labdao / docs

Powering docs.labdao.xyz. All LabDAO project documentation is deployed via this repository.

LabDAO Docs

This repository powers docs.labdao.xyz. It pulls together all LabDAO/OpenLab documentation together into a single site using Docusaurus.

Writing documentation

We've established some conventions around writing documentation that make it easy to integrate new projects' docs into this repository and deploy those docs to docs.labdao.com. Here's what you need to know:

• All documentation should live in a folder named docs/ in the root of your repository.
• When making references between documentation files, use relative paths.
• Each Markdown page should have a front matter section at the beginning, which at minimum should define the document's title and description.
• If you want to control the order in which the documents in a directory show up in the sidebar, add sidebar_position: <x> to the front matter for each document in the directory.
• If you want to customize the sidebar label for a particular directory, add a _category_.json file in the relevant directory with the contents { "label": "My Label" }. All the options available via _category_.json are documented here.

To add your repository's documentation to docs.labdao.com, make a pull request adding your repository as a Git submodule inside of this repository's docs/_projects folder. The submodule should be referenced in .gitmodules using an HTTPS repository link, not an SSH link (for Vercel compatibility).

Development

$ yarn
$ yarn start

This command starts a local development server and opens up a browser window. Most changes are reflected live without having to restart the server.

Build

$ yarn build

This command generates static content into the build directory and can be served using any static contents hosting service.

Deployment

This repository is deployed using Vercel, which has a Docusaurus V2 template. Just create a new Vercel project, connect it to this repository, and click deploy, and you're off to the races!

Misc

We collect anonymized analytics information from visitors to the documentation site to help us write better docs and understand which documentation is most important to our users.

docs's Issues

code example for diffdock+gnina

TODO: code example

undefined

extend tutorials

• move tutorials into separate section
• add an additional "level 2" with famous protein examples
• add an additional "run on your own data" model
• add more copy for the visualisation part of the installation tutorial

nextflow integration

tier-1 three tiers

• nf-core just like within a DAO the central core
• nextflow production
• nextflow developer hello world

tier-2 lab-developer grade application

• docker compose yaml file - map 1:1 to helm charts for kubernetes
• main.py

tier-3 lab-minimalist grade application

• command-line executable "main.py argument_1"
• Dockerfile with dependencies

does your tool have a command line interface?
docker
docker compose -
nextflow workflow -
nf-core workflow -

restify-service for any API (or any python library really that does not have a ton of dependencies)

rename doc directory

add information about the Jupyter Lab to the docs

content might include:

• how to access the lab - email dao @ labdao . com to be added to the github org
• [..]
• architecture diagram
• roadmap
• faq

Create copy for affinity prediction challenge page

Update Community docs

Hi @lilyhg - I think it would be good if we updated the docs on community activities and ways to contribute. Right now projects have their own section, so we should probably keep the focus in this section on groups and events.

I might delete some notes before our upcoming milestone to make sure we have clean docs with up-to-date information. The old notes should still be in the commit history.

Add coordinape documentation to docs

create an example for the updated docs for the discourse graph team

update all branded assets in docs

reorganise the docs into three sections as we prepare for Affinity Ranking launch

add admonitions to current Tutorial

resurface the "how to write documentation" page

smaller task branch

add docs for histology image analysis

Hi @hossam-zaki - could you add a set of docs for the pathology image processing tool that you have built? In terms of the target audience - I think there is a lot of potential if we speak to a college-CS and high-school-bio community.

update the symbol for the docs page

Make contributor editing experience WYSIWYG -> markdown

typeform for API key

how to write docs documentation

update logo in docs section with new symbol

reformat table of contents

might look better like this:

• labdao
  • what is labdao?
  • mission
  • get involved
  • contributing
• openlab
  • what is openlab?
  • running a service
  • adding a service

I am personally not a fan of concatenating these atoms into large molecules within the docs (probably because we have pretty big atoms right now, cc @blahah). I would drop all molecules right now, until we have worked out a more intuitive structure.

create documentation on how to use projects most effectively

Create copy for "Affinity Prediction"

Implement Staging Branch for docs and make sure it points to staging.labdao.xyz

create a events category in the community section

Reaction Loom for wireframes

Create a reaction Loom for preliminary wireframes.
no right/wrong way to do this, just try to speak about what is on your mind as you look at them.
What did you expect to see that's there or isn' there? Would you want an action to be in a different location? What features do you think should be highlighted more/less?
There are a number of different designs, so please mention any preferences!

get feedback on docs.labdao.xyz draft

expand the getting_started.md document for publishing

We want to create an article/wiki entry that helps get first-time users of the protocol up to speed quickly.

integrate assets/docs into a subsection for community group on docs.labdao.com

cc'ing @lilyhg
take note that this will only integrate the markdown within docs - the README (currently identical) will not be synced. Perhaps we should simplify the README file so people do not confuse the two.

update the organigram for LabDAO roles

We should update the chart of roles both in terms of the design and content.

can you team up with Curve?

remove docs/README from docs.labdao.com

review the copy of available grants for community members

@mithrauki created a set of funding sources and I added additional information. @el-ea can you add additional grant opportunities that you have been keeping track of?

https://github.com/labdao/docs/blob/b4d8ad2c3fa4cea060fb87577524c420f7b9f3ae/docs/projects/project_funding.md

how do we create capitalised directory names on the sidebar

Currently sidebar subsection names are automatically defined based on the corresponding directory names. Is there a low-overhead way to change the capitalisation of these sections?

For example "dna-seq" turns to "DNA-Seq" (will require some manual definition, or renaming of the directories?)

discord bot docs

creating a blank page for docs on the discord bot useage - ideally we move this file into the bot repository.
https://github.com/labdao/docs/blob/main/docs/labdao/_discord_bots.md

Docs minor structure update

Hey Aakaash, as discussed, minor updates:

1. At the moment, when you click "welcome", it only drops down what's underneath, and you have to click "welcome to labdao" to read anything. Infuriating!

Can we make the text on the "Welcome to labdao" page visible directly when you click "Welcome"? So no dropdown under Welcome.

2. Similarly, can you create a page for Affinity Binding too. Just put a bit of filler text saying "Our first toolset is for Affinity Binding", and I'll update the copy. [I'll add a short intro, with links to the subpages e.g. Introduction, Tools etc].

3. As a temporary measure, while we only have 1 toolset and 1 tutorial, can we move the Installation tutorial back underneath Affinity Binding, and just call it "Tutorial". As soon as we have multiple tutorials, we'll rethink this.

Thanks!

After this, I'll make some minor polishing updates to copy.

Remove outdated pages

Per @lilyhg, the following pages should be removed from the docs:

• What are Groups?
• What are Labs?
• Join a Lab

update the tools page

• include example code, incl. diffdock

creating a dedicated learn_more.md document for both labdao and openlab

add doc section on discourse graphs

remove the chmod step

ways to guide the UX could be:

• chmod confirmation message
• API key confirmation message

remove banner in "mission" section of the docs

create / identify a space in our notion that is used for all things app and UX research, owned by the team doing the work

Here: https://www.notion.so/labdao/Product-Home-30e9e684633242a4b42367d1ad600160

possibility to change browser miniature icon?

can we move from the old D to the green dots?

Record Loom video of interacting with CLI

@NiklasTR @tohrnii @acashmoney

add information about discourse graphs to the docs

how do we embed images within the assets repository within the served docusaurus?

enable mermaid based graphs for docs

Problem: Mermaid is a graph plotting tool in markdown that enables fast and easy generation of flowcharts of dependencies. This has value for application docs. Mermaid is not available in docusaurus.

Proposed Solution: To include mermaid to docusaurus, an actively maintained project exists: https://github.com/sjwall/mdx-mermaid

I propose we integrate mermaid support.

share the zoom recording from our workshop in a Notion base

Link is here: https://www.notion.so/labdao/Competitor-tools-d9954fd05e7842379cb2d0bb7e807704

Direct link to grain with transcript: https://grain.com/share/recording/7dc5b630-54d0-4544-bc2f-66da103a9cbb/Nx7ELZ747Dj36qizwgbZ87zoQu6qva5gIOCImXa0

Let me know if you can't access it

General review and updating the "how to contribute" section

Hi team - I think the current docs need an update to make it clear how people can engage with the organisation. I would love to hear your feedback after taking a pass through the docs on how we can improve them and where we need to make updates.

reorganising the docs

toplevel:

• Welcome to LabDAO
• LabDAO
  • Quickstart Guide
  • Mission
  • Org structure
  • LAB token
• Contributing to LabDAO
  • skills and roles
  • Teams, Guilds, and Working Groups
  • Offering laboratory services
  • Receiving funding and rewards
  • Meetings
  • Governance
  • Contributor guidelines
• Technology
  • lab-exchange
  • lab-standards
  • lab-NFTs
  • dry-lab applications
  • wet-lab applications
• Community
  • Onboarding
  • Lab Meeting
  • Lab Retreats
• Coordination
  • Tokenomics group
  • Legal
• Ressources
  • LabDAO memo
  • LabDAO onepager
  • Reading list