<h1 id="2024-04-26"><a aria-hidden="true" class="anchor-heading icon-link" href="#2024-04-26"></a>2024-04-26</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>I've got a Mail from Lisa Jeske (Brenda Database). </p>
<ol>
<li>take the structure file (molfile) from Brenda</li>
<li>Convert it to a SMART (<a href="https://docs.chemaxon.com/display/docs/molconvert_index.md">https://docs.chemaxon.com/display/docs/molconvert_index.md</a>)</li>
<li>annotate it with the organism</li>
</ol>
<p>I wanted to find out, how the mines database is build (where is the code?).
The paper <a href="https://doi.org/10.1186/s13321-015-0087-1">https://doi.org/10.1186/s13321-015-0087-1</a> provides some information about it.
Also a Github account is given: <a href="https://github.com/JamesJeffryes/MINE-API">https://github.com/JamesJeffryes/MINE-API</a>.
But it is not possible to find the code, how they put the reactions togheter.
It looks like they are working with the BNICE methode (database?) which is comming from the University of Lausanne.</p>
<p>To get access to the BNICE database, you have to sign up. This you can only do, if you are a professor.</p>
<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)

2024-04-26

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



2024-04-26

PAMREIN's daily Open Notebook (COMMONS Lab)

Todo - Check Github

Meetings

Daily report (What did I learn?)

Future perspective

Keywords