<h1 id="2024-04-18"><a aria-hidden="true" class="anchor-heading icon-link" href="#2024-04-18"></a>2024-04-18</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><strong>How to use JupyterLab on the cluster</strong>  </p>
<ol>
<li>start the correct environment and jupyter lab (Maybe you want also activate a specific environment with <code>poetry shell</code>)</li>
</ol>
<pre class="language-bash"><code class="language-bash">srun --partition<span class="token operator">=</span>pibu_el8 --cpus-per-task<span class="token operator">=</span><span class="token number">10</span> --mem<span class="token operator">=</span>30G --time<span class="token operator">=</span><span class="token number">10</span>:00:00 --pty /bin/bashun
micromamba activate jup_lab
jupyter lab --no-browser --ip<span class="token operator">=</span><span class="token number">0.0</span>.0.0 --port<span class="token operator">=</span><span class="token number">8879</span>
</code></pre>
<ol start="2">
<li>start a new ssh connection from your pc</li>
</ol>
<pre class="language-bash"><code class="language-bash"><span class="token function">ssh</span> -N -f -L localhost:4000:binfservas22:8879 pamrein@login8.hpc.binf.unibe.ch
</code></pre>
<ol start="3">
<li>login with a browser (localhost:4000). The first time, you will be asked for a token. This you can find on the terminal (cluster), where the "server" is running. [my current password: jupyterlab]</li>
</ol>
<ol start="4">
<li>close jupyter-lab</li>
</ol>
<pre class="language-bash"><code class="language-bash"><span class="token function">lsof</span> -ti:4000 <span class="token operator">|</span> <span class="token function">xargs</span> <span class="token function">kill</span> -9   <span class="token comment">#for the pc-terminal</span>
</code></pre>
<p>With <code>Ctrl + C</code> you can close the jupyter-lab session on the cluster.</p>
<p>total generelized rules: 1224
total indermediate: 7358
intermediat with underline: 6746
Intermediat without underline should be: 612</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)

2024-04-18

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



2024-04-18

PAMREIN's daily Open Notebook (COMMONS Lab)

Todo - Check Github

Meetings

Daily report (What did I learn?)

Future perspective

Keywords