<h1 id="2024-11-28"><a aria-hidden="true" class="anchor-heading icon-link" href="#2024-11-28"></a>2024-11-28</h1>
<h1 id="this-is-pmass-commons-lab-daily-open-notebook"><a aria-hidden="true" class="anchor-heading icon-link" href="#this-is-pmass-commons-lab-daily-open-notebook"></a>This is PMAS's COMMONS Lab daily Open Notebook.</h1>
<p>Today is 2024.11.28</p>
<h2 id="todo-today"><a aria-hidden="true" class="anchor-heading icon-link" href="#todo-today"></a>Todo today</h2>
<h3 id="have-a-look-at-the-commons-research-discussion-forum"><a aria-hidden="true" class="anchor-heading icon-link" href="#have-a-look-at-the-commons-research-discussion-forum"></a>Have a look at the COMMONS research discussion forum</h3>
<pre><code>- https://github.com/orgs/commons-research/discussions
</code></pre>
<h3 id="daily-work-on-the-open-science-for-natural-products-research-viewpoint"><a aria-hidden="true" class="anchor-heading icon-link" href="#daily-work-on-the-open-science-for-natural-products-research-viewpoint"></a>Daily work on the Open Science for natural products research Viewpoint</h3>
<p>See <a href="/commons-dws-public/notes/43p60vv8btyhaclugl93jok">Viewpoint</a></p>
<h3 id=""><a aria-hidden="true" class="anchor-heading icon-link" href="#"></a></h3>
<h3 id="-1"><a aria-hidden="true" class="anchor-heading icon-link" href="#-1"></a></h3>
<h2 id="doing"><a aria-hidden="true" class="anchor-heading icon-link" href="#doing"></a>Doing</h2>
<h2 id="paused"><a aria-hidden="true" class="anchor-heading icon-link" href="#paused"></a>Paused</h2>
<h2 id="done"><a aria-hidden="true" class="anchor-heading icon-link" href="#done"></a>Done</h2>
<h2 id="notes"><a aria-hidden="true" class="anchor-heading icon-link" href="#notes"></a>Notes</h2>
<ul>
<li>Meeting with Daniel Probst</li>
</ul>
<h3 id="junction-tree-variational-autoencoder-for-molecular-graph-generation"><a aria-hidden="true" class="anchor-heading icon-link" href="#junction-tree-variational-autoencoder-for-molecular-graph-generation"></a>Junction Tree Variational Autoencoder for Molecular Graph Generation</h3>
<p><a href="https://arxiv.org/pdf/1802.04364">https://arxiv.org/pdf/1802.04364</a></p>
<h3 id="rxn-insight-fast-chemical-reaction-analysis-using-bond-electron-matrices"><a aria-hidden="true" class="anchor-heading icon-link" href="#rxn-insight-fast-chemical-reaction-analysis-using-bond-electron-matrices"></a>Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices</h3>
<p><a href="https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00834-z">https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00834-z</a></p>
<h2 id="todo-tomorrow-one-day--or-never"><a aria-hidden="true" class="anchor-heading icon-link" href="#todo-tomorrow-one-day--or-never"></a>Todo tomorrow, one day ... or never</h2>
<h3 id="bigsmarts-a-topologically-aware-query-language-and-substructure-search-algorithm-for-polymer-chemical-structures"><a aria-hidden="true" class="anchor-heading icon-link" href="#bigsmarts-a-topologically-aware-query-language-and-substructure-search-algorithm-for-polymer-chemical-structures"></a>BigSMARTS: A Topologically Aware Query Language and Substructure Search Algorithm for Polymer Chemical Structures</h3>
<p><a href="https://pubs.acs.org/doi/10.1021/acs.jcim.3c00978">https://pubs.acs.org/doi/10.1021/acs.jcim.3c00978</a></p>
<h3 id="-2"><a aria-hidden="true" class="anchor-heading icon-link" href="#-2"></a></h3>
<h3 id="-3"><a aria-hidden="true" class="anchor-heading icon-link" href="#-3"></a></h3>
<h2 id="today-i-learned-that"><a aria-hidden="true" class="anchor-heading icon-link" href="#today-i-learned-that"></a>Today I learned that</h2>
<ul>
<li>o</li>
</ul>

BigSMARTS: A Topologically Aware Query Language and Substructure Search Algorithm for Polymer Chemical Structures

Daily work on the Open Science for natural products research Viewpoint

Have a look at the COMMONS research discussion forum

Junction Tree Variational Autoencoder for Molecular Graph Generation

Rxn-INSIGHT: fast chemical reaction analysis using bond-electron matrices

This is PMAS's COMMONS Lab daily Open Notebook.

2024-11-28

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

