Introduction to E-Notebook:A Q i k St t T t i lA Quick-Start Tutorial

Richard Strauss and Jesse Gordon CambridgeSoft Directors ofCambridgeSoft Directors of Software Marketingrstrauss@cambridgesoft.comjgordon@cambridgesoft.com (617) 588-9133(617) 320-6989 Skype: jessegordon

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E-Notebook Tutorial outline: Introduction

This video tutorial presents a step-by-step process for you to be able to quickly tour and use CambridgeSoft's electronic lab notebook or "ELN "electronic lab notebook, or ELN.

The tutorial is presented in three sections:

1) Introduction 2) E-Notebook Content3) Using E-Notebook3) Using E Notebook

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E-Notebook Tutorial outline: Intro & Basics

1) Introduction1) Introduction

2) E-Notebook Content

3) Using E-Notebook

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Why a lab notebook?

• To a Researcher - A place to record science– The primary lab data & experimental observations

recordrecord– Documentation of references to external data and

literature sources– Record of interpretations, distilled data and finalRecord of interpretations, distilled data and final

experimental conclusions and reports for other researchers or management.

• Expected to be convenient, easy to use, portableM t h it ith l l d l t th iti– Must have merit with legal and regulatory authorities.

– Required that it is non-reputable, and that courts consider to be standard business records

– Basis for US PTO issues patents based upon date ofBasis for US PTO issues patents based upon date of invention

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1. E-notebook introduction:Key Points

→ The burden of using conventional paper notebooks The burden of using conventional paper notebooks increases as a company grows. Eventually a critical point is reached when conversion to electronic is required which typically involves costly capital investment and loss of legacy data.

→ It is a great advantage to have a dedicated, integrated E-Notebook which has low implementation costs and provides a scalable, long term solution usable across the spectrum of organization sizes to avoid this critical juncture That is Eorganization sizes to avoid this critical juncture. That is E-Notebook from CambridgeSoft.

→ Case studies at many customers from major pharmaceutical companies to smaller biotech companies show that scientistscompanies to smaller biotech companies show that scientists can achieve a 10-25% increase in individual productivity with a break-even point at 10-19 months post-deployment by implementing E-Notebook.

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1. E-notebook introduction:Benefits of ELN

• Find what you looking for when you need to see it. • Manage and report on scientific data in a consistent way• In your notebook or your associates’• In your notebook or your associates • Legal protection for IP • Supports many disciplines (medicinal Supports many disciplines (medicinal, polymer, etc.) • Chemical and biological intelligence

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1. E-notebook introduction: Reaction Page

Tool Bar

Explorer & Offline buttonsExplorer & Offline buttons(new in version 11.5)

Navigation

History Panel

gPanel

Work Panels

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Work Panels

1. E-notebook introduction: Getting Started

Your system configuration determines the type of collections and sections that you can create delete, move etc within E-Notebook and the rules that define their contents The permission to viewand the rules that define their contents. The permission to view, edit, and create collections can be set up on a per-collection basis.

Each user has a user collection associated with them The userEach user has a user collection associated with them. The user collection is your home collection, and appears at the top of the Collection Tree when you first log into E-Notebook.

•Launch the E-Notebook from the start menuLaunch the E Notebook from the start menu.•Enter your Login information and click Connect.

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1. E-notebook introduction: User’s collections

For the first time, wizard steps you through initializing the notebook and creating identity.

Collections under the user “User1”:

The appropriate User configuration and Offline folder for each f

pp p guser is created automatically when the user first logs in.

Select User collection “User1” in the Collection Tree

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1. E-notebook introduction: Home Page

The right frame displays the User’s home page in addition to summary information about your open pages/reactions, Waiting Documents and list of Submitted documentsWaiting Documents and list of Submitted documents.

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1. E-notebook introduction: Browsing

Selecting the Notebook collection displays Table of contents. As you add pages/experiments to your notebook this list will grow –it can also display some summary data from your experiment p y y y p

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1. E-notebook introduction: User Configuration

User Configuration folders are configuration dependent. Within your user collection, there is a User Configuration Folder, which can contain collections of commonly used items ascontain collections of commonly used items as well as user entered additions, to expedite the creation of notebook pages.

These are the shared items such as salt listsThese are the shared items such as salt lists, reagents, and rendering templates. Here, you can create your own custom items such as reagents, templates, folders etc.

Note: By default, the E-Notebook is configured so that you cannot delete some specific collections such as, User Collection, User Configuration Folder, Notebook Collections and Offline Folderand Offline Folder.

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1. E-notebook introduction: User Configuration

Reactants Folder: Contains reactants whose structures and properties you can add to Reaction and Compound section. New Reactants can be added to existing reactant listsgSalt Codes Folder: Contains a read only list of salts whose structures and properties you can add to Reaction and Compound Sections.Solvents Folder: Contains read only list of 55 most commonly usedsolvents whose names and properties you can add to reaction andsolvents whose names and properties you can add to reaction and Compound sections.Solvate Codes Folder: Contains a read only list of solvates whose names and properties you can add to Reaction Sections.T l t f ld All t t t i d t l t fTemplates folder: Allows you to create user customized templates of various types that saves and stores commonly used procedures and experimental pages that can be used to avoid unnecessary reentry of data.M dCh A t T t D fi iti All t tMedChem AutoText Definitions: Allows you to create user customized autotext definitions to be used in various sections of E-Notebook.Tasks Folder: Contains the “Search” and the “Batch Explorer” folders

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Rendering Folder: Contains read only templates for the export files.

E-Notebook Tutorial outline: Intro & Basics

1) Introduction1) Introduction

2) E-Notebook Content

3) Using E-Notebook

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2. E-Notebook Content:User Collection

Select User

CollectionCollection

Opens User’s Homepage and

table of contents

Collection= a set of related items in E-Notebook, e.g.

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, gnotebook, folder, experiment page, etc.

2. E-Notebook Content: To add new Collection

Right click User

ll iCollection

Select new Notebook to

tcreate new collection

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2. E-Notebook Content: To add new Notebook page

Right clickRight click Notebook

Select new Page to create new

page in notebooknotebook

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2. E-Notebook Content: Specify Notebook page

Specify type of

section on page

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2. E-Notebook Content: Reaction page

Use ChemDraw Active-X to draw structures or just select reagents from dropdown list

2 ways to ddadd

molecules to reaction

panel

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Reaction page-Filling in the information

Use ChemDraw Struct-to-Name*

to automatically nameto automatically namethe reaction compounds

* Requires ChemDraw Ultra application!

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Reaction page-Adding Compounds

Use filter to narrow list of compounds to choose from based on a word or combination of letter

Type in name ofname of

compound to locate it

Select compound pfrom large

list of reagents

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Reaction page-Stoichiometry Table

Stoichiometry Table records data about the reactants and productsabout the reactants and products

and allow users to enter experimental reaction parameters

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Reaction page-Auto Text

Right click to insert items from stoichiometry table

Autotext l ti tselection to assist in writing

protocols. Mouse over

Double click phrase to have text entered in field. It will be automaticallyupdated when changes are made to reaction, either in drawing or

stoichiometry grid

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items to see text

stoichiometry grid

Reaction page-Add Solvent

•Select Solvent from the displayed list and click Add•Double click in the Molecular formula box•Select Salt or solvate from the dropdown list to add to the molecule

You can also create new salts and solvates using the “New Salt Code” and the “New Solvate” buttons on the right.

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Reaction page-AutoText Fill-ins

Right click to insert items from list to fill in undefined items in color

Link to other pages or

collectionscollections

Users can add to existing AutoText by editing the files,

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g y g ,located in the User Configuration folder

MS Word page

Standard MS Word toolbarsImport existing

Word document or object

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MS Excel Spreadsheet page

Import existingImport existingExcel table

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MS PowerPoint Slideshow page

Import existingPP slideshow

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Standard MS PP layout

Image import page

Import existingImport existingimage or PDF

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Spectrum page

Add Properties to accompany spectrum

Import Spectrum onto page

Add Properties to accompany spectrum

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Ancillary data page

Create link to file which is not importable to E-Notebook

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History Panel

To view the history details of a collection, select the collection in thell ti t d li k th Hi t i At th b tt f th ll ticollection tree and click the History icon At the bottom of the collection

tree, you can view the history (details of when it was created, saved etc)of a particular collection.

.

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E-Notebook Tutorial outline: Intro & Basics

1) Introduction1) Introduction

2) E-Notebook Content

3) Using E-Notebook

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Search Types: Collection / Structure / Section

* Collection Search by:M t d tMetadataOwnerCreation dateLocation

* Chemical Structure Search by:SubstructureSubstructureAdvanced molecule queriesReactions

* S ti S h* Section SearchLocationType of Section

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Setting Up Your Search: Search Type

1. Switch toSearch mode

2. Select type of search: ypCollections, Sections or Structures

3 Select New Query3. Select New Query

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Setting Up Your Search: Conduct Search: 3 types

• Simple Text Query: Enter the text string for which you want to search.• Advanced Text Query: Advanced Text Query allows you to obtain more precisesearch results In addition to specify the text associated with the experiment yousearch results. In addition to specify the text associated with the experiment, youcan also specify Search Location. You can also specify the metadata about theexperiment.• Reaction Query: Using a reaction query, you can search for the structures. You.

can also specify other criteria such as reactant name, product name, solventsand reaction conditions.

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Search Types: Text / Structures / Criteria

• Chemical StructureSt i f T t• Strings of Text

• Numerical values in property fieldsC ll i d/ i h• Collections and/or sections that meet specified criteria (date, owner…)

• Structure search means ONE search for ONE t tONE structure,even when it’s storedunder lots of valid but dissimilar names

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but dissimilar names…

Viewing Your Search Results

• Click Search Now to execute the query• Click the name of the item to view• A results list appears in the results tab.pp

Click the name of the item to view

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Collection Search

To specify collection attributes for the search

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Advanced Search

Some new options:

(The search includes full text! )full text! )

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Introduction to E-Notebook:A Q i k St t T t i lA Quick-Start Tutorial

Richard Strauss and Jesse Gordon CambridgeSoft Directors ofCambridgeSoft Directors of Software Marketingrstrauss@cambridgesoft.comjgordon@cambridgesoft.com (617) 588-9133(617) 320-6989 Skype: jessegordon

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