Computational Lab Notebooks

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Documentation for installing and using cln, a command line program to help you set up and manage a computational lab notebook using git and git-annex.

It's inspired by Rails ActiveRecord migrations, in that it helps you prepare, run, and commit actions.

This documentation is a work in progress. For suggestions, corrections, and pull-requests, please visit the issue tracker or the documentaion GitHub repository.


Keeping a good lab notebook for your work is key for data scientists and computational biologists. We know it is important, but it can be challenging to implement in practice. The cln program helps to automate some of the more tedious aspects of managing a computational lab notebook using git and git-annex. It helps implement a workflow that gives you a nice, searchable git history and provenance tracking for your files.

For more background information and motivation, see my blog post introducing the software and workflow.



license MIT or Apache 2.0

The cln program is licensed under the Apache License, Version 2.0 or the MIT license, at your option. This program may not be copied, modified, or distributed except according to those terms.

You can view the license files here: MIT and Apache v2.0.


Creative Commons License

© Ryan Moore, 2021. This work is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.