<h1 id="2024-02-20"><a aria-hidden="true" class="anchor-heading icon-link" href="#2024-02-20"></a>2024-02-20</h1>
<h1 id="this-is-pamreins-commons-lab-daily-open-notebook"><a aria-hidden="true" class="anchor-heading icon-link" href="#this-is-pamreins-commons-lab-daily-open-notebook"></a>This is pamrein's COMMONS Lab daily Open Notebook.</h1>
<p>Today is 2024.02.20</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>
<h2 id="doing"><a aria-hidden="true" class="anchor-heading icon-link" href="#doing"></a>Doing</h2>
<ul>
<li>introduction to <a href="https://www.dendron.so">dendron</a>
<ul>
<li>Ctrl + L or daily lab book Ctrl + Shift + D</li>
<li>Links are made with double brackets "[[]]"</li>
</ul>
</li>
<li>info slides from PMA <a href="https://doi.org/10.5281/zenodo.8137605">https://doi.org/10.5281/zenodo.8137605</a></li>
<li>Zulip for chatting <a href="https://commons-lab.zulipchat.com/">https://commons-lab.zulipchat.com/</a></li>
<li>Mine, Smart and others (Datatypes for proteinstuff)</li>
<li>poetry (like conda but better)</li>
</ul>
<h3 id="meeting-zoom---annothons"><a aria-hidden="true" class="anchor-heading icon-link" href="#meeting-zoom---annothons"></a>Meeting Zoom - Annothons</h3>
<p><a href="https://mibig.secondarymetabolites.org/">https://mibig.secondarymetabolites.org/</a></p>
<p>MIBiG 1.0 (2015)
MIBiG 3.0 (2022)
MIBiG 4.0 (2024)</p>
<p>separate biosynthesis vs. compound classifications (Kai Blin)</p>
<p>MITE - Minimum Informationabout at Tailoring Enzyme (database crosslinks - <a href="https://github.com/INTABiotechMJ/MITE-Tracker">https://github.com/INTABiotechMJ/MITE-Tracker</a>)
describes reactions of molecules.</p>
<p>Trello (Kanban boards for work coordinations) - Toyota is using it</p>
<p>MIBiG Literature table (<a href="http://tinyurl.com/mibig-literature">http://tinyurl.com/mibig-literature</a>)
<a href="http://tinyurl.com/mibig-literature-explanation">http://tinyurl.com/mibig-literature-explanation</a></p>
<p>Licensing: <a href="https://www.contributor-covenant.org/">https://www.contributor-covenant.org/</a></p>
<h2 id="keywords"><a aria-hidden="true" class="anchor-heading icon-link" href="#keywords"></a>Keywords</h2>
<p>Pickaxe</p>
<h1 id="-head"><a aria-hidden="true" class="anchor-heading icon-link" href="#-head"></a>&#x3C;&#x3C;&#x3C;&#x3C;&#x3C;&#x3C;&#x3C; HEAD</h1>
<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>
<blockquote>
<blockquote>
<blockquote>
<blockquote>
<blockquote>
<blockquote>
<blockquote>
<p>f268f10 (update dendo daily report)</p>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
</blockquote>

Have a look at the COMMONS research discussion forum

This is pamrein's COMMONS Lab daily Open Notebook.

2024-02-20

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

