this post was submitted on 12 Jul 2025
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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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[–] Guenther_Amanita@slrpnk.net 7 points 16 hours ago* (last edited 16 hours ago) (1 children)

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

[–] JustEnoughDucks@feddit.nl 2 points 14 hours ago

Also with the excalidraw plugin, hand drawing images and such is also possible.

It is not as good for flowcharts and diagrams since there are only like 5 non-specified font sizes, but also usable for notes

[–] SheeEttin@lemmy.zip 13 points 1 day ago

If your university uses Office 365, G Suite, or a similar product, I would examine those options first.

[–] illusionist@lemmy.zip 9 points 1 day ago* (last edited 1 day ago) (1 children)

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?

[–] Scrath@lemmy.dbzer0.com 3 points 15 hours ago (1 children)

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.

[–] illusionist@lemmy.zip 1 points 15 hours ago (1 children)

Markdown is just a universal language. Using WYSIWYG editors it's even better than using common word processors. Evreything is consistent, easy and beautiful.

[–] Scrath@lemmy.dbzer0.com 2 points 15 hours ago (1 children)

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.

[–] illusionist@lemmy.zip 1 points 15 hours ago (1 children)

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.

[–] Scrath@lemmy.dbzer0.com 1 points 15 hours ago (1 children)

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

[–] illusionist@lemmy.zip 2 points 14 hours ago (1 children)

Oh shit. I'd try pandoc md to docx conversion. No idea if it works for your case

[–] Scrath@lemmy.dbzer0.com 2 points 14 hours ago (1 children)

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

[–] illusionist@lemmy.zip 2 points 13 hours ago (1 children)

Ok, sounds not so good. What about only using the converson for the snippets?

[–] Scrath@lemmy.dbzer0.com 2 points 12 hours ago (1 children)

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

[–] illusionist@lemmy.zip 1 points 7 hours ago

Why doing it manually when you can simply automate it /s

[–] Holli25@slrpnk.net 4 points 1 day ago

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!