<h1 id="mongo"><a aria-hidden="true" class="anchor-heading icon-link" href="#mongo"></a>Mongo</h1>
<h1 id="mongo-db-related-infos"><a aria-hidden="true" class="anchor-heading icon-link" href="#mongo-db-related-infos"></a>Mongo DB related infos</h1>
<p>A pres by Matt Swain
<a href="https://speakerdeck.com/mcs07/chemical-structure-handling-in-mongodb">https://speakerdeck.com/mcs07/chemical-structure-handling-in-mongodb</a></p>
<p><a href="https://matt-swain.com/blog/2014-06-03-chemical-similarity-search-in-mongodb">https://matt-swain.com/blog/2014-06-03-chemical-similarity-search-in-mongodb</a></p>
<p>Associated repo <a href="https://github.com/mcs07/mongodb-chemistry">https://github.com/mcs07/mongodb-chemistry</a>
And a derived notebook <a href="https://mnowotka.github.io/notebooks/mongo.html">https://mnowotka.github.io/notebooks/mongo.html</a></p>
<p><a href="https://mnowotka.github.io/notebooks/">https://mnowotka.github.io/notebooks/</a></p>
<p>Bunch of chembl related info here also
<a href="http://chembl.blogspot.com/">http://chembl.blogspot.com/</a> n</p>

Mongo

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

