<h1 id="2024-04-24"><a aria-hidden="true" class="anchor-heading icon-link" href="#2024-04-24"></a>2024-04-24</h1>
<h1 id="pamreins-daily-open-notebook-commons-lab"><a aria-hidden="true" class="anchor-heading icon-link" href="#pamreins-daily-open-notebook-commons-lab"></a>PAMREIN's daily Open Notebook (COMMONS Lab)</h1>
<h2 id="todo---check-github"><a aria-hidden="true" class="anchor-heading icon-link" href="#todo---check-github"></a>Todo - <a href="https://github.com/orgs/commons-research/projects/2/views/1">Check Github</a></h2>
<p>-[]</p>
<h2 id="meetings"><a aria-hidden="true" class="anchor-heading icon-link" href="#meetings"></a>Meetings</h2>
<h2 id="daily-report-what-did-i-learn"><a aria-hidden="true" class="anchor-heading icon-link" href="#daily-report-what-did-i-learn"></a>Daily report (What did I learn?)</h2>
<p>Today I received an answer from the BRENDA database: </p>
<p>vielen Dank dass du BRENDA verwendest! Aktuell gibt es keine Möglichkeit die Reaktionen in BRENDA als SMARTS darzustellen/runterzuladen. Eine einfach Lösung für dein Problem sehe ich aktuell nicht. Für die Zukunft ist geplant eine umfangreichere API anzubieten, die mehr Informationen bereitstellt.</p>
<p>Folgendes könnte ich mir allerdings vorstellen: Jeder Ligand hat eine spezifische Seite (z.B. <a href="https://brenda-enzymes.org/ligand.php?ligand_name=heme+b">https://brenda-enzymes.org/ligand.php?ligand_name=heme+b</a>), wo es auch die Mol Files zum Download gibt. Diese Mol Files könnten verwendet werden um SMILES zu generieren (z.B. mit RDKit) um daraus dann die SMARTS zu generieren. Allerdings wäre es dazu nötig die BRENDA Webseite zu parsen um die  Mol Files zu erhalten.</p>
<p>parsen: analysieren, bzw. in Teile zerlegen</p>
<blockquote>
<p>Molfile: <a href="https://de.wikipedia.org/wiki/Molfile">https://de.wikipedia.org/wiki/Molfile</a></p>
</blockquote>
<h2 id="future-perspective"><a aria-hidden="true" class="anchor-heading icon-link" href="#future-perspective"></a>Future perspective</h2>
<h2 id="keywords"><a aria-hidden="true" class="anchor-heading icon-link" href="#keywords"></a>Keywords</h2>
<p><a href="/commons-dws-public/notes/3ca85tg6eqf78kgql1mj3vl">Abbreviations</a></p>

PAMREIN's daily Open Notebook (COMMONS Lab)

2024-04-24

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



2024-04-24

PAMREIN's daily Open Notebook (COMMONS Lab)

Todo - Check Github

Meetings

Daily report (What did I learn?)

Future perspective

Keywords