<h1 id="2025-07-01"><a aria-hidden="true" class="anchor-heading icon-link" href="#2025-07-01"></a>2025-07-01</h1>
<h1 id="this-is-pmass-commons-lab-daily-open-notebook"><a aria-hidden="true" class="anchor-heading icon-link" href="#this-is-pmass-commons-lab-daily-open-notebook"></a>This is PMAS's COMMONS Lab daily Open Notebook.</h1>
<p>Today is 2025.07.01</p>
<h2 id="todo-today"><a aria-hidden="true" class="anchor-heading icon-link" href="#todo-today"></a>Todo today</h2>
<h3 id="have-a-look-at-the-commons-research-discussion-forum"><a aria-hidden="true" class="anchor-heading icon-link" href="#have-a-look-at-the-commons-research-discussion-forum"></a>Have a look at the COMMONS research discussion forum</h3>
<pre><code>- https://github.com/orgs/commons-research/discussions
</code></pre>
<h3 id="daily-work-on-the-open-science-for-natural-products-research-viewpoint"><a aria-hidden="true" class="anchor-heading icon-link" href="#daily-work-on-the-open-science-for-natural-products-research-viewpoint"></a>Daily work on the Open Science for natural products research Viewpoint</h3>
<p>See <a href="/commons-dws-public/notes/43p60vv8btyhaclugl93jok">Viewpoint</a></p>
<h3 id=""><a aria-hidden="true" class="anchor-heading icon-link" href="#"></a></h3>
<h3 id="-1"><a aria-hidden="true" class="anchor-heading icon-link" href="#-1"></a></h3>
<h2 id="doing"><a aria-hidden="true" class="anchor-heading icon-link" href="#doing"></a>Doing</h2>
<h2 id="paused"><a aria-hidden="true" class="anchor-heading icon-link" href="#paused"></a>Paused</h2>
<h2 id="done"><a aria-hidden="true" class="anchor-heading icon-link" href="#done"></a>Done</h2>
<h2 id="notes"><a aria-hidden="true" class="anchor-heading icon-link" href="#notes"></a>Notes</h2>
<h2 id="todo-tomorrow-one-day--or-never"><a aria-hidden="true" class="anchor-heading icon-link" href="#todo-tomorrow-one-day--or-never"></a>Todo tomorrow, one day ... or never</h2>
<h3 id="-2"><a aria-hidden="true" class="anchor-heading icon-link" href="#-2"></a></h3>
<h3 id="-3"><a aria-hidden="true" class="anchor-heading icon-link" href="#-3"></a></h3>
<h2 id="today-i-learned-that"><a aria-hidden="true" class="anchor-heading icon-link" href="#today-i-learned-that"></a>Today I learned that</h2>
<ul>
<li></li>
</ul>
<h3 id="chat-with-scorfi"><a aria-hidden="true" class="anchor-heading icon-link" href="#chat-with-scorfi"></a>Chat with Scorfi</h3>
<p><a href="http://www.metabolomexchange.org/site/">http://www.metabolomexchange.org/site/</a></p>
<p><a href="https://masswiki.metabolomics.us/aOC06HM">https://masswiki.metabolomics.us/aOC06HM</a></p>
<ul>
<li>
<p>Get in touch with MetabolomExchange </p>
</li>
<li>
<p>INSDC (<a href="https://www.insdc.org/">https://www.insdc.org/</a>) wants to go <a title="Private" href="https://wiki.dendron.so/notes/hfyvYGJZQiUwQaaxQO27q.html" target="_blank" class="private">metabolomics (Private)</a> -> MetaboBank (<a href="https://www.ddbj.nig.ac.jp/metabobank/index-e.html">https://www.ddbj.nig.ac.jp/metabobank/index-e.html</a>) ... IDF: Investigation Description Format... MAF: metabolite assignment file (<a href="https://www.ddbj.nig.ac.jp/metabobank/datafile-e.html#maf">https://www.ddbj.nig.ac.jp/metabobank/datafile-e.html#maf</a>)</p>
</li>
<li>
<p><a title="Private" href="https://wiki.dendron.so/notes/hfyvYGJZQiUwQaaxQO27q.html" target="_blank" class="private">Thomas Hankemeier (Private)</a> <a href="/commons-dws-public/mailto:hankemeier@lacdr.leidenuniv.nl">hankemeier@lacdr.leidenuniv.nl</a></p>
</li>
</ul>
<p><a href="https://www.nature.com/articles/s42255-025-01239-4/figures/1">https://www.nature.com/articles/s42255-025-01239-4/figures/1</a></p>
<p><a href="https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/14.md">https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/14.md</a></p>
<p><a href="https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/18.md">https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/18.md</a></p>

Daily work on the Open Science for natural products research Viewpoint

Have a look at the COMMONS research discussion forum

This is PMAS's COMMONS Lab daily Open Notebook.

2025-07-01

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

