<h1 id="2024-03-08"><a aria-hidden="true" class="anchor-heading icon-link" href="#2024-03-08"></a>2024-03-08</h1>
<h1 id="this-is-marcos-daily-open-notebook"><a aria-hidden="true" class="anchor-heading icon-link" href="#this-is-marcos-daily-open-notebook"></a>This is Marco's daily open-notebook.</h1>
<p>Today is 2024.03.08</p>
<h2 id="notes"><a aria-hidden="true" class="anchor-heading icon-link" href="#notes"></a>Notes</h2>
<p>Talk with PMA</p>
<h3 id="nextflow"><a aria-hidden="true" class="anchor-heading icon-link" href="#nextflow"></a>Nextflow</h3>
<h3 id="text-for-experimentcom"><a aria-hidden="true" class="anchor-heading icon-link" href="#text-for-experimentcom"></a>Text for experiment.com</h3>
<p><strong>about this project</strong> : , we want to predict the molecules of life. No introduction to EMI.
See <a href="/commons-dws-public/notes/8ElFvQBDYuPdyHJeLaRNS">Scientific_paper</a>
See <a href="https://docs.google.com/document/d/1M2tU1GmtFWkD05RSsxgKfchrQRhUnmf_q77IV8wyBMk/edit">https://docs.google.com/document/d/1M2tU1GmtFWkD05RSsxgKfchrQRhUnmf_q77IV8wyBMk/edit</a></p>
<h3 id="anticipated-lotus-new-predictions"><a aria-hidden="true" class="anchor-heading icon-link" href="#anticipated-lotus-new-predictions"></a>Anticipated LOTUS new predictions</h3>
<p>Todo : add a display of probabilites
strangly the model predicts all species to be around 0.8 at minimum.
Call Luca to discuss this ! --> TODO today</p>
<p>investigate interactive phylogenetic plots </p>
<h2 id="todo-today"><a aria-hidden="true" class="anchor-heading icon-link" href="#todo-today"></a>Todo today</h2>
<ul>
<li></li>
</ul>
<h2 id="doing"><a aria-hidden="true" class="anchor-heading icon-link" href="#doing"></a>Doing</h2>
<h2 id="done"><a aria-hidden="true" class="anchor-heading icon-link" href="#done"></a>Done</h2>
<ul>
<li></li>
</ul>
<h2 id="todo-tomorrow"><a aria-hidden="true" class="anchor-heading icon-link" href="#todo-tomorrow"></a>Todo tomorrow</h2>

2024-03-08

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

