Register a strain collection in Benchling¶
🎯 This guide will show you how to upload an entire strain collection from a spreadsheet to Benchling following a Notebook template.
You may want to do this if…
You have an externally stored collection (for example, in a spreadsheet) and you’re interested in sharing with others through Benchling
You want to be able to link strains in your Notebook entries (also referred as “tagging” in Benchling, e.g., @MyStrain)
You want to keep track of the links between parental and child strains, therefore create a lineage of your strains
You’d like to keep a record of where all your strains are stored and when they are used
You’d like to upload strain-related metadata to Benchling at the end of a project or before leaving Biosustain, to make sure that data is not lost over time
You’d like to promote FAIR data! 😄
⚠️ If you need to register only a few strains, and not an entire strain collection, you might find it easier to follow this guide instead.
Before starting¶
The only prerequisite to the following steps is to have a spreadsheet with metadata related to your strains.
Template overview and guide¶
Create a Notebook entry based on the template.
You will need the Registration of Strain Collection template, which you can find under the LIMS Support folder, as seen in the picture below.
The template should look like this:
Watch the video to understand how to use the template.
Troubleshooting¶
If you run into any issues while registering your collection, read through this list and see if you can find a solution.
General tip: Refresh the Benchling tab you are working on. This can help when entity links are not being detected properly.
“I submitted a registration table and realized the entities were saved to an unwanted place.”
By default, the entities will be saved to the folder where the template ELN is located. This can be changed in the Registration table settings.
These settings can only be modified before submitting entities. If you made a mistake, you will have to move them manually to the desired location; and create a new table for future entities of the same schema that you’d like to register.
“While setting up a registration table, I deleted a column that is important for me. How do I bring it back?”
This can be done easily by following these steps:
Right click > Insert column left/right > Select the column you’d like to bring back
“I can’t find a field that matches my spreadsheet on the registration table.”
First option: look for a field that could allow for the type of data you want to store and add a note on your ELN regarding this.
Second option: Add a custom field/column
This only supports the following data types: text, integer, decimal, boolean, date, and datetime.
Third option: Reach out to us to potentially add a new field to the schema. This may or may not be possible.
“I registered some plasmids that are not in Benchling, and now I’d like to upload the sequences to the corresponding entities. How can I do this?”
You can update your registered plasmid entities with the “Reimport DNA sequences in bulk” option.
You only need to upload a file with the same filename as the entity name, and the entity will be updated accordingly, keeping the fields that had already been filled.
If you have any other problem, don’t hesitate to contact us at lims_support@biosustain.dtu.dk!
Additional resources¶
Links that could be helpful
Once your collection is uploaded to Benchling, you can use lookup tables to easily find specific information related to your strains in your experiment ELNs.
If you’d like to know more about the inventory system in Benchling and how you can use it to track your strains, you can check out the Benchling guides.