This topic is under construction for the 23.7 (July 2023) release of LabKey ELN. For the previous version of this documentation, click here.
— Available in LabKey Biologics LIMS and the Professional Edition of Sample Manager. Learn more
or contact LabKey
Notebooks give you a place to collaboratively record your research. You can have as many notebooks your team requires. Use custom tags to categorize them by project, team, or any other attribute you choose. This topic covers the process of authoring a notebook, including creating it, adding to it, editing it, and submitting it for review.
Create New Notebook
To create a new notebook, click Create Notebook
from the Notebooks Home
- Enter a Notebook Title.
- Select the Tag from the dropdown. Available in LabKey Biologics LIMS only. Whether this field is required or optional is controlled by an administrator setting.
- If you are a Biologics LIMS administrator, you can click Create new tag to add a new one.
- Enter a Description.
- Select Start and end dates.
- By default, You are an author. Use the selection menu to add more Co-authors.
- If you have templates defined, you can choose one to use by clicking Browse Templates.
Notebook ID Generation
When you create a new notebook, a unique ID value is generated for it. This can be used to help differentiate notebooks with similar names, and cannot be edited later. The format of this ID is:
For example, the user creating the notebook here has assigned User ID "1006", the date it was created was November 30, 2022, and it is the second one created on this server.
Expand and Collapse Detail Panel
The left panel of the notebook screen displays a table of contents, full listing of references to this notebook as well as items this notebook references, and attachments for the notebook and any entries. This section can be collapsed by clicking the
and expanded again by clicking the
Create New Tag (Biologics Only)
During notebook creation in LabKey Biologics, the author can select an existing tag. If that author is also an administrator, they have the option to click Create new tag to add a new one
Learn more about tags in this topic:
Add Custom Fields (Experimental Feature)
To define and use custom fields for your notebooks to support additional classification that is meaningful to your team, you must first enable the experimental feature "Notebook Custom Fields"
Once enabled, you will see a Custom Fields
section. Use Add custom field
to select an existing field to add to this notebook. Type ahead to narrow the list of existing fields to find the one you want. Shown here, the "ColumnTemperature" field is added and you can now provide a value for this field for this notebook.
To manage the set of custom fields available in your application, click Manage custom fields
. In the popup you can see the existing defined fields and how many notebooks are currently using them. Here you can also add new fields, and edit or remove any fields not currently in use. Click Done Editing Fields
Rename a Notebook
A notebook author can click the
to rename a notebook. Non-authors will not see the edit icon. While the system does not require names to be unique, you will want to choose something that will help your colleagues identify it on lists and dashboards.
Copy a Notebook
Once you have created and populated a notebook, you can copy it to create a new notebook with the same details. This is similar to creating a new notebook from a template
, except that templates do NOT include the value of any custom fields, and copied notebooks do include these values. You do not need to be a notebook author to make a copy of it. Select Save As > Copy
Give your new notebook a name, and if using within Biologics, you can select a tag (the tag of the one you copied is the default). Click Yes, Copy Notebook
to create the new one.
Add to a Notebook
A notebook lets you record your work in a series of entries
, each of which can have a custom name, span multiple days, include references to data in the application, and support entry-specific comment threads.
The Table of Contents
on the left lists the entries, references (both to this notebook and from this notebook to other entities), and attachments. On the right, the header section lists the name and ID, the authors, shows the tag (if any), creation details, and status. A new empty notebook looks like this:
As you complete your notebook, everything is saved automatically. Note that refresh is not continuous, so if you are simultaneously editing with other authors, you may need to refresh your browser to see their work.
Add to an Entry
The New Entry
panel is where you can begin to write your findings and other information to be recorded.
The formatting header bar for an entry includes:
- Insert: Select to add:
- Styling menu: Defaults to Normal and offers 3 heading levels.
- Font size: Defaults to 14; choose values between 8 and 96 point type.
- Special characters: Add mu, delta, angstrom, degree, lambda, less than or equal, greater than or equal, and plus minus characters.
- Bold, Italics, Underline, Strikethrough
- : Link selected text to the target of your choice.
- / : Make a text selection a super- or sub-script.
- Text color. Click to select.
- Alignment selections: Left, center, or right alignment; indent or dedent.
- : Numbered (ordered) lists
- : Bullet (unordered) lists
- : Checkboxes
- and : Undo and Redo.
- : Clear formatting.
Rename an Entry
next to the "New Entry" title to rename it.
Add a Reference
Within the entry panel, you can use the Insert > Reference
menu, or within the text, just type a '/' forward slash to reference
an available resource.
The / menu lets you select the category you want to reference:
If you click Samples
you will next be able to click one of the existing Sample Types
, then can type ahead to Search
within that category, or the most recent entries in that category are shown.
When referencing Assays, if the Assay Type you choose includes Batch fields, you'll have the option to reference either runs or batches.
Once added, the reference appears as a color-coded lozenge in the text, and is also added to the Referenced Items
list in the Table of Contents
panel. Click the
to expand the Samples
Add References in Bulk
After selecting the type of reference you want to add, you can click Reference multiple [type of reference]
In the popup, you can:
- Paste (or type) your references into the box, one per line. Use Sample IDs as shown below, for example.
- Click Upload file to upload a file of references, supported formats include .csv, .tsv, .txt
- In the case of samples, assays, media, or registry entity references, click Change [category] to switch types within that category.
Click Add References
to add them.
If any pasted or uploaded references cannot be found, you'll see a warning listing the invalid references (valid references are not shown in the warning.
You can either:
- Correct any errors and click Recheck References
- Or click to Skip and Add References, proceeding without the ones not found.
Add a New Day
Place the cursor where you want to add a marker for a new date. Select Insert > New Day
. A date marker
will be added to the panel for today's date.
Hover to reveal a
delete icon. Click the day to open a calendar tool, letting you choose a different day to reference. Record activities for that day below the marker.
Comment on an Entry
Click Start a thread
to add a comment to any entry. Each entry supports independent comment threads, and an entry may have multiple independent comment threads for different discussions.
By default you will enter comments in Markdown Mode
; you can switch to Preview
mode before saving. Other dashboard options include bold, italic, links, bullets, and numbered lists. Click the
button to attach a file to your comment.
Type and format your comment, then click Add Comment
Once your comment has been saved, you or other collaborators can click Reply
to add to the thread. Or Start a thread
to start a new discussion.
For each thread, there is a
menu offering the options:
- Edit comment (including adding or removing files attached to comments)
- Delete thread
Attachments, such as image files, protocol documents, or other material can be attached to the notebook.
- To add to the notebook as a whole, click the Attachments area in the Table of Contents area on the left (or drag and drop attachments from your desktop).
- To add an attachment to an entry, select Insert > Attachment. You can also paste the image directly into the entry; it will be added as an attachment for you.
Once a notebook has attachments, each will be shown in a selector box with a
- Copy link: Copy a link that can be pasted into another part of an ELN, where it will show the attachment name already linked to the original attachment. You can also paste only the text portion of the link by using CMD + Shift + V on Mac OS, or CTRL + Shift + V on Windows.
- Remove attachment
Note that the details panel on the left has sections for attachments on each entry, as well as "Shared Attachments" attached to the notebook as a whole. Each section can be expanded and collapsed using the /
Add a Table
You can add a table directly using the Insert > Table
menu item, directly entering content. You can also paste directly from either Google Sheets or Excel either into that table, or into a plain text area and a table will be added for you.
Adjust Wide Tables
After adding a table to an ELN
, you can use the
table tools menu to add/remove columns and rows and merge/unmerge cells. Drag column borders to adjust widths for display.
When configured, you'll be able to export to PDF and adjust page layout settings
to properly show wider tables.
Entry Locking and Protection
Many users can simultaneously collaborate on creating notebooks. Individual notebook entries are locked while any user is editing, so that another user will not be able to overwrite their work and will also not lose work of their own.
While you are editing an entry, you will periodically see that it is being saved in the header:
Other users looking at the same entry at the same time will be prevented from editing, and see your updates 'live' in the browser. A lock icon and the username of who is editing are shown in the grayed header while the entry is locked.
Your notebook can contain as many entries as needed to document your work. To add additional panels, click Add Entry
at the bottom of the current notebook. You can also add a new entry by copying an existing entry.
You cannot completely delete an entry in a notebook. Archiving an entry collapses and hides the entry.
- You can immediately Undo this action if desired.
- Note that when an entry is archived, any references in it will still be protected from deletion. If you don't want these references to be 'locked' in this way, delete them from the entry prior to archiving. You could choose to retain a plain text description of what references were deleted before archiving, just in case you might want to 'unarchive' the entry.
Once multiple entries have been archived, you can display them all again by selecting Archive > View Archived Entries
at the top of the notebook. Each archived entry will have an option to Restore entry
Return to the active entries using Archive > View Active Entries
Create a duplicate of the current entry, including all contents. It will be placed immediately following the entry you copied, and have the same name with "(Copy)" appended. You can change both the name and position
Select to open a panel where you can drag and drop to rearrange the entries. Click Save
to apply the changes.
You cannot delete a notebook (just as you cannot fully delete a notebook entry
, but you can Archive
it so that it no longer appears active. Archived notebooks will be locked for editing, removed from your list of recently accessed notebooks, and will no longer show in your active notebooks. They can be restored at a later time.
To archive a notebook, select Archive > Archive Notebook
from the top of the notebook editing page.
Access Archived Notebooks
From the Notebook Dashboard
, select Manage > Archive
. You'll see a grid of archived notebooks making it easier to restore them or otherwise access their contents.
(i.e. undo the archiving of) a notebook, open it from the archived Notebooks list
and click Restore
Submit for Review
When your notebook is ready for review, click Submit for Review
You'll review your entries, references, and attachments to confirm you have included everything necessary, then click Go to Signature Page
- Select one or more reviewers from the Request review by dropdown. You'll see individual users as well as any project groups that have been assigned the "Editor" role.
- You can also provide a deadline, and comments if needed.
- Verify your identity by providing your LabKey login, i.e email address and password. This verification positively identifies the submitter.
- Check the box to certify that the data contained in the notebook and all attachments are accurate.
Click Submit Signed Notebook
Learn more about the notebook review process in this topic: