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?
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Obsidian or Logseq.
I’ve used Logseq for my lab journal, thoughts, and whatsoever, and it works excellent for that.
- You can link different things/ dates with each entry
- Markdown
- Functions and querys
- Local
- Very flexible
- And you can find pretty much every thought you’ve ever had, nothing is lost.
It can be tricky tho if you want to collaborate, because the sync isn’t perfect yet, but the devs are working really hard on it
It depends on what you guys do.
Markdown is very easy to use. It can be learned within a couple of minutes.
Do you calculate stuff? -> quarto
Modern, comprehensible latex? --> typst
Do you want trackable research? --> git
A git server (forgejo, radicle) can also be used to track issues. Or you may want to try openproject.org
Why is latex not easy to collaborate? Because others don’t know it?
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.
If your university uses Office 365, G Suite, or a similar product, I would examine those options first.
The group I did my PhD in used eLabFTW after I was gone. I heard only positive things and am trying to implement it in my current job (can not really selfhost as the IT department does all services). It should have a system to log experiments as well as have basic (maybe even more) inventory management. As far as I remember it dous not need any “big” hardware, so just using an older computer with a good backup strategy should work fine.
Idk if latex is optimal for note taking, or if others will warm to it if forced, but overleaf is obv collaborative though not selfhosted.
I’ve liked Outline https://www.getoutline.com/ and while I haven’t used it collaboratively, it really highlights that it’s a primary goal. It’s supposed to be a collaborative/dynamic wyswyg wiki thing. You need a SSO service like authentik or authelia for it, it doesn’t do login. But that’s good for security anyway!
