How do we organise, archive, and communicate our collective knowledge?

Hey everyone, I’ve also been following along this conversation.

To add into the mix, after GOSH 2022 a few of us have been discussing creating a database similar to what was mentioned. We were a little frustrated because there seemed to be a lot of interesting projects happening but we had difficulty finding documentation.

On top of that, we noted that there were most likely many academia/student projects that are not publicly published that could be, but were not due to neglect (i.e. a student graduates start into a job and forgets to upload/share their work, even though they were open to sharing). We actually are having a meeting with some developers from to discuss the possibility of adding another section on their site for open science hardware. Though I have seen the project database that @kaspar made which is really nice.

We were only having a introductory discussion with the developers to see what they could provide and how (maybe they can be partial archivers). The goal was to organize this new section in a way that people unfamiliar with OSrH can find projects and, ideally, get involved or add their own. Though we will be aware of propriety concerns as mentioned earlier in this forum.

Maybe they could link their database to the wikis that @naikymen mentioned. The documentation could be based in a centralized self-hosted GOSH wiki site (as mentioned here) with each project on it’s own individual page. Or it could redirect to the GOSH forums. These are just ideas. Open for more input from you all and what else to include in our discussion!


What interesting discussions as of late! I think @dusjagr and @naikymen both make good points. Whatever we decide to do, I think we need people who are willing to put in the sustained work needed to tend this digital garden.

I am also interested in @Sarah’s suggestions as to how a loose, international community like GOSH can find the people to come together for this gardening. Happy to follow up in early 2023.

As for the directory of interesting OScH projects that @NKArranz mentioned, I think it would first of all be a good showcase of why GOSH is important. If we successfully create this directory, it would be good to give it some visibility on GOSH’s website. One possibility is to use this directory as a starting point for knowledge management. Once we have it set up, we can start thinking about how we add other bits of knowledge to this garden. On the other hand, maybe it will be simpler to keep this OScH directory independent.

Also somewhat randomly, I was skimming through the Open Scientist Handbook by Bruce Caron, and it’s got a chapter on idea gardening, though it’s more about how ideas cross-pollinate and how current academic institutions are not conducive to great ideas…


Stumbled upon this book: Connecting the Knowledge Commons — From Projects to Sustainable Infrastructure edited by Leslie Chan and Pierre Mounier. Among other things:

How do we move from an approach entirely based on temporary projects to an approach based on community-based sustainable infrastructure?
What kinds of social and technical infrastructures could support the Knowledge Commons?

Yet another book we could read together

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And here my friend just posted a great article on Wiki gardening:

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A few ideas from a fellow gardener.

These sites are made from Obsidian Publish:

Welcome to The Quantum Well - The Quantum Well - Obsidian Publish!
publish homepage - Obsidian Publish
+ Start Here - LYT Kit
Welcome to my digital garden - Alexis Rondeau - Obsidian Publish
Welcome - Eleanor's Notes - Obsidian Publish
00 - Start here - Obsidian Hub - Obsidian Publish

  • There are free alternatives to Publish. 0. 1. 2. 3.
  • The Obsidian graph interface is similar to @Paul 's link above.
  • @jarancio above mentions Zotero, which I agree is a great resource. I generally just drag notes/annotations from Zotero into Obsidian (which auto-generates a link back to that note), but there are other integrations. 1. 2.

If I can use it (albeit poorly), it can’t be too difficult. I’m not necessarily pushing for obsidian, but perhaps some git system here that leverages links between .md files, tagging, graphs, etc. with a simple jekyll site might be more active and easier/nicer to navigate than a wiki.


Dear Colleagues,

When I get to it this summer, I will collate the open source hardware information into
something akin to The One Card Deck to Rule Them All that I generated several years ago at

I could definitely use some help organizing all that information!
Jim Brenner

2 Likes is an option, but more for a self hosted wiki on a usb-stick, or self contained file.

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Really love how comprehensive @eric’s post is about Obsidian! It looks like an amazing tool, though I’m concerned that it’s closed source which not only does not respect my digital freedoms, but also risks costly vendor lock in and forced obscelesence.

I wonder if there’s a way to achieve what Obsidian can do with TiddlyWiki as @DrBrian suggests? I’ve known about TiddlyWiki but hesitated when I learned that it uses its own mark up language instead of Markdown. Though I also know that TiddlyWiki is highly extensible, and maybe there’s a way to make it work for me.

Also looking forward to @jbrennerFIT’s “One Card Deck to Rule Them All”, which is a curious name!

Lastly, I just want to link to this thread about negative case studies of closed source hardware which is receiving useful responses. It would be good to collect these stories for our collective knowledge!

The One CardDeck to Rule Them All is at
What I want to do this summer is something like this for GOSH.

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Let’s keep The One CardDeck to Rule Them All simpler. Login | Engineering Unleashed

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Thanks! But this link you shared takes me to a log in page:

While this one seems to work:

Are they supposed to take me to the same place?

On a separate note, I had an interesting chat at the Turing Way Collaboration Cafe today, including a brief discussion about collective knowledge.

Instead of wikis, etc., they cultivate their digital garden through The Turing Way “book” here:

The contents of their garden is managed in a GitHub repository.

Which other communities have remixed for their purposes, such as for an environmental data science community:

Apparently, they are also still working on how to manage this gardening, just like for us in this thread.

Not saying we should or shouldn’t use this to manage our knowledge, but I’m putting this here for reference!


Logseq is a good open-source alternative to Obsidian. I’m a happy daily user. The main difference between the two (besides open vs closed source) is Logseq is block-based (in the outliner sense) and Obsidian is page-based. They each have their pros and cons for that reason.

Anyhow, happy to answer any questions folks might have. Feel free to DM.

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Here’s a related and useful web standard: Robust Links

As you know, hyperlinks on the web are subject to link rot, where the pages they point to might change or disappear over time. Robust links is a proposed standard for the <a href> </a> HTML tag for hyperlinks to embed an additional link to an archived version of the target page. The archived page could, for example, be a snapshot on the Internet Archive’s Wayback Machine.

I love this idea! Something to keep in mind, though it’s not supported in Markdown or other mark up languages at the moment.

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I just posted here community governance documents by 2i2c. They have an extensive knowledge base called the “Team Compass” (looks like a Jupyterbook) where they manage their collective knowledge! Worth checking out…


Here’s an interesting open source tool called Danswer, which “allows you to ask natural language questions against internal documents and get back reliable answers… You can connect to a number of common tools such as Slack, GitHub, Confluence, amongst others.” Another discussion thread is on Hacker News.

Sadly it currently uses OpenAI LLMs to works its magic, which is not open source, but plans work with other models in the future.

I probably won’t start using this right now, but such a tool could help partially solve the discoverability problem of a large knowledgebase/digital garden by helping you query it using natural language. I.e. “Tell me where in my notes I wrote about X.”

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Learning from mistakes i.e. the Verica Open Incident Database [for software service incidents]:


I just randomly noticed that Discourse has a knowledge base feature called “Docs”:

Is this something available to our forum, that could be turned on? This might even be where the OScH directory can live? @briannaljohns??


@briannaljohns more info here on installation/usage: Discourse Docs (Documentation Management) - plugin - Discourse Meta

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I’m at the FOSDEM 2024 Open Research Devroom online session today, and am learning about the Open Life Science knowledge management system:

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