I won a new grant (yaay!) and dipping my toes in the role of PI in my university. For now, I will have a PhD, a post doc and a couple of masters students in my team.
In all my previous labs, everything was on paper and very poorly documented (…don’t ask). I myself used to use LaTeX to keep a “neat” labnote. Obviously, it is not easy to collaborate and work with others.
Any researchers here who have experience hosting their own e-lab book in their labs?
I’m gonna upvote the git + plain markdown solution simply because it is a very basic solution that does not depend on a lot of specific software in case you want to switch in the future. I had a look at obsidian in the past but discarded that idea because it required a license for commercial use back then which it seems they either changed or I misread the terms at the time.
Still I am a fan of going as low-tech as possible with note formats so that I can easily hand down my notes to whoever comes after me and they won’t need a special program to open anything.
Quarto looks nice and would be something I would look into if I did more data heavy work. As it is I only write technical notes and documentation for software for which plain markdown is perfectly suitable.
Markdown is just a universal language. Using WYSIWYG editors it’s even better than using common word processors. Evreything is consistent, easy and beautiful.
Oh yes definitely. I currently have to write the technical documentation for a project I am working on in MS Word because that’s the format my supervisor wants (since everyone in the organisation already has word installed by default and knows how to use it at least somewhat). Probably a quarter of the time I spend writing is lost to fighting the formatting in word. I managed to have stuff happen that my coworkers have never seen word do before like taking the content of all my textfields (which I use for pasting code snippets) and having it duplicated inside each textfield…
I wished I could use LaTeX for it but I understand the argument that some people after me may have to work on the project who don’t know LaTeX.
I feel you. Using word is like going backwards.
Especially technical docs should never be in word. Converting markdown to html is so easy but I get where you are.
The code snippets are the worst part. God forbid I ever have to update them because I have to manually indent every line in them correctly
Oh shit. I’d try pandoc md to docx conversion. No idea if it works for your case
Unfortunately not because the word document is meant to be the “master” document. We aren’t even supposed to export PDF versions because in the future people may see the PDF in the folder and use that as a reference instead of the main word document even though the word doc was updated and the PDF wasn’t. Also I tried pandoc md conversion to docx in the past for another document and it didn’t go very well. The formatting of the headers was all over the place which made it impossible to generate the Table of Contents in word
Ok, sounds not so good. What about only using the converson for the snippets?
I guess that might work. I’ll have to try it on monday though it’s probably more effort this way compared to just doing it manually since the snippets I have to add currently are mostly single functions with less than 20 lines