<h1 id="2023-02-28"><a aria-hidden="true" class="anchor-heading icon-link" href="#2023-02-28"></a>2023-02-28</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>
Today is 2023.02.28
<h2 id="notes"><a aria-hidden="true" class="anchor-heading icon-link" href="#notes"></a>Notes</h2>
<h3 id="watched-madleinas-presentation-on-presentation-about-sex-determination"><a aria-hidden="true" class="anchor-heading icon-link" href="#watched-madleinas-presentation-on-presentation-about-sex-determination"></a>Watched Madleina's presentation on presentation about sex determination</h3>
let us denote <math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>n</mi><mrow><mi>i</mi><mi>c</mi></mrow></msub></mrow><annotation encoding="application/x-tex">n_{ic}</annotation></semantics></math>nic​ the number of reads in individual i in contig c. We have :
<div class="math math-display"><math xmlns="http://www.w3.org/1998/Math/MathML" display="block"><semantics><mrow><msub><mi>n</mi><mrow><mi>i</mi><mi>c</mi></mrow></msub><mo>∝</mo><mi>M</mi><mi>u</mi><mi>l</mi><mi>t</mi><mi>i</mi><mi>n</mi><mi>o</mi><mi>m</mi><mi>i</mi><mi>a</mi><mi>l</mi><mo stretchy="false">(</mo><msub><mi>N</mi><mi>i</mi></msub><mo separator="true">,</mo><msub><mi>π</mi><mrow><mi>i</mi><mi>c</mi></mrow></msub><mo stretchy="false">)</mo><mspace linebreak="newline"></mspace><mover accent="true"><msub><mi>π</mi><mrow><mi>i</mi><mi>c</mi></mrow></msub><mo>~</mo></mover><mo>=</mo><msub><mi>γ</mi><mi>c</mi></msub><mo stretchy="false">(</mo><msub><mi>p</mi><mrow><mi>i</mi><mi>c</mi></mrow></msub><mo>+</mo><mi>ϵ</mi><mo stretchy="false">)</mo><mspace linebreak="newline"></mspace><mover accent="true"><msub><mi>π</mi><mrow><mi>i</mi><mi>c</mi></mrow></msub><mo>~</mo></mover><mo>=</mo><mfrac><mover accent="true"><msub><mi>π</mi><mrow><mi>i</mi><mi>c</mi></mrow></msub><mo>~</mo></mover><mrow><munderover><mo>∑</mo><mrow><mi>c</mi><mo>=</mo><mn>1</mn></mrow><mi>c</mi></munderover><mover accent="true"><msub><mi>π</mi><mrow><mi>i</mi><mi>c</mi></mrow></msub><mo>~</mo></mover></mrow></mfrac></mrow><annotation encoding="application/x-tex">n_{ic} \propto Multinomial(N_i, \pi_{ic}) \\ \tilde{\pi_{ic}} = \gamma_c (p_{ic} + \epsilon) \\ \tilde{\pi_{ic}} = \frac{\tilde{\pi_{ic}}}{\sum_{c=1}^c \tilde{\pi_{ic}}}</annotation></semantics></math>nic​∝Multinomial(Ni​,πic​)πic​~​=γc​(pic​+ϵ)πic​~​=∑c=1c​πic​~​πic​~​​</div>
<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>
<ul>
<li>meeting with Pierre-Marie</li>
</ul>

Watched Madleina's presentation on presentation about sex determination

2023-02-28

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

