Using Org Mode as a Lab Notebook

Erik Clarke over at pleiotropy has a couple of nice posts on using Org mode as a lab notebook. The first post lays out his requirements for a digital lab notebook. As you can probably guess, these include

  • Permanence
  • Citations
  • Ease of use
  • Discoverability

By citations he means the ability to include BibTeX-like citations in the notebook and have the full citation included when the notebook is exported. Discoverability means that it should be easy for him or others to search the notebook to find entries on some desired topic.

The second post is the code and configuration data that he used to implement his notebook. It's straightforward and easy to understand and is therefore easily adapted to your particular needs. Clarke uses Papers, a research paper repository tool, and added a bit of applescript to export his bibliography from Papers1. He also added a hook to automatically commit his notebook to version control whenever he saves it. That last step is an important part of the permanence requirement.

If you're in the sciences and the idea of an easily searchable and printable lab notebook is appealing to you, you'll want to take a look at these posts. Clarke's solution probably won't fit your needs exactly but his ideas constitute an excellent infrastructure for you to build your own solution on.



Papers is also available for Windows but I don't know what scripting ability it has there.

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  • Skywalker

    Ah, Papers, always Papers... OSX software (ported to windows, unavailable for linux), proprietary, expensive...

    It turns out that there is a bibliography manager for emacs (ebib)... I never got the hang of using it (or any other bibliography manager) and I just keep copy/pasting stuff in my .bib files manually. I you want to use one, I suggest you try this one, though. At least for the scripting part, emacs being emacs, it should be, hu... possible.

    On the other hand, you will probably miss some features from graphical paper managers (like linking the bibliography to a pdf version of the article), but that's something you can do directly from org.

  • ajsteven130

    I started using emacs in order to use org as an electronic lab notebook. I especially like the ability to freely flow from text to data to analysis where everything is clear, simple, and searchable. The ability to put analysis code directly into the prose is the killer feature. I also use org-mode to write papers, so the gap between data collection/exploration etc. and finished product is much smaller