1. Core LIMS Training: Electronic Laboratory Notebook

2. Course Topics Navigating to Notebooks and Entries Creating Notebooks
Creating Entries
Entering Data
Making Notebook Templates
Registering Samples to the LIMS
Editing Notebook Entries
Closing and Signing Entries
Searching Notebooks
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3. What is an ELN?
An Electronic Laboratory Notebook (ELN) is a software program intended to capture raw discovery data traditionally stored in paper laboratory notebooks
It records signatures through user-authenticated passwords and automatically records an electronic audit trail of all data events
An ELN enables electronic searching of chemical structures and other data to leverage your current knowledge base
An ELN can increase access to raw data between scientists working collaboratively on a project
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4. How Do I Get To My ELN?
If you are not already there by default, select the ELN application from the application menu OR click on the ELN icon from the home page
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5. The Tree Viewer Panel
You can see the notebooks in a folder structure from any page in the system in the Tree Viewer panel on the left side.
If the Inventory or History section was last displayed, you will need to click on the plus icon in the ELN bar to expand the ELN section
Click on the left facing arrow between panes to minimize the Tree Viewer panel. Click on the right facing arrow to expand it again.
Notebook Type (Public/Private/Notebook/Template)
Notebook Name
Barcode: Entry Name 1
Barcode: Entry Name 2
Section Name 1
Section Name 2
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6. How Do I Find A Notebook?
You can click on the folder of an existing notebook in the Tree Viewer to open the notebook record in the main panel.
OR you can also select List All under the Notebooks menu. You can then follow the hyperlink to your desired notebook.
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7. How Do I Find the Table of Contents?
The Notebook Details page has general information about the notebook (name, author, number of pages, etc.)
The View Entries hyperlink will send you to the Table of Contents
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8. How Do I Find an Entry?
In the Tree Viewer, you can click on a gear icon to open a page
OR in the Table of Contents, you can follow a hyperlink to the desired entry
OR you can type in the barcode into the Quick Find Tool and click the black arrow
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9. Key Notebook Concepts A notebook is a collection of pages or entries
A notebook entry is the page where you store and sign off on the actual data; it can contain one or many sections to logically organize similar data together
A template notebook is a collection of template pages that contains sections or default data that you can copy to save time entering data into a notebook page
There is no limit to the number of notebooks or templates you can create (unless you have corporate rules in place); ideally one notebook per user per project works well for searching
There is no limit to the number of entries you can have in a notebook (unless you have corporate rules in place)
A user can have multiple notebooks and can add entries to any active notebook as needed (you do NOT need to fill notebooks one at a time in sequential order)
You can assign multiple authors to a notebook (but they do need to sign their own entries)
Notebooks can be public (viewable by all users) or private (viewable to author only in tree viewer, but can be accessed by directly entering barcode); administrators can also configure project-based security to limit access when needed
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10. How Do I Create a New Notebook?
Select Create under the Notebooks > Notebook menu (remember you should be in the ELN application)
Enter a descriptive name – it will appear in the Tree Viewer
Tip: It is a good idea to develop a standard naming convention for notebooks in your company
Unless you want to limit access to yourself, leave the private box unchecked
Select the notebook author(s)
Select a queue so that your witness will know when to sign your notebook
Click Create New to save
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11. How Do I Create a New Entry?
Note that your user notebooks will be stored under the My Notebooks folder (If you made it public, other users will see it in the Public folder)
OR you can click on the New Entry hyperlink on the Notebook Details page
You can create a new entry by right clicking on your notebook folder in the Tree View Panel and selecting the Add New Entry menu
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12. Define the Page Layout
By choosing a template (or not), you are roughly defining the outline of the notebook entry; you can still add sections later
A title is optional; however the title is displayed in the Tree Viewer and can be used in searches later
The top option lets you select from an existing notebook template collection and template page
OR you can use the bottom option to create a blank page and add the sections you need to it later
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13. Entering Data Concepts
You are not required to enter data in every section, but an administrator may define a field within a section as mandatory (must be filled before section can be saved – it will be marked with an asterisk)
You can always leave a record partially complete and return later to enter more data
Be sure to save each section before moving to a new one
Unless the system has been configured to enforce section order, you can enter data in any order
Data is viewable by anyone with access as soon as it is entered
You can add or remove sections as needed
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14. Enter Reaction Data Draw or copy/paste structures in the sketch window
Tip: You can paste SMILES strings into the sketch and they will automatically render
Click on the double down arrows to expand a section
Click the Save button (there are more than one) to populate the reactant/product tables below
Tip: Use the “Clean” tool under Structure>Clean 2D menu to standardize bond angles and lengths
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15. Entering Registered Reagents
Instead of drawing a structure, you can also search for reagents/agents/solvents registered in the database and select items to add to the reaction sketch above
3) Click on the desired row in the pop-up search results window (Note: hits may be sample, lot, or container records)
4) Reagent structure will be added to the sketch and data will be added to the Reactant table
1) Type in the reactant barcode in reactant table search box
2) Click the Search button
Solvents and Agents can be searched by name
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16. Reactant and Product Tables
Enter the amount of reactants you added to the reaction and the mmols will automatically be calculated (Note: the limiting reagent and # of equivalents needs to be defined first)
If you enter the amount for the limiting reagent, the other reagents will automatically populate, but they can be modified if you want to add the actual amount used later
Don’t forget to save your changes!
You can move/hide columns on the fly or an administrator can change default table layout
Click on cells to edit # of equivalents of which reagent is limiting 2 1 3
The theoretical mass will automatically be calculated based on the limiting reagent; Enter the actual mass and the % yield will automatically be calculated
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17. Filling Out Stoichiometry Tables
The recommended workflow to filling out reactant and product tables is:
Save the reaction sketch or lookup reagents to populate the molecular weights in the stoichiometry tables
Verify the default limiting reagent is correct; modify it if needed
Enter the quantity of limiting reagent first; this will automatically calculate amounts you need to measure out for other reagents
If not a solid, you can add densities to automatically calculate the desired volume
Verify the desired equivalents of other reactants are correct and modify if needed; the amounts of other reagents will adjust
Save your results and physically complete the reaction
If you need to adjust the reagent amounts actually used in the experiment, update the values; mmols and equivalents should adjust; Save any changes
Once the product is isolated, enter the recovered amount of product and the purity; yield will automatically be calculated
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18. Stoichiometry Table Notes
Prior to saving, values that have been manually entered will be displayed in blue text; Values that were previously saved or automatically calculated will be displayed in black text
Reagents that are mixtures (for example, 10% Pd/C) should fill the quantity in the Substrate column (instead of mass) and enter the percentage of active agent in the Subs. Wt % column
The number of digits you enter for the mass will dictate how many significant figures will be returned for the mmols
If you need to modify table values in the middle of the process, you may need to clear the cell that you want to calculate in order to trigger the automatic update
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19. Uploading Images
In an Image section you can upload image file formats (jpg, gif, etc) to be displayed directly in the section (instead of as an attached document which would have a hyperlink to view the image in another page)
Click on the upload hyperlink and browse to the file
The image will be displayed in the section
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20. Office Tools
The ELN incorporates Think Free applets to let you type formatted documents, build spreadsheets, and slide presentations right in your notebook.
You can import files you have already created using standard office tools
OR you can copy/paste or create content directly within the section
Use the save buttons on the web page instead of within the applet
Tip: This can be a good way to add annotations to images and control image size
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21. Attaching Other Documents
Files will make and store a local copy (file updates not recorded automatically)
Database may impose limits on size and number of attachments, but no theoretical limit
Users will need application on their computer to view file content
OR you can attach unstructured generic files (literature references, etc.) to the entry (click on Files icon)
The ELN can be configured to have specific files be attached to certain sections for more structured searching later (click on Upload link to browse to file – this will create a hyperlink to view the file contents)
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22. Reusing Data Action Description When To Use Copy
You can make a copy of any closed entry (from any public notebook) or any entry from your private notebook into your own notebook
If you have similar data that is easier to modify from another single experiment than to enter it from scratch
Add To Template
You can make a copy of any closed public entry or any of your private entries into your own notebook template
If you have a general experiment that you run many times with only small amounts of new data values to enter
Create or Use Public Template Notebook
You can build your own template notebook and entries from scratch and share them for anyone to use
If you want to have everyone in a group follow a standard entry format with the same section organization
Create or Use a Private Template Notebook
You can build your own template notebook and entries from scratch and add default data that you frequently use
If you want to pre-enter the data and section organization you always enter for almost all experiments
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23. How Do I Copy Entries?
To make a copy of this page into your own notebook click on Copy
To see the Copy/Add to Templates hyperlinks the entry must be closed or be created by you
To make a copy of this page into your own notebook template click on Add to Templates
You will be asked to select from a list of your notebooks or notebook templates where the copy should go
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24. How Do I Create a New Notebook Template?
Select Create under the Notebooks > Template Notebook menu (remember you should be in the ELN application)
Enter a descriptive name – it will appear in the Tree Viewer
The major difference between creating a notebook and a template notebook is that you do NOT need a signature workflow for a template;
Since you will probably have fewer template entries than notebook entries you may want to just store all template pages in a single notebook
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25. How Do I Create a New Template Page?
Select the New Template link when you are on the Template Notebook Details page
You can modify another predefined template to create your own template in the top section
OR you can create your own template from scratch in the bottom
Enter a descriptive name – it will appear in pull down lists
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26. Select A Section or Template
Choose the first section type for the page and select the Add Section button
Sections have pre-defined functionality that can be modified by an administrator, but users only need to select sections
OR you can add a group of sections at once by copying a template entry
Tip: Users can enter data in any section and any order they want unless section rules are enforced. However, you cannot reorder how the sections are displayed so select them in display order
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27. Adding More Sections
If you return to this page and are missing the Add New Section, click on the Add/Edit Sections hyperlink to get it back
You can view (and enter data) into the first section by expanding the down arrows
Add as many new sections as you want using the same pull down menus
Tip: If there is data you commonly enter for many pages, you can save it as default data in your template sections to minimize your typing time
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28. Hands-On Practice
In a TEST system (don’t use your production environment, if possible),
Create a new notebook template
Create a template entry (you may copy from a template or start from scratch)
Add a reaction section and an image section
Create a new notebook
Create a notebook entry using your notebook template
Enter a sample reaction
Enter the mass of the reactants added and products recovered in the stoichiometry table
Upload a dummy image file
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29. How Do I Register a Sample to the LIMS?
Final products that you want to test in biological assays should be registered as small molecules. Click on the Register hyperlink which will transfer you to the sample registration.
Most chemistry ELN’s should choose small molecule
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30. Register the Sample
For compound registration you need to enter sample details on one page and once that is registered, you enter lot information on the second page.
For more detailed information on compound registration in general, see the Compound Registration training slides.
Leave the name blank if you want the system to automatically assign a barcode (also ignore name on lot page)
Do NOT modify the structure here (make any changes in the ELN before registration)
When you click Create New, the system will check to see if a duplicate structure has already been registered, register the sample if it is new, and then bring you to a page to register the lot
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31. Register the Lot and Container
On the lot registration page you can:
enter any details about the lot
add a hyperlink to the ELN entry
create container records
Add the barcode of the ELN if you want to have a hyperlink on the page link back to the ELN page
You can always create a container later, but it may save time to create the container record now (the Create New Lot button will create both the lot and container record if you enter container information)
Tip: You can drag and drop a location from the Inventory folder in the Tree Viewer if you don’t know the barcode
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32. Links Between ELN and LIMS
Once the sample, lot, and any containers are registered, you will be returned to the ELN entry
You should see hyperlinks to any newly created records in the Products table
If you added the association to the Lot you will see a hyperlink from the Lot Details page or any Container Details pages
From Sample or Lot Details pages, click on the ELN icon
Follow the View Details hyperlink to get a link to the ELN page
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33. Editing Notebooks
You can only edit notebook entries when they are open – entries that are closed or signed can not be modified unless they are reopened
You can not permanently remove a notebook, template or a notebook entry from the database, but you can deactivate a record to remove it from view and searches
A deactivated notebook will remain viewable if there is an active entry within it
When open, you can add or remove sections and change content within sections
You can only edit your own entries (not even an administrator can write to your entry)
Every time an entry is opened or re-opened for editing the event is logged
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34. How Do I Deactivate a Record?
Click on the Edit Icon
Tip: If you are editing a record, you may want to add a comment to explain why
Deselect the Active Checkbox and save changes
If you are deactivating an entry, it must first be open and you must be the original author
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35. How Do I Change Sections?
Use the Reopen hyperlink to enable editing if an entry is closed
Click on hyperlink to add new sections
The record must be open
Click on Remove to delete sections (you will not be able to “undo” and restore original content)
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36. How Do I Change Content? The record must be open
Don’t forget to save your changes before leaving the page
Just add or modify content in text boxes as needed
Non-editable fields (like Barcode) will not give you a place to enter or change data
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37. How Do I Change Reactions?
If the record is open, you can modify the reaction sketch and stoichiometry tables
When you save changes to the sketch, the molecular weight and mmols will update in the stoichiometry tables
Note: If you modify a registered product, you will need to edit the small molecule record too!
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38. How Do I Change Attached Docs?
For uploaded files and images, click on the edit hyperlink to browse to a new or updated file
The display or hyperlink to view file will be replaced with the most recent uploaded file
The original files can still be viewed from the edit hyperlink
For docs attached under the Files icon, click on the View Details and deactivate the File Details record to remove the file.
Add new docs if needed
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39. Compare Versions
If a notebook has been reopened after it was closed, there will be a Compare Versions report in the Events section so you can drill down to see what was edited
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Open the PDF records for snapshot of data at that time

40. Hands-On Practice
In a TEST system (don’t use your production environment, if possible),
Register the product into the LIMS (create a lot and a container)
Navigate between the Lot/Container/ELN pages
Make some edits to your entry (modify content, upload a new image, modify the reaction, remove or add a section, etc.) and save the changes
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41. Closing and Signing Entries
Closing Entries
Takes an entry out of editable mode (prevents accidental modification)
Can still be reopened to allow edits
Adds an entry to an author’s signature queue (if in a signature workflow)
Executed by clicking on a hyperlink
Signing Entries
Entry needs to be closed first before it can be signed
Each entry needs to be signed by an author and a manager (or other witness)
Requires a password to execute
When an author signs an entry it will move into manager’s signature queue (if in a signature workflow)
You can only sign one notebook page at a time
You can still reopen your own signed entries, but you will need to close and resign them again
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42. Closing an Entry Open entries have a plain gear icon
Closed entries have a pencil on the gear icon
Click on the Close hyperlink to close the entry
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43. Sample Closed Entry
Add/Edit Sections and Close hyperlinks replaced by Download PDF, Sign, and Reopen
Can view data in PDF or in a non-editable web page
Closed status updated to Yes
Entry is not marked complete until it has the author signature
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44. Closed Entries Added to Author Signature Queue
1) Click on My Queues icon on the main home page
2) Click on your author signature queue to view Queue Details
3) The entry you just closed should be at the bottom of the task list
4) Entries that are signed or reopened will automatically be moved out of this queue
Tip: You can view this list to find any entries you have forgotten to sign
Note: Your administrator can configure either a shared queue/signature workflow (where all authors/managers use the same task lists) or individual queues/signature workflows (where authors or managers might see only their work but might have to go to multiple queues to see all work tasks
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45. Signing an Entry (Author)
Click on the Sign hyperlink (it will be missing if you are not the author or the entry is not closed)
A PDF of all data is automatically generated and displayed at the top
Tip: Mouse over the title to get a menu to print the PDF
Use the scroll bar to view entire PDF
Scroll to the bottom and click on the Sign This Entry hyperlink to enter password
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46. Enter Electronic Signature
Use the same user name and password as you do to log into the system
Be sure to check the check box
Click on Create New to execute the signature
Entry will be moved to the Management Signature Queue
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47. Signing an Entry (Manager)
Tip: Check your Management Signature Queue to find all pages you need to sign
Click on the Sign hyperlink (it will be missing if the author has not signed the page yet)
Only the author can reopen the entry so hyperlink is not live
Scroll to the bottom and click on the Sign This Entry hyperlink to enter password like the author
If you do not have permissions, you will get an error message
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48. Completed Entry
Green Check Icon indicates completed entry with 2 signatures
The author can still reopen a signed entry, but must close and resign again to complete entry
Entry is closed
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49. How Do I Search For An Entry?
Select Query under Entries>Entry Menu to get a query interface
This search filters for entries by Demo User that contain Amidation in the title (multiple filters are an AND query)
Naming entries with keywords makes it easier to find them using an Entry Query
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50. How Do I Do A Structure Search?
Use the Query under the Sections>Reaction menu
Note: You can use filters on other tabs to fine tune the query
Substructure is the default, but exact and similarity searches are also supported
Use an arrow to indicate whether you are searching for reactants or products
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51. Query Results Returned In Interactive Table
Different columns can be on different tabs (this is configured by your administrator)
Click on a hyperlink to view the entry you want
Tip: You can drag and drop column order or hide columns on the fly
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52. Hands-On Practice
In a TEST system (don’t use your production environment, if possible),
Close your entry
Find your author signature queue
Sign your entry
Search for an entry created by you after a certain date
Do a substructure search for your entry
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