A Guide to Using the Benchling Notebook

Roger Pellegrini

Cutting edge research requires cutting edge tools. Here's a short guide to help you transition from a paper notebook to the Benchling platform.

1. Projects are for long term goals

Projects are the central hub of all the work you do on Benchling. Projects can help you:

  • Organize all data in one place for a research goal

  • Share data with your whole lab

  • Manage who can access and edit your data

I created project folders for the two goals I'll be working towards in the next month:


2. Create an entry for each experiment

Entries are the system of record on Benchling and replace pages in a paper notebook. You should:

  • Create a notebook entry for every experiment

  • Use the Insert New Days feature to plan multi-day experiments

  • Use the @-symbol to reference any Benchling file

  • Make todo lists for daily tasks

I will be cloning some CRISPR guides today - Benchling makes it easy to reference my DNA sequences for ligation.


3. Create and reference protocols

Protocols allow you to standardize written procedures. Here's what I did for my gRNA cloning experiment:

  • Created a master protocol for my ligation step with T4 DNA Ligase

  • Attached my protocol to my BRCA2 gRNA Cloning entry to get a copy of the master protocol

Tip: Turn up your speaker volume and use Benchling's inline timers for time sensitive methods.

4. Use organizations to share data with your lab

Create an organization for your lab to easily share your data and notes. I use organizations to share my protocols with the lab. You can too:

  • Create an organization from the organization section on the right side of the home screen

  • In the left navigation bar, you'll see a new default shared project for the organization based on your org's name (i.e [Lab Name] Shared Project)

  • Put all your protocols in your shared project - your lab mates can now use your protocols!

5. Export your notebook in a few clicks

All data can be exported - notebook pages will be exported as pdfs.

  • Right click on a project and select Export

  • Select the projects that you want to export and select a date range

  • Click Export to receive an email of your exported notes


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