THERMO FISHER SCIENTIFIC INC. AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL,INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT,INCLUDING YOUR USE OF IT.

Revision history: Pub. No. MAN0013444

Revision Date DescriptionC.0 October 2, 2018 This revision includes information to:

• Connect an Ion Chef™ Instrument to an Ion GeneStudio™ S5Sequencer

• Share Planned Runs using Ion Mesh

• Monitor consumables using Ion Mesh

B.0 December 18, 2015 Various revisions.

A.0 January 27, 2015 New document.

Important Licensing Information: These products may be covered by one or more Limited Use Label Licenses. By use of these products, you acceptthe terms and conditions of all applicable Limited Use Label Licenses.TRADEMARKS: All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.

©2018 Thermo Fisher Scientific Inc. All rights reserved.

Contents

■ CHAPTER 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5About the Torrent Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5Networking guidelines and best practices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6Network setup workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6Collect the required network information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

■ CHAPTER 2 Connections between Torrent Server and theIon Chef™ Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

General requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7Direct connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7DHCP IP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8Static IP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Add the Torrent Server IP address . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Edit the Torrent Server firewall tables to allow the LAN port IP . . . . . . . . . . . . . . . . . . . . . . 10Create a firewall exception for the Torrent Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Connect directly to the Torrent Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Connect by network to the Torrent Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

■ CHAPTER 3 Connections between the Ion S5™ or IonGeneStudio™ S5 Systems and the Ion Chef™ Instrument . . . . . . . . . . . . . 15

General requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15Direct connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15DHCP IP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16Static IP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Add the sequencer IP address . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Edit the Torrent Server firewall tables to allow the LAN port IP . . . . . . . . . . . . . . . . . . . . . . 18Create a firewall exception for the Torrent Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Connect directly to the Ion S5™, Ion GeneStudio™ S5, or Ion GeneStudio™ S5Plus Sequencer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Connect by network to the Ion S5™ or Ion GeneStudio™ S5 Sequencer . . . . . . . . . . . . . . . . . 20

Ion Chef™ Instrument Network Connection User Guide 3

■ CHAPTER 4 Monitor runs, share Planned Runs, and manageconsumables with Ion Mesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Set up Ion Mesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

View sequencing runs on multiple sequencers with Ion Mesh . . . . . . . . . . . . . . . . . . . . . . . . 22

Transfer a Planned Run to a Torrent Server with Ion Mesh . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Remove a server from an Ion Mesh configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Change server nickname in an Ion Mesh configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Enable or disable an Ion Mesh connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Track Ion Chef™ flexible workflows for Ion 550™ chips with Ion Mesh . . . . . . . . . . . . . . . . . . 25

Related documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Customer and technical support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Limited product warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Contents

4 Ion Chef™ Instrument Network Connection User Guide

Introduction

If your Torrent Server, Ion S5™, Ion GeneStudio™ S5, or Ion GeneStudio™ S5 Plussequencer was not connected to the Ion Chef™ Instrument during installation, or ifyou move the equipment in your laboratory, the procedures in this guide might applyto you.

Overview

This document describes how to configure the Ion Chef™ Instrument to connect with aTorrent Server. The guide also explains how to connect an Ion Chef™ Instrument tothe internal Torrent Server in Ion S5™, Ion GeneStudio™ S5, and Ion GeneStudio™ S5Plus sequencers. When you connect to a Torrent Server, you can use Torrent Suite™

Software to plan and monitor instrument runs, review run reports, and download runresults from the connected instruments.

You can use the following types of network connections to connect a Ion Chef™

Instrument to a Torrent Server or a Torrent Server that is embedded in an IonGeneStudio™ S5 Sequencer:

• A local area network (LAN) by DHCP IP connection• A direct connection• A local area network (LAN) by Static IP connection

If you add multiple Torrent Servers to a network, you can configure connectionsbetween servers, if you use Torrent Suite™ Software 5.6 and later. Connections that usean Ion Mesh configuration, enable you to do the following:

• Share Planned Runs with Torrent Servers that are included in the Ion Meshconfiguration.

• Track reagent and cartridge usage across Ion Chef™ Instrument flexibleworkflows from different Ion Chef™ Instruments connected to different TorrentServers.

• View and monitor all runs of interest across multiple Torrent Servers on thescreen in Torrent Suite™ Software.

Torrent Server in this guide refers to the server component of the PGM™, Ion Proton™,Ion S5™ XL, or Ion GeneStudio™ S5 Prime System. Torrent Suite™ Software is thesoftware that resides on the Torrent Server. You can transfer Planned Runs betweenservers that use the same versions of Torrent Suite™ Software and are connected to thesame subnet.

The Ion S5™, Ion GeneStudio™ S5, and Ion GeneStudio™ S5 Plus sequencers haveembedded Torrent Servers and this guide describes how to target the sequencer IPaddresses to form network connections.

1

About the TorrentServer


We recommend that you consult a network administrator before connecting theIon Chef™ Instrument to your laboratory network. See the Ion Chef™ System SitePreparation Guide (Pub. No. MAN0007956) for more information about the Ion Chef™

Instrument networking requirements.

Collect the required network information.

q

Connect the Ion Chef™ Instrument to the configured LAN port.q

Configure the Ion Chef™ Instrument with the required information.q

Monitor the Ion Chef™ Instrument to test the network connection.

q

Share Planned Runs and monitor consumables with Ion Mesh.

Before you begin the procedures in this guide, obtain the following information fromyour network administrator:

• Network policy for obtaining IP addresses (DHCP IP or static IP).• If the network requires static IP addresses, obtain the static IP address, subnet

mask, gateway address, and DNS server name for the LAN port.

Note: For the Planned Run sharing and file transfer protocol (FTP) functionality to besuccessful, the subnet must be the same on all Torrent Servers and Ion Chef™

Instruments on the LAN.

Networkingguidelines andbest practices

Network setupworkflow

Collect therequired networkinformation

Chapter 1 IntroductionOverview1


Connections between Torrent Serverand the Ion Chef™ Instrument

This chapter describes how to connect the standalone Torrent Server component of thePGM™, Ion Proton™, Ion S5™ XL, or Ion GeneStudio™ S5 Prime System to an Ion Chef™

Instrument.

General requirements

The following diagrams illustrate common network configurations to which anIon Chef™ Instrument and Torrent Server might be added. See the Ion Chef™ SystemSite Preparation Guide (Pub. No. MAN0007956) for more information.

For a direct connection, the Ion Chef™ Instrument is connected directly to the TorrentServer.

1

2 3

1 Network2 Ion Chef™ Instrument3 Torrent Server

2

Direct connection


In a DHCP IP network, the Ion Chef™ Instrument and the Torrent Server connect tothe network.

1

3 4

2

1 DHCP Server2 Network3 Ion Chef™ Instrument4 Torrent Server

In a static IP network, the Ion Chef™ Instrument and the Torrent Server are connectedto the network.

1

2 3

1 Network2 Ion Chef™ Instrument3 Torrent Server

To share Planned Runs and successful FTP functionality, the subnet must be the samefor all Torrent Servers and Ion Chef™ Instruments on the LAN.

DHCP IP

Static IP

Chapter 2 Connections between Torrent Server and the Ion Chef™ InstrumentGeneral requirements2


Add the Torrent Server IP address

The first time that an instrument is connected to a Torrent Server, or any time theconnection configuration is changed, for example from a direct connection to aconnection over a network, you must add the IP address of the server to theinstrument. To add the Torrent Server IP address from the Ion Chef™ Instrument.After you complete this procedure the IP address is available to select on theIon Chef™ Instrument.

1. Sign in to Torrent Suite™ Software.

2. Click (Settings)4Services.

3. Record the server IP address that is displayed on the System Services screen.Later you will enter the IP address on the instrument screen.

4. Return to the Ion Chef™ Instrument user interface, then tap Manage. TheManage Connections dialog opens.

Chapter 2 Connections between Torrent Server and the Ion Chef™ InstrumentAdd the Torrent Server IP address 2


5. Enter the server IP address or Torrent Server host name in the Server field andrepeat for Update site. Click Save.

The Torrent Server host name or IP address is linked to the Ion Chef™ Instrument.

Edit the Torrent Server firewall tables to allow the LAN port IP

When connecting through a LAN, the Torrent Server firewall settings need to bemodified for both DHCP and Static LAN connections.

Note: When directly connected, instruments are on the 192.168.20x.x subnet fromwhich all traffic is enabled, so modification of firewall settings is not required.

Any exception would mean that editing the local firewall tables to include the LAN IPis required. Also, if the Ion Chef™ Instrument is getting a DHCP address from yournetwork, you need to create an exception for the entire DHCP subnet.

Consult your system administrator or Thermo Fisher Field Service Engineer (FSE) orField Application Specialist (FAS) for this procedure. On the Torrent Server, editthe /etc/iptables.custom file and add a firewall rule to allow all traffic from the IPaddress of the Ion Chef™ Instrument. (This is a blank file initially and is intended forcustom firewall configuration.)

IMPORTANT! Only edit the /etc/iptables.custom file and not /etc/iptables.rules,because /etc/iptables.rules is overwritten when software is updated.

1. Enter sudo^nano^/etc/iptables.custom, then add the three lines below:

*filter-A INPUT -s xxx.xxx.xxx.xxx -j ACCEPTCOMMIT

Note: -A INPUT -s xxx.xxx.xxx.xxx -j ACCEPT adds the rule to theformat. Enter the IP address of the Ion Chef™ instrument in place of"xxx.xxx.xxx.xxx". When finished editing, save changes by pressing CTRL +O and CTRL + X.

Create a firewallexception for theTorrent Server

Chapter 2 Connections between Torrent Server and the Ion Chef™ InstrumentEdit the Torrent Server firewall tables to allow the LAN port IP2


2. After this command, manually apply the change:sudoîptables-restore^--noflush^<^/etc/iptables.customNote: You can also list the firewall rules with: sudoîptables-L.

If this command returns with no output, it means it succeeded.

3. If the Ion Chef™ Instrument is getting a DHCP address from your network, createthe exception for the entire DHCP subnet.The example below assumes that the DHCP address for the Ion Chef™

Instrument is 172.16.48.0 and the DHCP subnet range is 172.16.48.1 to172.16.48.254. Add these three lines:

*filter-A INPUT -s 172.16.48.0/24 -j ACCEPTCOMMIT

4. Restart the server.

5. (Optional) If you need to make corrections, repeat this process and completelydrop all rules and start fresh. Enter the following:

sudoîptables-Fsudoîptables-restore^<^/etc/iptables.rulessudoîptables-restore--noflush^</êtc/iptables.custom

Removing a rule from either of these files would remove it from the activefirewall rules, because the iptables-restore command does not overwriterules, it adds them to all active rules.

Connect directly to the Torrent Server

You can directly connect the Torrent Server to the Ion Chef™ Instrument.

1. Verify Torrent Server connection to Ion Chef™ Instrument.a. Plug the connector from the Ion Chef™ Instrument directly into one of the

available ports on the back of the server.The Ion Chef™ Instrument is assigned a default IP address, for example192.168.201.1, based on the Torrent Server port you connect to.

Chapter 2 Connections between Torrent Server and the Ion Chef™ InstrumentConnect directly to the Torrent Server 2


b. On the Home screen, tap Settings4Instrument Settings4About4AboutInstrument, then verify the IP address for the server connection on the IonChef™ Instrument.

2. Connect the Ion Chef™ Instrument.a. On the Home screen, tap Settings4 Torrent Server.

b. Verify that the server settings are correct. Ensure that the Torrent Suite™

Software password is correct.The Torrent Suite™ Software URL is the IP address of the port you connectedto on the back of the server (192.168.20x.1).

The server and instrument are now connected.

Chapter 2 Connections between Torrent Server and the Ion Chef™ InstrumentConnect directly to the Torrent Server2


3. To set the password, tap Manage, then enter the password to the ionadminaccount password on the selected Torrent Server.

4. Tap Save.

The Torrent Server is directly connected to the Ion Chef™ Instrument, an icon ( ) onthe lower left side of the home screen appears. You can now use Ion Mesh to sharePlanned Runs and monitor consumables.

Connect by network to the Torrent Server

To connect to the Torrent Server through the company LAN, you need to targetServerPortIP (Eth1), see “Add the Torrent Server IP address“ on page 9 for moreinformation. When the LAN is set to DHCP, the IP, Gateway, Netmask, and DNSName Servers populate automatically. You will also need to modify the Torrent Serverfirewall settings. See “Edit the Torrent Server firewall tables to allow the LAN portIP“ on page 10 for more information.

1. On the Home screen, tap Settings4Instrument Settings4NetworkConfiguration.

2. Select the appropriate IP configuration:

Option Description

DHCP Dynamic Host Configuration Protocol is a client/server protocol thatautomatically provides an Internet Protocol (IP) host with its IP addressand other related configuration information such as the subnet mask andthe gateway.

Static IP Static Internet Protocol (IP) address is a permanent number assigned to acomputer by an Internet Service Provider (ISP).

Chapter 2 Connections between Torrent Server and the Ion Chef™ InstrumentConnect by network to the Torrent Server 2


3. Ensure that the information is correct, then tap Done.

The Torrent Server is connected to the company LAN, an icon ( ) on the lower leftside of the home screen appears. You can now use Ion Mesh to share Planned Runsand monitor consumables.

Chapter 2 Connections between Torrent Server and the Ion Chef™ InstrumentConnect by network to the Torrent Server2


Connections between the Ion S5™ orIon GeneStudio™ S5 Systems and the

Ion Chef™ Instrument

This chapter describes how to connect an Ion Chef™ Instrument to the internal TorrentServer component in an Ion S5™, Ion GeneStudio™ S5, or Ion GeneStudio™ S5 PlusSequencer.

General requirements

The following diagrams illustrate common network configurations to which anIon Chef™ Instrument and a Ion S5™, Ion GeneStudio™ S5, or Ion GeneStudio™ S5 PlusSequencer with an internal Torrent Server might be added. See the Ion Chef™ SystemSite Preparation Guide (Pub. No. MAN0007956) for more information.

For a direct connection, the Ion Chef™ Instrument is connected directly to an Ion S5™,Ion GeneStudio™ S5, or Ion GeneStudio™ S5 Plus Sequencer with an embedded server.

1

2 3

1 Network2 Ion Chef™ Instrument3 Ion S5™, Ion GeneStudio™ S5, or Ion GeneStudio™ S5 Plus Sequencer with an embedded

server

3

Direct connection


In a DHCP IP network, the Ion Chef™ Instrument and the Ion S5™, Ion GeneStudio™

S5, or Ion GeneStudio™ S5 Plus Sequencer with an embedded server connect to theDHCP IP network.

1

3 4

2

1 DHCP Server2 Network3 Ion Chef™ Instrument4 Ion S5™, Ion GeneStudio™ S5, or Ion GeneStudio™ S5 Plus Sequencer with an embedded

server

In a static IP network, the Ion Chef™ Instrument and the Ion S5™, Ion GeneStudio™ S5,or Ion GeneStudio™ S5 Plus Sequencer with embedded server are connected to thenetwork.

1

2 3

1 Network2 Ion Chef™ Instrument3 Ion S5™, Ion GeneStudio™ S5, or Ion GeneStudio™ S5 Plus Sequencer with an embedded

server

To share Planned Runs and successful FTP functionality, the subnet must be the samefor all sequencers and Ion Chef™ Instruments on the LAN.

DHCP IP

Static IP

Chapter 3 Connections between the Ion S5™ or Ion GeneStudio™ S5 Systems and the Ion Chef™ InstrumentGeneral requirements3


Add the sequencer IP address

The first time that an instrument is connected to an Ion S5™, Ion GeneStudio™ S5, orIon GeneStudio™ S5 Plus Sequencer with an embedded Torrent Server or any time theconnection configuration is changed, for example from a direct connection to aconnection over a network, you must add the IP address of the sequencer to theinstrument. After you complete this procedure the IP address is available to select onthe Ion Chef™ Instrument.

1. If you are connecting the Ion Chef™ Instrument to a Ion S5™, Ion GeneStudio™ S5,or Ion GeneStudio™ S5 Plus Sequencer with an embedded Torrent Server over anetwork, click Settings4Instrument Settings4About on the sequencer andlocate the target IP address displayed on the sequencer user interface screen.

2. Return to the Ion Chef™ Instrument user interface, then tap Manage. TheManage Connections dialog opens.

3. Enter the sequencer IP address or host name in the Server field and repeat forUpdate site. Click Save.

The sequencer IP address is linked to the Ion Chef™ Instrument.

Chapter 3 Connections between the Ion S5™ or Ion GeneStudio™ S5 Systems and the Ion Chef™ InstrumentAdd the sequencer IP address 3


Edit the Torrent Server firewall tables to allow the LAN port IP

When connecting through a LAN, the firewall settings of an Ion S5™, Ion GeneStudio™

S5, or Ion GeneStudio™ S5 Plus Sequencer with an embedded Torrent Server need tobe modified for both DHCP and Static LAN connections.

Note: When directly connected, instruments are on the 192.168.20x.x subnet fromwhich all traffic is enabled, so modification of firewall settings is not required.

Any exception would mean that editing the local firewall tables to include the LAN IPis required. Also, if the Ion Chef™ Instrument is getting a DHCP address from yournetwork, you need to create an exception for the entire DHCP subnet.

Consult your system administrator or Thermo Fisher Field Service Engineer (FSE) orField Application Specialist (FAS) for this procedure. On the Ion S5™, IonGeneStudio™ S5, or Ion GeneStudio™ S5 Plus Sequencer with an embedded TorrentServer, edit the /etc/iptables.custom file and add a firewall rule to allow all traffic fromthe IP address of the Ion Chef™ Instrument. (This is a blank file initially and isintended for custom firewall configuration.)

IMPORTANT! Only edit the /etc/iptables.custom file and not /etc/iptables.rules,because /etc/iptables.rules is overwritten when software is updated.

1. Enter sudo^nano^/etc/iptables.custom, then add the three lines below:

*filter-A INPUT -s xxx.xxx.xxx.xxx -j ACCEPTCOMMIT

Note: -A INPUT -s xxx.xxx.xxx.xxx -j ACCEPT adds the rule to theformat. Enter the IP address of the Ion Chef™ instrument in place of"xxx.xxx.xxx.xxx". When finished editing, save changes by pressing CTRL +O and CTRL + X.

2. After this command, manually apply the change:sudo^iptables-restore^--noflush^<^/etc/iptables.customNote: You can also list the firewall rules with: sudo^iptables-L.

If this command returns with no output, it means it succeeded.

3. If the Ion Chef™ Instrument is getting a DHCP address from your network, createthe exception for the entire DHCP subnet.The example below assumes that the DHCP address for the Ion Chef™

Instrument is 172.16.48.0 and the DHCP subnet range is 172.16.48.1 to172.16.48.254. Add these three lines:

*filter-A INPUT -s 172.16.48.0/24 -j ACCEPTCOMMIT

Create a firewallexception for theTorrent Server

Chapter 3 Connections between the Ion S5™ or Ion GeneStudio™ S5 Systems and the Ion Chef™ InstrumentEdit the Torrent Server firewall tables to allow the LAN port IP3


4. Restart the server.

5. (Optional) If you need to make corrections, repeat this process and completelydrop all rules and start fresh. Enter the following:

sudoîptables-Fsudoîptables-restore^<^/etc/iptables.rulessudoîptables-restore--noflush^</êtc/iptables.custom

Removing a rule from either of these files would remove it from the activefirewall rules, because the iptables-restore command does not overwriterules, it adds them to all active rules.

Connect directly to the Ion S5™, Ion GeneStudio™ S5, or IonGeneStudio™ S5 Plus Sequencer

The Ion S5™, Ion GeneStudio™ S5, and Ion GeneStudio™ S5 Plus sequencers include abuilt-in server. You can connect an Ion Chef™ Instrument and the sequencer directlyand plan runs for both instruments through the Torrent Suite™ Software.

Before you can complete this procedure the Ion Chef™ Instrument and the Ion S5™,Ion GeneStudio™ S5, or Ion GeneStudio™ S5 Plus Sequencer must be connecteddirectly through a cable connection. See the your site administrator or the Ion Chef™

System Site Preparation Guide (Pub. No. MAN0007956) for more information about thisconnection and Ion Chef™ Instrument networking requirements.

1. Connect the Ion Chef™ Instrument directly to the Ion S5™, Ion GeneStudio™ S5, orIon GeneStudio™ S5 Plus Sequencer, then click Settings4Instrumentsettings4Torrent Server.

2. Record the following information from the screen:

Setting Example Value

Update site 192.168.201.1

Server 192.168.201.1

Username (browser) ionadmin

Password (browser) ionadmin

Username (ftp) ionguest

Password (ftp) ionguest

3. To connect the instruments for the first time, tap Manage on the Ion Chef™

Instrument, then enter the recorded information in the Manage Connectionsdialog, and click Save.

The Ion Chef™ Instrument is now connected to the Ion S5™, Ion GeneStudio™ S5, orIon GeneStudio™ S5 Plus Sequencer, an icon ( ) on the lower left side of the homescreen appears. You can now use Ion Mesh to share Planned Runs and monitorconsumables.

Chapter 3 Connections between the Ion S5™ or Ion GeneStudio™ S5 Systems and the Ion Chef™ InstrumentConnect directly to the Ion S5™, Ion GeneStudio™ S5, or Ion GeneStudio™ S5 Plus Sequencer 3


Connect by network to the Ion S5™ or Ion GeneStudio™ S5 Sequencer

To connect to an Ion Chef™ Instrument to an Ion S5™, Ion GeneStudio™ S5, or IonGeneStudio™ S5 Plus Sequencer with an embedded Torrent Server through thecompany LAN, you need to target ServerPortIP (Eth1), see “Add the sequencer IPaddress“ on page 17 for more information. When the LAN is set to DHCP, the IP,Gateway, Netmask, and DNS Name Servers populate automatically. You will alsoneed to modify the Ion S5™ or Ion S5™, Ion GeneStudio™ S5, or Ion GeneStudio™ S5Plus Sequencer firewall settings. See “Edit the Torrent Server firewall tables to allowthe LAN port IP“ on page 18 for more information.

1. On the Home screen, tap Settings4Instrument Settings4NetworkConfiguration.

2. Select the appropriate IP configuration:

Option Description

DHCP Dynamic Host Configuration Protocol is a client/server protocol thatautomatically provides an Internet Protocol (IP) host with its IP addressand other related configuration information such as the subnet mask andthe gateway.

Static IP Static Internet Protocol (IP) address is a permanent number assigned to acomputer by an Internet Service Provider (ISP).

3. Ensure that the information is correct, then tap Done.

The Ion S5™, Ion GeneStudio™ S5, or Ion GeneStudio™ S5 Plus Sequencer is connectedto the company LAN, an icon ( ) on the lower left side of the home screen appears.You can now use Ion Mesh to share Planned Runs and monitor consumables.

Chapter 3 Connections between the Ion S5™ or Ion GeneStudio™ S5 Systems and the Ion Chef™ InstrumentConnect by network to the Ion S5™ or Ion GeneStudio™ S5 Sequencer3


Monitor runs, share Planned Runs,and manage consumables with Ion

Mesh

The Ion Mesh network capability was introduced in Torrent Suite™ Software 5.6 tomake Planned Run sharing and run monitoring easier. It also enables consumablestracking.

Set up Ion Mesh

Ion Mesh is a feature in Torrent Suite™ Software that allows you to form a connectionbetween Torrent Servers.

Note: Torrent Servers must be running the same software version.

When using Ion Mesh, you can:• View all runs of interest across multiple Torrent Servers on the Completed Runs

and Reports screen.• Transfer Planned Runs between sequencers that are connected to different

Torrent Servers.• Track reagent and cartridge usage across Ion Chef™ Instrument flexibleworkflows from different Ion Chef™ Instruments connected to different TorrentServers.

Follow these steps to connect (link) your Torrent Server to another Torrent Server.

1. In any tab, click (Settings), then click Ion Mesh.

4


2. Select one of the following options.

Option Description

Link a selected Torrent Server. Select a Torrent Server from the dropdown listmenu, then click Link Selected TS.

Manually link a Torrent Server. Click Link TS Manually.

3. Enter the following information in the Setup Mesh Computer dialog.

Parameter Definition

Hostname/Address Host name or address of the server.

Note: If linking a selected Torrent Server, this field isautomatically populated and cannot be edited.

Nickname A common name that is assigned to the Torrent Server.

Username Your username.

Password Your password.

4. Click Setup.The linked and enabled Torrent Servers are available to be used in the PlannedRuns and the data from the linked and enabled Torrent Servers can be viewed onthe same Data page.

View sequencing runs on multiple sequencers with Ion Mesh

Before viewing runs on multiple servers, you must first connect the servers using IonMesh. See “Set up Ion Mesh“ on page 21 for more information.

1. In the Data tab, click Completed Runs and Reports.

2. Select one or more Torrent Servers that you want to view data from in the Serverdropdown list.Notice that the server name is now reflected in the Run Name column. Yourresults across multiple sequencers are ready for your review.

Chapter 4 Monitor runs, share Planned Runs, and manage consumables with Ion MeshView sequencing runs on multiple sequencers with Ion Mesh4


Transfer a Planned Run to a Torrent Server with Ion Mesh

You can transfer Planned Runs that are created on one Torrent Server and transferthem to another Torrent Server with Ion Mesh. This is useful if the sequencerconnected directly to the origin Torrent Server is offline or busy.

Before Planned Run transfer, first connect the Torrent Servers with Ion Mesh. See “Setup Ion Mesh“ on page 21 for more information.

Note: The Torrent Servers must have the same version of Torrent Suite™ Softwareinstalled in order for this Planned Run transfer to be successful.

1. Sign in to Torrent Suite™ Software on the origin Torrent Server.

2. In the Plan tab, click Planned Runs.

3. Find the row of the Planned Run you want to transfer, then click (Actions)4Transfer.

4. Select the Torrent Server that you want to receive the Planned Run.

5. A confirmation dialog appears. Check the information, then click Transfer.

Note: You can no longer access this Planned Run on the origin server after it hastransferred.

A status appears in the dialog with the results of the transfer.• A green box lists the Planned Runs that are successfully transferred.

• A red box lists any failed Planned Run transfers.

Chapter 4 Monitor runs, share Planned Runs, and manage consumables with Ion MeshTransfer a Planned Run to a Torrent Server with Ion Mesh 4


Remove a server from an Ion Mesh configuration

You can permanently remove a Torrent Server from an Ion Mesh configuration.


2. In the Configure Mesh dialog box, click (Actions) in the row of the server youwant to unlink, then click Unlink.

3. On the confirmation window, click OK.

Note: Unlinking a Torrent Server permanently removes that server from IonMesh.

The Torrent Server is removed from the Ion Mesh configuration.

Change server nickname in an Ion Mesh configuration

You can edit the nickname of a Torrent Server linked by Ion Mesh.


2. In the Configure Mesh dialog box, click (Actions) in the row of the server youwant to edit, then click Edit.

3. Change the nickname of the linked Torrent Server, then click Setup.

The Torrent Server nickname is changed.

Enable or disable an Ion Mesh connection

You can enable or disable any Torrent Server that is connected through an Ion Meshconfiguration. The Torrent Server must be included in the configuration before you dothis procedure.

In any tab, click (Settings), then click Ion Mesh.

Option Action

Enable aTorrent Server

To enable a Torrent Server: select the checkbox in the Enable column ofthe Configure Mesh table in the row of the server.

Disable aTorrent Server

To disable a Torrent Server: deselect the checkbox in the Enable columnof the Configure Mesh table in the row of the server.

Note: Disabling a Torrent Server hides that server from Planned Runsactions and Data menus so the unlinked server cannot be used by theTorrent Suite™ Software.

Chapter 4 Monitor runs, share Planned Runs, and manage consumables with Ion MeshRemove a server from an Ion Mesh configuration4


Track Ion Chef™ flexible workflows for Ion 550™ chips with Ion Mesh

To use the flexible workflow feature and enable cartridge use tracking betweenTorrent Servers across multiple Ion Chef™ instruments, Torrent Servers must be linkedin an Ion Mesh configuration. For further information on how to link Torrent Serversin an Ion Mesh setup, see “Set up Ion Mesh“ on page 21. For more information onconfiguring a flexible workflow on the Ion Chef™ instrument, see the Ion 550™

Kit − Chef User Guide (Pub No. MAN0017275).

IMPORTANT! If you have Torrent Servers that are connected in an Ion Meshconfiguration, and the connection to one Torrent Server is disrupted or lost, cartridgetracking between servers is disabled. In this situation, an error message appears if youattempt to start a run. The run is not allowed to start because cartridge use status isnot trackable. Ion Mesh communication must be restored to verify that cartridge usestatus before the run can start.

1. In the Data tab, click Completed Runs & Reports.

2. Click a completed report.

3. In the run report, scroll down to Details section, then select Chef Summary andS5 Consumable Summary tabs to track the cartridge use.

Chapter 4 Monitor runs, share Planned Runs, and manage consumables with Ion MeshTrack Ion Chef™ flexible workflows for Ion 550™ chips with Ion Mesh 4


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Customer and technical support

Visit thermofisher.com/support for the latest service and support information.• Worldwide contact telephone numbers• Product support information

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• Order and web support


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• Product documentation– User guides, manuals, and protocols– Certificates of Analysis– Safety Data Sheets (SDSs; also known as MSDSs)

Note: For SDSs for reagents and chemicals from other manufacturers,contact the manufacturer.

Limited product warranty

Life Technologies Corporation and/or its affiliate(s) warrant their products as set forthin the Life Technologies' General Terms and Conditions of Sale at www.thermofisher.com/us/en/home/global/terms-and-conditions.html. If you haveany questions, please contact Life Technologies at www.thermofisher.com/support.

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Ion Chef Instrument Network Connection

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Transcript of Ion Chef Instrument Network Connection