<h1 id="2023-03-28"><a aria-hidden="true" class="anchor-heading icon-link" href="#2023-03-28"></a>2023-03-28</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 2023.03.28
<h2 id="notes"><a aria-hidden="true" class="anchor-heading icon-link" href="#notes"></a>Notes</h2>
<h2 id="todo"><a aria-hidden="true" class="anchor-heading icon-link" href="#todo"></a>Todo</h2>
<ul>
<li>simulate <math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>ϵ</mi><mi>c</mi></msub></mrow><annotation encoding="application/x-tex">\epsilon_c</annotation></semantics></math>ϵc​ from multivariate normal distribution with mean = 0 and cov <code>prob_sigma</code></li>
<li>from x simulate Lotus from x and P and Q --> R </li>
<li>from R draw Bernoulli with P = R</li>
<li>--> simulated data</li>
<li>from simulated data try to do the opposite :
<ul>
<li>try to infer <math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>γ</mi></mrow><annotation encoding="application/x-tex">\gamma</annotation></semantics></math>γ and <math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>δ</mi></mrow><annotation encoding="application/x-tex">\delta</annotation></semantics></math>δ from MCMC --> should find our <math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>δ</mi></mrow><annotation encoding="application/x-tex">\delta</annotation></semantics></math>δ and <math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>γ</mi></mrow><annotation encoding="application/x-tex">\gamma</annotation></semantics></math>γ</li>
</ul>
</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>

2023-03-28

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

