This topic is under construction for the 22.3 (March 2022) release of LabKey Biologics. For the previous version of this documentation, click here.
Notebooks give you a place to collaboratively record your research. You can have as many notebooks for as many projects as your team requires.
Create New Notebook
To create a new notebook, click Create New Notebook
from the Notebooks
- Enter a Name.
- Select the Project from the dropdown. Whether this field is required or optional is controlled by an administrator setting.
- If you are an administrator, you can click Create new project to add a new project to the system.
- 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 "1003", the date it was created was June 21, 2021, and it is the first one created in this project.
Create New Project
During notebook creation, the author can select an existing project. If that author is also an administrator, they have the option to click Create new project
to add a new one.
- Give the project a name, description, and set a color.
- Click Create Project.
Learn more about projects in this topic:
Rename a Notebook
A notebook author can select Rename
menu next to the name. Non-authors will not see the Rename
option on this menu. 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.
Give your new notebook a name, select a project (the project of the one you copied is the default), and 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 Biologics application, and support entry-specific comment threads.
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.
A new empty notebook looks like this:
The header section lists the name and ID, the authors, shows the project (if any), and shows the status. A details panel to the right summarizes references for all entries, may include attachments, and can be hidden by clicking Hide details
(and shown again by clicking show details).
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 a table, attachment, new day, or reference
- Styling menu: Defaults to Normal and offers 3 heading levels
- Special characters: Add mu, delta, angstrom, degree, or lambda characters
- Bold, Italics, Underline
- : 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 or bullet lists
- : 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
anything in the Biologics registry.
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.
Once added, the reference appears as a color-coded lozenge in the text, and is also added to the Referenced Items
list in the details panel.
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 sampleIDs 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 of reference.
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.
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 an attachment to an entry, select Insert > Attachment
. To add to the notebook as a whole, click the Attachments
area in the Details panel on the right (or drag and drop attachments from your desktop).
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.
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
in the popup to apply the changes.
Export Notebook as PDF
To export a notebook as a PDF, you must have correctly configured the Puppeteer
service. Learn more in this topic: Configure Puppeteer
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, provide a deadline, and comments if needed. You'll sign with your display name or email (click Configure name
to set the display name to use). Check the box to certify that the data contained in the notebook is accurate. Click Submit Signed Notebook
Learn more about the notebook review process in this topic: