<h1 id="28"><a aria-hidden="true" class="anchor-heading icon-link" href="#28"></a>28</h1>
<h1 id="present"><a aria-hidden="true" class="anchor-heading icon-link" href="#present"></a>Present</h1>
<ul>
<li>Edouard</li>
<li>Heloise</li>
<li>Marco</li>
<li>Colin</li>
<li>Pascal</li>
</ul>
<h1 id="colin"><a aria-hidden="true" class="anchor-heading icon-link" href="#colin"></a>Colin</h1>
<ul>
<li>
<p>established a list of standards for the MAPP platform</p>
</li>
<li>
<p>How do we store sample ?</p>
</li>
<li>
<p>Moved to 9x9 boxes</p>
</li>
</ul>
<p>Coordinate with Edouard on the best way to </p>
<ul>
<li>
<p>Noni sample for analysis to be treated </p>
</li>
<li>
<p>Legal disclaimer is done </p>
</li>
</ul>
<h1 id="edouard"><a aria-hidden="true" class="anchor-heading icon-link" href="#edouard"></a>Edouard</h1>
<p>Last week.
Directus update, running on a docker.</p>
<p>Last directus version.
/docker </p>
<p>Docker is automatically restarted</p>
<p><a href="http://directus.dbgi.org">http://directus.dbgi.org</a></p>
<p>Nocodb is also running on the same server docker
For MAPP </p>
<p>PG is version each 2 hours (for 48h) + weekly backup.</p>
<ul>
<li>Mass Spectrometry manager </li>
<li>iNat-fetcher (takes info from iNat to Directus)
didnt link it back to the lab part of the</li>
</ul>
<p>NocoDB.</p>
<p><a href="https://www.inaturalist.org/observations/153546334">https://www.inaturalist.org/observations/153546334</a></p>
<p>Example of a wrongly tagged observation
The user is no longer part opf the lab ...</p>
<h1 id="heloise"><a aria-hidden="true" class="anchor-heading icon-link" href="#heloise"></a>Heloise</h1>
<ul>
<li>Collected entire Greenhouse</li>
<li>Doing extraction (half done)</li>
<li>Personal project, checked with FIBL for the long term experiment</li>
</ul>
<p>Call Hans. When ? </p>
<p>Problem with iNat.</p>
<p>Next week absent. </p>
<h1 id="marco"><a aria-hidden="true" class="anchor-heading icon-link" href="#marco"></a>Marco</h1>
<p>Two week
Finding a chemical classifier
NPClassifier and Classyfire.</p>
<p>Quite bad.
MCCS</p>
<ul>
<li>Irreproducibility of the results</li>
</ul>
<p>pythonChebiAI</p>
<p>Linking molecule through chemical similarity </p>
<p>Monorepo</p>
<h1 id="pascal"><a aria-hidden="true" class="anchor-heading icon-link" href="#pascal"></a>Pascal</h1>
<p>4 week ago with the dataset extractor</p>
<ul>
<li>MINE dataset extractor</li>
</ul>
<p>Reading about MongoDB
NoSQL database using JSON string </p>
<p>Doctring
MKDocs build from the readme</p>

Concrete steps to access and contribute to the DBGI Dendron


![](/assets/images/allard-lab.jpg)

Welcome the the COMMONS Lab Open Dendron !

In the [COMMONS Lab](https://www.unifr.ch/bio/en/groups/allard/) we intent to follow the [Open Notebook Science](https://en.wikipedia.org/wiki/Open-notebook_science) approach to document our research.

For this we use the [Dendron](https://www.dendron.so/) system as a mean to efficiently capture notes and publish them.

## What is this note

This note is a succinct tutorial note aiming to get you started in the use of the COMMONS Lab Dendron.

## Tutorial

### Dendron. 

#### What is Dendron ?

> Dendron is an open-source, local-first, markdown-based, note-taking tool. Think of it as a cache for everything that you care about - if you've spent more then five minutes solving a problem, you should never spent any more time solving the same exact problem.
> 
> Dendron is a knowledge base built by and for developers and integrates natively with IDEs like VS Code and VSCodium.

#### Where to get more info on Dendron ?

- You can get more information in the Dendron system at the official website www.dendron.so
- All the Dendron documentation is hosted here https://wiki.dendron.so/. It is, obviously, a Dendron itself.

#### Concrete steps to access and contribute to the DBGI Dendron

1. Install [VSCode](https://code.visualstudio.com/download)
2. Install [Dendron](https://marketplace.visualstudio.com/items?itemName=dendron.dendron) from the VSCode marketplace 
3. Clone the COMMONS Dendron repo

    In your terminal
    ```
    git clone https://github.com/commons-research/commons-dws-public.git
    ```
4. In VSCode open (File/Open) the cloned repository.
5. Voila ! You should now be in the COMMONS Lab Open Dendron.

Feel free to explore and contribute.
A first, important step could be to configure VSCode so that you can easily add a daily note. See steps described at [[open-notebook.commons.setup]]


## Questions, comments, suggestions ?

Feel free to contribute here https://github.com/orgs/commons-research/discussions

