Desktop E-Notebook 12.0 User Guidesgpwe.izt.uam.mx/files/users/uami/jpn/Lab_de_Quimica_I/ENotebook_Guide.pdfchemical structure drawing, a table of reactants, a table of solvents, a

E-Notebook User Guide

1. Introduction E-Notebook Features

• Facilitates daily record-keeping for the scientists (Managing data, organizing information, streamlining workflow).

• Conducts searches by substructure, key word, date, full-text and so on.

• Is configurable, you can create a customized E-Notebook that matches your workflow.

• Allows you to copy and paste commonly used protocols in order to save time.

• Creates a valuable resource for sharing the information amongst the research scientists.

• Allows you to set up templates to avoid reentering information that you often use.

• Fully automates the stoichiometry calculations.

• Allows you to electronically sign a PDF version of your completed page/reaction page.

• Offline data management allows you to work in the offline mode and get the data synchronized at a later time.

• Allows you to view a reaction tree showing successors and predecessors of a selected batch or compound.

2. Terminology: Collection: A set of related items in E-Notebook. Collections are the items that appear in the E-Notebook Collection Tree.

Section: A set of related pieces of data. Each piece of data is described by a field. For example, a reaction section might contain a chemical structure drawing, a table of reactants, a table of solvents, a table of products and a description of the procedure used to create the drawing.

Field: A description of a unit of data within a section type. Each field has a type, which describes the type of data stored in the field, and a name. Property: A unit of data.

Experiment: A collection of sections. Form: The layout of a section is determined by the Form, which contains Fields, Boxes, and possible Form Tools.

Form Tool: A Form Tool is used to perform particular function in an E-Notebook section, such as data analysis or data import/export. History: A list of the versions and transitions that have been made to a collection. Home: The collection that appears when you first log into E-Notebook. It is the collection associated with you as a user.

Meta Data: The data that describes the other data. For example, you can use meta-data such as creation date or owners name as the parameters when searching for the data and information in the E-Notebook. User: A person who uses E-Notebook. User is also a term that E-Notebook uses to identify a person.

Version: The contents of a collection saved at a particular time.

Figure 1: Conceptual Overview

Sections are the second order of

organization

Collections are the first order of

organization


Figure 2: E-Notebook- A Big Picture

15. Operations relative to Experiment collection

16. Rendering

20. History

Form

8. Field

4. Notebook

18. E-Signature Transitions

5. Experiments

3. User Collection

9. Form tools

6. Sections

Property

7. Section Operations

Data13. Annotation rules

11. Export/Import

17. Close transition

21. Session Manager

23. Collection/Transition Security

1. E-Notebook

22. Work Offline

14. Restore Changes


Figure 1&2 depicts the ‘Conceptual Overview’ and ‘E-Notebook Operations’ respectively

1. E-Notebook Organizes information via collections.

2. Groups (e.g. Users) are also collections that contain one or more Users (e.g. User1).

3. A User (User1) is also a collection that manages Notebooks

(e.g. Chemistry Notebook, Biology Notebook).

4. Notebook (e.g. Chemistry Notebook-01) contains Experiments

(e.g. Chemistry Notebook-01-001, 002, 003 etc)

Note: Your system configuration determines the types of collections that you can create

5. Experiment (e.g. Chemistry Notebook-01-001) contains sections (e.g. Reaction, MS Word, Excel, Power Point, Spectra, Ancillary Data, Image)

Note: Your system configuration determines which types of sections can be added to which types of collections.

6. Section (e.g. Reaction) contains fields (e.g. Reaction, Reactants&Products, Preparation, Solvents, Reaction conditions).

7. Each section (e.g. Reaction section) associated with a collection (Chemistry Notebok-01-001) shows several different behaviors such as the add, duplicate, remove, move and rename behaviors.

Note: Your system configuration determines the types of traits that should be shown by the sections.

8. Field (e.g. Reaction conditions) contains properties (e.g. Reaction Morality, Pressure, and Temperature).

9. User1 will have a form tool (e.g. New Section) associated with a

Experiment (Chemistry Notebook-01-001) that allows him to add new Sections (e.g. Reaction, MS Word, Excel, Power Point, Spectra, Ancillary Data, Image).

Notebook collections within User collection

Experiment collections within Notebook collection

User collection within Group

collection

Group collection


Note: Your system configuration determines the collections to which this form tool can be added

10. User1 may browse up to the next highest level i.e. Users group in the collection tree. This requires access privilege to be granted by the system administrator

11. Import/Export menu commands allows you to export and import

the collections as XML files. Each XML file contains all of the data and formatting associated with the collection.

12. User1 will be prompted to enter annotation whenever a version of the Experiment is saved.

Note: Enabled only if Required Annotation rules are defined by the system administrator)

13. Annotate Last change.. provides an optional annotation for the

last change you made to a collection (Biology Notebook-01-001)

14. In the event of a network failure, you can save your changes

locally using Restore Changes.., and then add them to the E-Notebook at a later time using the Restore command.

15. Operations relative to Experiment collection

(a) Paste reference creates a shortcut that allows an E-Notebook user to view an original from elsewhere in the Collection Tree. Any changes made to the original are reflected in the reference.

Predefined sections for Chemistry Experiment

Biology Experiment reference within Chemistry Notebook


Note: Your system configuration determines which collections can be referenced within which container collections

(b) Copy: You can copy a collection in the Collection Tree.

Note: Your system configuration determines which type of collections you can copy, and into which type of container collections you can copy them

(c) Duplicate: You can duplicate a collection within its container collection in the Collection Tree. The duplicate you create contains references to all of the collections that are contained within the collection at the time the copy is made.

Note: Your system configuration determines which collections can be duplicated, and where the duplicates can reside in the Collection Tree.

(d) Delete: You can delete a collection from the Collection Tree so that you can manage only the information that is relevant to your current needs.

Note: Your system configuration determines which types of collections can be deleted.

(e) Delete Modified collections: In some cases, you may delete the collections only if they have not been modified since they were created. Once the collection is modified, the Delete option in the collection menu is inactive when collections of that type are selected.

Note: Your system configuration determines which types of collections cannot be deleted after modification

(f) Rename: You can rename a collection to avoid a duplicate name. Your system administrator may configure some specific collections that prevents you from renaming them once they have been created. For example a Chemistry Experiment (Chemistry Notebook-01-001) whose name is generated by the auto-numbering feature gives the following error message.

Note: Your system configuration determines naming conventions for various types of collections

(g) Move Up/Down: Collections can be moved up and down within a container collection. In some cases, the collections can be moved from one container collection to another.

Note: Your system configuration determines which items can be moved into which types of collections.

16. The contents of a collection (Chemistry Notebook-01-001) can be Rendered/Exported to a PDF or MS Word file, or to a printer

Note: Your system configuration contains templates that determine exactly how the printed page appears.

17. Notebooks/Experiments may have states (Open/Close) that defines the life cycle of the collection. A “Close” transition may allow a User to move his Experiment (Chemistry Notebook-01-001) from an “Open” state (in which edits are permitted) to a “Closed” state (in which close is read only).

Note: These options may vary based upon your system configuration

18. E-signature allows you to electronically sign a PDF version of your completed page/reaction page

19. User Information provides you specific information about the user who is currently logged in. File -> User Info

Login ID - the Login ID of the user who is currently logged into E-Notebook.


Password - Depending upon the type of login authentication your system uses, this field may be used to change the password for the logged-in user.

Administrator - A checkbox that indicates whether the user has administrative privileges. Note: this checkbox is only visible if the logged-in user is an administrator.

20. A version of the collection is created each time the collection is saved. For each version, the history pane shows the date, time, and the action name - which may be save, autosave, or a transition name.

21. Session manager allows you to end your old sessions, and release any collection that may be locked by it.

22. User1 can work in offline mode in E-Notebook 12.0 when server or network connection is not available. The changes or the data you have added during the offline mode will get synchronized as soon as the network or server is available

23. User1 can change the access permission that other E-Notebook users have to his specific collection (Chemistry Notebook-01-001). For this you must have Full Control privileges to the collection (Chemistry Experiment)

(a) User1 can change the Collection Security of a collection by granting access permission to Groups and Users

(b) User1 can change the transition Security of Chemistry Notebook-01-001 by granting access permission to Groups and Users. For example, some users may be allowed to close a collection while others can also reopen the collection.

Note: Your system configuration determines which transitions may be performed, and by whom.

24. User1 can view a reaction tree showing successors and predecessors of a selected batch or compound using Batch Explorer form tool.

25. User1 can perform the Collection search and Chemical Structure search.

Full control privilege assigned to User1 for ‘Chemistry

Notebook01-001’ Assigned by system administrator

Privileges granted by User1 for ‘Chemistry Notebook01-001’ collection to User2 and User3

E-Notebook User Guide Figure 3: View Menu Items

Figure 4: Toolbar New: Context sensitive operations relative to user collection

Transition: Electronically sign a PDF version of your completed page/reaction page Save: Saves your data

Back: Move to the last state of the application Forward: Move to the next state of the application

Home: Move to Home page Up: Move to the higher level collections in the collection tree

Collections: Show/hide the hierarchy of the collections in the left History: Show/hide the history of selected collection

First: Move to the first experiment of the current notebook. Previous: Move to the experiment previous to the selected experiment in a notebook

Next: Move to the experiment next to the selected experiment in a notebook Last: Move to the last experiment of the current notebook Search: Find information in E-Notebook that meets the criteria you specify Batch Explorer: View a reaction tree showing successors and predecessors of a selected batch or compound Work Offline: Work when server or network is not connected and get the data synchronized when you work in the online mode Help: Online Help

Browse to your home collection

Hide | Show History Panel

Browse at a higher level in the collection tree

Hide | Show Collection Tree

Hide | Show Toolbar

Browse the entire collection tree (if you have the read privilege for the collection at the top of the collection hierarchy).


3. 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 view, edit, and create collections can be set up on a per-collection basis.

Each 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.

1. Launch the E-Notebook from the start menu.

2. Enter your Login information and click Connect.

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

The appropriate User configuration and Offline folder for each user is created automatically when the user first logs in.

3. Select User collection “User1” in the Collection Tree

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 documents.

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

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 Folder.

Open Pages

Submitted documents

Waiting documents

Hyperlink to open this experiment

Collections under the user


4. User Configuration Folder User Configuration folders are configuration dependent. Within your user collection, there is a User Configuration Folder, which can contain 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 lists, reagents, and rendering templates. Here, you can create your own custom items such as reagents, templates, folders etc.

Reactants Folder: Contains reactants whose structures and properties you can add to Reaction and Compound section. New Reactants can be added to existing reactant lists

Salt 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 used solvents 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.

Templates 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.

MedChem 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

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

5. Managing and Organizing Collections and Sections 5.1. Add New Collection 1. Right-click the User Collection “User1” and select New ->

Chemistry Notebook

2. Enter “Chemistry Notebook-01” as the name of the collection

The Table of Contents section of the Notebook appears in the right frame.

3. Right-click the “Chemistry Notebook-01” and select New-> Chemistry Experiment

Similarly add the Biology Notebook to the User collection and further add Biology Experiment to the Biology Notebook

5.2. Add New Section E-Notebook comes preconfigured with a number of useful Sections that you can add to your pages. Your system administrator may have modified these Sections, eliminated them, or added new Sections that more closely match your workflow.

Custom folder for solvents

Notebook created

Experiment created


1. Browse to the Chemistry Notebook-01 -> Chemistry Notebook-01-001 and select the “New Section” form tool

2. Select the type of section (Reaction page, Property Table

page, MS Word, MS Excel, MS PowerPoint, Capture Image, Spectrum, Ancillary data) on Chemistry Notebook-01-001

5.2.1. Reaction Page 5.2.1.1. Add a Reaction Section

1. Select “Reaction” from the “New Section” form tool

2. Right-click the Reaction tab and select “Rename Section”

3. Enter “Reaction-AB-10001”,as the name of the section, click OK

5.2.1.2. Add Reaction Scheme

You can use the ChemDraw Active-X to draw structures or just select reagents from the dropdown list that can be further added to your reaction panel. When you draw a reaction, the stoichiometry grid is automatically populated with the properties of the reactants and products. If you remove a reactant or product from the stoichiometry grid, the corresponding structure will be removed from the reaction drawing.

(A) Using ChemDraw Active-X

You can draw a reaction using the Chem & Bio Draw reaction field.

(B) Using Reaction Toolbar

You can add the reactants and products from your Acronyms collections in the E-Notebook. There are two methods for adding a structure with the reaction toolbar namely Add and Quick Add

i. Add: Filter, Select and Add

1. Click the Add in the reaction toolbar, the Select and Add Structure dialog appears

2. Select the structure list from the Search in dropdown list

3. Use filter to decrease the number of compounds to choose from, based on a word or combination of letters

OR Type in the name of compound to locate it

4. Select Compound

5. Click the Add down arrow and select Left of Arrow as reactant

Preconfigured sections that can be added to Chemistry Experiment


The structure is added to the reaction drawing to the left of the arrow and also to the reactants table in the grid

ii. Quick Add

You can bypass the Add Structure dialog and remove several steps from the process of adding a structure to your reaction

1. Select the compound from the dropdown list that appears in the reaction toolbar

2. Click the down arrow by the Quick Add in the reaction toolbar and select Left of Arrow as reactant

Similarly add a product by selecting “Right of Arrow as Product” at step 2

5.2.1.3. Generate Name for Reaction Compounds

1. Select a Reactant, right-click within the reaction area

2. Select the Structure -> Convert Structure to Name

5.2.1.4. Add Experimental Data

Stoichiometry table records the data about the reactants and products and allows the users to enter the experimental reaction parameters. It calculates and stores the amount, M.Wt, moles, density, and many other variables. This table is populated automatically as you modify the reaction drawing. Blue values indicate the values typed in by the user; grey cells indicate the values not to be edited.


Reaction Conditions records the pressure, temperature and other conditions of the reactions

5.2.1.5. Adding Solvents

1. Right-click within a cell in the Solvents table and select Add Solvent option

2. Select Solvent from the displayed list and click Add

5.2.1.6. Adding Salts and Solvates

1. Double click in the Molecular formula box

2. Select Salt or solvate from the dropdown list to add to the molecule, click OK

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

5.2.1.7. Add Preparation using Autotext

Enter the procedure for the reaction in Preparation field. Add predefined fragments of text to this field using the AutoText feature

5.2.1.7.1. Creating New AutoText

Users can add their own autotext by editing the files located in the User Configuration folder (Depends on the system configuration)

1. Browse to the User1 -> User configuration folder -> MedChem Autotext Definition

2. Select the New AutoText Item form tool, enter “My AutoText Item” as the name of the item and click create

3. Specify your AutoText. Click Save

5.2.1.7.2. Using AutoText Item

1. Browse to the Reaction section

2. Move the mouse over the items to see the text

3. Double-click the “My AutoText Item” item

4. Double click the phrase to have text entered in field. (Automatically updated when changes are made to reaction)


OR right-click to insert items from the stoichiometry table or reaction conditions OR choose to insert the Custom autotext

5.2.2. Property Table Page

You can use table sections to organize the chemical properties of compounds of your interest. You can add properties to a table, pivot a table, resize columns and rows, and organize columns and rows. You can also insert links to other sections or collections into a table.

For example, you can use Table to organize the chemical properties of the products that are synthesized in reaction section of Chemistry Notebook-01-001 and can further add a Reaction Section (Reaction-AB-10001) link to table cell AB-10001 OR a Biology Notebook-01-001 collection link to table cell AB-10001, where the biological activity from screening assays are stored for the compound (AB-10001) OR an external link.

5.2.2.1. Create and Add Data to Table:

1. Select “Table” from the “New Section” form tool

2. Enter the Compound ID

3. Double-click a table cell corresponding to a structure

The Edit Structure dialog box appears, you can use the Chem & Bio Draw tools to draw the structure. Or, you may copy a standard image file into the field.

4. Draw the structure or paste in the image and click OK

Molecular Formula, Molecular Weight and Molecular Mass fields will be populated automatically

5. Right-click the table and select the “Add Row After” option

6. Follow step 2-4 to add new entries

5.2.2.2. Add a Link to a Table Cell from a Collection in the E-Notebook:

1. Select the Table Section placed under Chemistry Notebook-01 -> Chemistry Notebook-01-001

2. Click the table cell to which you wish to add the reference

3. Click the collection (Biology Notebook-01-001) you would like to reference and, holding the mouse down, drag the collection into


the upper-left corner of the table cell (AB-10001).

Release the mouse, the reference is created, and the text in table cell is converted into blue colored hyperlink.

You may also use the Copy Collection/Paste reference functionality to add the reference (Please refer section 5.2.2.3 for details)

5.2.2.3. Add a link to a Table Cell from a Section in the E-Notebook:

1. Browse to the Chemistry Notebook-01 -> Chemistry Notebook-01-001

2. Right-click the Reaction-AB-10002 section menu icon, and select Copy Section

3. Go to Table Section and right-click within a table cell (AB-10002) and select Paste Reference from the menu that appears

5.2.2.4. Add a Link from a Property List to an External URL

1. Go to Table Section and right-click within a table cell (AB-10003) and select Edit Reference

2. Enter the URL and click OK

The reference is added to the table cell.

Clicking the hyperlink will display the URL you have referenced.

5.2.3. MS Word Sections


You can use the MS word sections to manage the information related to your experiments.

5.2.3.1. Create/Import a Word Document:

1. Select “MS Word Document” from the “New Section” form tool

2. Add information to the MS Word document or alternatively select the Import/Export icon in the right frame

3. Select the Import MS Word Document option

4. Browse to the file to be imported and click Open

5.2.3.2. Export a Word Document:

1. Open the Word section to be exported

2. Select the Import/Export icon in the right frame and choose the “Export MS Word Document” option

3. Enter a name for the file and click Save

5.2.3.3. Clear a Word Document:

4. Open the Word section to be cleared

5. Select the Import/Export icon in the right frame and choose the “Clear MS Word Document” option

6. Click OK for the confirmation message

5.2.4. MS Excel Sections Microsoft Excel sections can be used to manage the Excel spreadsheets in E-Notebook. For example, structural features and biological activity of the studied compounds are manipulated and stored in excel. This allows sorting and helps in identifying most active hits

5.2.4.1. Create/Import a MS Excel section:

1. Select “MS Excel Spreadsheet” from “New Section” form tool

2. Add information to MS Excel section or alternatively select the

Import/Export icon in the right frame

3. Select the Import MS Excel Spreadsheet option


4. Browse to the file to be imported and click Open

5.2.4.2. Export a MS Excel Spreadsheet

1. Open the MS Excel sheet to be exported

2. Select the Import/Export icon in the right frame and choose the “Export MS Excel Spreadsheet” option

3. Enter a name for the file and click Save

5.2.4.3. To clear a MS Excel sheet:

1. Open the Excel section to be cleared

2. Select the Import/Export icon in the right frame and choose the “Clear MS Excel Spreadsheet” option

3. Click OK for the confirmation message

5.2.5. MS PowerPoint Slideshow

You may add MS PowerPoint slideshow section to your Chemistry Notebook-01-001.

Like MS Word and MS Excel spreadsheet sections, it is possible to Import an existing PP slideshow, export the ppt file and delete the existing ppt file.

5.2.6. Capture Image Captured Image Sections let you import, export, view, and annotate images and documents, using the same tools as Adobe Reader software. The section supports a wide variety of file types, such as PDF, JPG, GIF, PNG, TIFF and BMP.

5.2.6.1. Create New Captured Image Section:

1. Select “Captured Image” from the “New Section” form tool

2. To add an image, select the “Import Image” icon. To add a document select the “Import PDF” icon and choose the “Import PDF” option


3. Browse to the file to import and click Open

Export and Clear functionalities are similar to MS Word/Excel section. Please follow section 5.2.3.2 and 5.2.3.3 for details

5.2.7. Spectrum Allows you to view and analyse the spectrum images. You can manage your spectra data easily and effectively using the spectrum and the spectra sections. While Spectrum section can contain a single spectrum, the Spectra section can contain multiple spectrums, organized in subsections or sub tabs

5.2.7.1. Add Spectrum

1. Select “Spectra” from the “New Section” form tool and select the “New Spectrum” option

2. Select Import/Export tool -> Import Spectrum

3. Browse to the Galactic Data file to be imported and click Open

4. Right-click within the “Spectrum Properties” box and select the

“Add property” option

5. Select fields you would like to add to this section, click Add

6. Enter information for the Analysts and Date fields


5.2.7.2. Replace Spectrum

1. From within the section containing the image you wish to copy, click the Import/Export tool -> Copy Spectrum

2. Browse to the section containing the spectrum image you wish

to replace.

3. Click the Import/Export tool -> Paste Spectrum

5.2.7.3. Clear Spectrum

1. Go to the Spectrum section to be cleared

2. Click the Import/Export tool -> Clear Spectrum

This removes only the Spectrum image. Data in the Spectrum properties and Notes will remain as such.

5.2.7.4. Zoom in on a Spectrum Peak

1. Click the spectrum image and drag your mouse to draw a box around the area you wish to zoom in.

2. Click within the box. The zoomed view appears.

3. To zoom out again, simply right-click in the spectrum image.

5.2.8. Ancillary Data


You can use the ancillary data section to associate a file, such as a PDF or PowerPoint file, with a page/reaction page.

5.2.8.1. Create New Ancillary Data Section: 1. Select “Ancillary Data” from the “New Section” form tool, go to

File>Save

2. Select Import/Export Tool and choose the "Import Ancillary Data" option

3. Select the file and click Open. The checksum, source path, and

source file name are populated automatically.

Although the file cannot be viewed or edited from within the E-Notebook, it can be exported to a selected location, and then opened and viewed or edited from there. Export and Clear functionalities are similar to MS Word/Excel section. Please follow sections 5.2.3.2 and 5.2.3.3 for details

5.2.9. History Panel To view the history details of a collection, select the collection in the

collection 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.

6. Searching

E-Notebook makes it possible to search for the Chemical Structures, Text, Collections - Notebooks, Folders, etc. - that meet specific criteria, such as creation date, owner's name, or state, Reaction Search, free Text Search AND Substructure Search

6.1. Setting up Search The sections must be saved before performing any search. For the TEXT search you need to have full text installed on SQL

6.1.1. Conduct Search:


1. Switch to search mode, the Query tab appears

2. Select type of search. The 3 types of search are as follows:

• Simple Text Query: Enter the text string for which you want to search.

• Advanced Text Query: Advanced Text Query allows you to obtain more precise search results. In addition to specify the text associated with the experiment, you can also specify Search Location. You can also specify the metadata about the experiment that you want to search. For example, Collection Name, Owner Name, Creation Date, and Status.

• Reaction Query: Using a reaction query, you can search for the structures. You can also specify other criteria such as reactant name, product name, solvents and reaction conditions associated with a reaction.

3. Select New query from the drop-down list

4. Enter the search parameters

5. You can do one of the following

5.a. Save the Query 1. Click Save Search to the left of the query form

2. Click a collection to select it as the location, and click the Save

The query will be saved under User Collection “User1”

3. Rename the query as “AB-10001 Search”

5.b. Execute the Query 1. Click Search Now to execute the query

A results list appears in the results tab.

6.1.2. Searching for Text with the Query Text Field You can search for the text that is contained in the E-notebook fields such as styled text fields, MS word fields, MS Excel, E-notebook property lists, tables and text in chemical structure fields

Simple Text Search

Advanced Text Search

6.1.3. Searching with Collection Attributes

Click the name of the item to view


6.1.4. Searching with Search Location Field

You can perform the collection search by selecting the location from the dropdown list or you can browse to the root collection over which your search will be run.

Advanced Text Query Reaction query

6.1.5. Chemical Structure Searching Substructure Exact structure Transformation

6.1.6. Reaction Searching

Product Reactants

6.2. Working with query results After executing query, results are displayed in a list, you can save the results list and/or view any item on the list.

6.2.1. To view items in Results list 1. Click the name of the item that you want to open

The Collection Tree appears, with the item displayed.

6.2.2. To save a results list 1. After executing the query, click Save search

2. Click a collection to select it as the location, and click the Save

The query will be saved under User Collection “User1”

3. You can also rename the query.

6.3. Running a saved query To run the query that was saved in the collection tree (Section5.a.): 1. Click Browse and select the query “AB-10001 Search”

2. Right-click the section and select Copy Section


3. Switch to the Search mode, from the More Options select the type of query that corresponds to the query form you are copying

4. Right-click “Simple Text Query” and select Paste Section

6.4. Refining a Search Once a search is conducted, you can further run a query on search results to refine it. The various options available are as follows:

1. Create a New Set of Search Results – Deletes the previous

results and replaces them with the search results generated by the new query.

2. Refine the Previous Search - Uses the previous search results to limit the collections in which a search is done. The stored hit list will contain the intersection of the previous search results and the results specified by the new query.

3. Exclude Collections from the Previous Search - Excludes collections from the stored hit list that are part of the previous search results. The stored hit list is completely replaced.

4. Add to the Previous Search - Adds the results specified in the search query to the previous search results. Duplicate collections and/or sections will not be added.

5. Remove from the Previous Search - Removes the results specified in the search query from the previous search results.

7. Working Offline You can work in offline mode in E-Notebook 12.0 when server or network connection is not available. Each User collection should have only one offline folder. It is created by default as soon as a User first logins in. All notebooks and reactions created will have a reference in the offline folder.

7.1. Working in Offline Mode 1. You can work in the offline mode either by Login to offline mode

from login screen

OR Switch from online to Offline mode on the upper right corner of the E-Notebook screen

You can see that User Collection contains only two collections i.e. User Configuration and Offline folder. All notebooks and reactions created will have a reference in the offline folder.


2. Select page from the Offline folder, make changes and additions as you did in online mode. Click Save

3. Click Connect on the upper right corner of the screen.

4. Specify password and click Connect, the Synchronization Change dialog appears

5. Click show details to review the changes you have done

Click OK to close the dialog

6. Click Synchronize to update all the changes Note: Offline Data is cached in files located in the Temp folder of the currently logged in user.

7.2. Limitation of Offline Mode There are certain limitations while working in offline mode.

1. You will not be able to create new notebooks or any new collections.

2. You will not be able to make any transition changes.

3. E-signature functionality will not be available in offline mode.

8. Batch explorer With the batch explorer, you can view a reaction tree showing successors and predecessors of a selected batch or compound.

Before performing the Batch Explorer, there are two requirements:

8.1. Create a Task: 1. Browse to the User Configuration folder -> Tasks

2. Right-click on the Tasks folder and select Batch Explorer.

8.2. Create a Template 1. In the Collection Tree, right-click Templates folder

2. Select New -> Chemistry Experiment Template, add a reaction section to the template


OR To use an existing template, click and drag the collection into Templates collection to create a new Page, Reactant, etc., and avoid creating a collection from scratch each time

OR Right-click the template in the Collection Tree and select Copy from the menu that appears. Then, right-click the container collection (for example, the Notebook) and select Paste from the menu.

8.3. Working with Batch Explorer

8.3.1. Create Page/Reaction Page As Next Step In Another Notebook

This allows you to create a Chemistry Experiment as Next Step in another Notebook

1. Go to a Notebook -> Chemistry Experiment -> Reaction section, select the product (NH3) of the reaction

2. Click the Batch Explorer tool icon in the reaction section and

select Create Chemistry Experiment as Next Step in Another 'Notebook'

3. Select the Notebook in which you want to create the reaction

page, click Select

4. Select the template to be used for the new Reaction Page, click

Select

Another dialogue appears which tells that a link is set and asks you to navigate to 'Reaction' section of selected Notebook collection.

5. Click Yes for navigation

A reaction page in another Notebook will be created. You can add data to this reaction section.


8.3.2. Create Page/Reaction Page As Next Step In same Notebook

This allows you to create a new page/reaction page within the same notebook.

1. Go to a Notebook -> Chemistry Experiment -> Reaction section, select the product of the reaction

2. Click the Batch Explorer; select “Create Page/Reaction Page As Next Step In same Notebook”.

3. Select a template for the New Experiment and click Select.

4. Click Yes for navigation.

Create your reaction scheme for the Next Chemistry Experiment and follow step 2-4 to complete your preparation.

8.3.3. Create Step Link to Existing Notebook To create a link between two existing ENotebook reactions in same/different notebooks such that the product of one reaction is a reactant in the other. Both the reaction sections should contain valid reactions. Hence a link is created between two pre-existing pages.

8.4. View Batch Explorer Displays a reaction tree showing successors and predecessors of a selected batch or compound.

1. Click the Batch Explorer tool icon in the Reaction Section.

2. Select View Batch Explorer. The Batch Explorer section appears

showing the reactants and products of the current page template in the form of reaction tree.

3. Right-click the molecule to view the options to display predecessors or successors or all steps of the batch.

Select Successors for this batch


Example 8.3.1

8.5. View Synthetic Path View Synthetic Path option allows you to view all the successors and predecessors of the current page template.

1. Click Batch Explorer tool icon in the reaction section

2. Select View Synthetic Path option from the Batch Explorer menu

9. E-Signature (Optional add-on)

With E-Signatures, you can electronically sign a PDF version of your completed page/reaction page. This page/reaction page rendition is then routed to co-authors (where applicable) and witnesses. Once all required parties have signed the page/reaction page rendition, it is stored in a separate database for protection of your intellectual property. E-Signature works on the pages/reaction pages created.

Pages/Reaction Pages have several states which define their lifecycles. You may perform transitions on a page or reaction page to move it from one state to another.

(a) Sign and Close (b) Sign and Keep Open (c) View Signed Versions

9.1. Signing a Document

9.1.1. Sign and Close 1. Right-click on any page/reaction page and select the sign and

close option.

2. Click Yes for the ‘Confirm Sign and Close’ dialog.

The ‘Witness Selection’ dialog appears so that s(he) can countersign it


3. Select witness(es) and click OK. The experiment is now

rendered to PDF and the experiment in PDF format appears which is now ready to submit.

4. Enter UserID and password, select “Reviewed” checkbox, and

click ‘Sign and Store’ that gives the chosen witness read permission to the experiment so that s(he) can countersign it.

5. You will receive a receipt, click OK for the ‘Receipt’ dialog

Once the page/reaction page is signed and closed, an icon is displayed (Lock Sign) in the collection tree. This state will be read-only

6. View -> History shows the status as Sign and Close

7. Select Home Page (User Collection ‘User1’)

The documents sent to you by some other author waiting for your action and a list of documents submitted by you that are still going through the signature process will be displayed

9.1.2. Sign and Keep Open 1. Right-click on any page/reaction page and select the sign and

keep open option


2. Depending on you E-Signatures configuration a witness selection dialog box may appear where you have to select the user and then click Add. Page/reaction page is rendered and displayed in PDF.

3. Enter the password, select “Reviewed” checkbox and click Sign and Store.

4. You will receive a receipt, click OK

5. View -> History shows the status as Sign and Keep Open.

This state may have an optional annotation; it is write only, so that you may provide a reason for a change you wish.

9.1.3. View Signed Versions The signed versions are writable and changes are visible on the screen that can be either printed or exported

1. Open a signed document, right-click and select the “View Signed version” option

2. Select a version to be displayed

3. For the complete version information, click “Show history”

9.2. Modifying a submission To review a document that has been submitted by you,

1. Select your user collection “User1”. Your home page appears in the right frame.

2. Right-click the document submitted by you from “Documents

Submitted by you” list and click the 'Review...’ option

3. Enter the password and select “Reviewed” checkbox

4. Click Modify Submission -> select the witness -> Add -> OK.


5. You will receive a Receipt, Click OK for the ‘Receipt’ dialog

9.3. Recall Document To recall a document that has been submitted by you,


2. Right-click the document submitted by you from “Documents Submitted by you” list and click the “Recall...” option

3. Enter the password, click OK for the ‘Recall Submission’ dialog

4. You Will receive a receipt. Click OK for the ‘Receipt’ dialog

9.4. Cancelling a Document Once a submission has been cancelled, there is no way to resubmit it. To cancel a document that has been submitted by you,

1. Follow steps 1-3 of section 9.2. 2. Click Canceling Submission button

3. You will receive a receipt, click OK for the ‘Receipt’ dialog

9.5. Countersigning a Document To countersign a document that has been submitted to you,


2. Right-click the document you wish to sign from “Waiting Documents” list, and select the “Countersign...” option

3. Enter the password and select “Reviewed” checkbox

4. Click 'Witness' button to verify your approval thus closing the signing process. Hence the document is also closed

5. You will receive a receipt, Click OK for the ‘Receipt’ dialog

9.6. Rejecting a Document To reject a document that has been submitted to you,

1. Follow step 1-3 of section 9.5. Countersigning a Document 2. Click ‘Reject’ to reject your approval to sign and close the

document sent to you.

3. You will receive a receipt, Click OK for the ‘Receipt’ dialog


The rejected submission can again be reviewed by the primary author to either resubmit or cancel the submission.

10. Security The items that are visible to the user in the collection tree are determined by the privileges assigned to you by your system administrator. Security determines which user has read, write, or full control access to that collection.

There are three levels of security permission:

1. Read-only access: only viewing permission, with no editing allowed

2. Read and Write access: editing permission

3. Full Control access: editing permission, and the ability to assign/remove permissions for other users

If a collection is in a read-only state, such as a closed state, no edits will be permitted.

Note: Each collection object may only be edited by one person at a time.

10.1. View Collection Properties You can see specific information about a collection by viewing the Collection Properties

1. Right-click the item whose properties you wish to view, select ‘Collection properties’

2. Click Collection Security or Transition Security tab to view Collection Security or Transition Security properties

10.2. Browsing up to the User Group If you have the required security permissions, you may browse up to the next highest level in the Collection Tree and view the user group at that level.

1. Right-click your user collection “User1”, and select Go Up To, and then the name of your user group “Users”.

Alternatively, you may select View from the menu bar, and then choose the Go Up To option

10.3. Change Access to a Specific Collection You can change the access that other E-Notebook users have to the specific collections. You must have Full Control privileges to the collection, assigned to you by your system administrator

To do this:

1. Right-click the Chemistry Notebook01-001 collection


2. Select Collection Properties -> Collection security tab

User1 has Full control privilege to Chemistry Experiments i.e. User1 can change the access that other E-Notebook users have to Chemistry Notebook01-001 (Chemistry Experiment) collection

By default, each collection inherits the security properties of its parent(s) in the Collection Tree.

10.3.1. To Disable Inherited Security: 1. Right-click the collection (e.g. Chemistry Notebook01-001) for

which you wish to disable inherited security. A menu appears.

2. If Inherits Security is checked, select it to clear the checkmark.

Inherits Security is disabled.

10.3.2. To Change the Security Properties/ Transition Security of a Collection:

1. Right-click the collection whose Security Properties you want to change

2. Select the Collection Properties option

3. Click the Collection Security /Transition tab

Groups and Users who have permission to access this item or to apply a transition to this item will be displayed under Inherited or Assigned permissions list

4. Click Grant, the ‘Grant Access To User Or Group’ dialog

appears

5. Select the User you wish to grant access, click Continue


6. Select Collections and click Grant

7. Highlight a User and select ‘Read and Write’ from ‘Type of Access for User3’ drop down list

8. Click OK to close the dialog Note: Inherited Permissions are permissions inherited from the parent collection in the collection tree. These permissions can not be changed from this dialog. Only the Assigned Permissions can be changed from this dialog.

11. Using the Session Manager

In certain situations an E-Notebook session may be left open. With the Session Manager, you can end your old session, and release any collection that may be locked by it.

11.1. Access the Session Manager 1. Right-click any blank area in the Collections Tree

2. Click the Session Manager....

This dialog shows the Users, Session numbers and Start Times for each current session.

11.2. Ending a Session

1. Click the session in the list.

2. Click the End Session

3. Click Yes.

The session is ended. Any record that was locked by the session is released.