<h1 id="2025-02-12"><a aria-hidden="true" class="anchor-heading icon-link" href="#2025-02-12"></a>2025-02-12</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 2025.02.12</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>
<p>Alison Bender's Matser thesis presentation</p>
<p>Concept of <a href="https://en.wikipedia.org/wiki/Eusociality" title="Eusociality (Greek εὖ eu &#x22;good&#x22; and social) is the highest level of organization of sociality. It is defined by the following characteristics: cooperative brood care (including care of offspring from other individuals), overlapping generations within a colony of adults, and a division of labor into reproductive and non-reproductive groups. The division of labor creates specialized behavioral groups within an animal society, sometimes called castes. Eusociality is distinguished from all other social systems because individuals of at least one caste usually lose the ability to perform behaviors characteristic of individuals in another caste. Eusocial colonies can be viewed as superorganisms.
Eusociality has evolved among the insects, crustaceans, trematoda and mammals. It is most widespread in the Hymenoptera (ants, bees, and wasps) and in Blattodea (termites). A colony has caste differences: queens and reproductive males take the roles of the sole reproducers, while soldiers and workers work together to create and maintain a living situation favorable for the brood. Queens produce multiple queen pheromones to create and maintain the eusocial state in their colonies; they may also eat eggs laid by other females or exert dominance by fighting. There are two eusocial rodents: the naked mole-rat and the Damaraland mole-rat. Some shrimps, such as Synalpheus regalis, are eusocial. E. O. Wilson and others have claimed that humans have evolved a weak form of eusociality. It has been suggested that the colonial and epiphytic staghorn fern, too, may make use of a primitively eusocial division of labor.">eusociality</a></p>
<ul>
<li>
<p>Do honeypots ants only occur in desert-like environments ?</p>
</li>
<li>
<p>You show metabolomics and proteomics differneces on the replete types.
Are they any behaviour / time differnces. E.g. do clear become amber ?</p>
</li>
<li>
<p>Are the replete feeding themselves or are they "filled" by others ?</p>
</li>
</ul>
<p>"Label-free metabolite annotation"</p>
<p>Triglycerides --- long term energy storage</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="-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>

Daily work on the Open Science for natural products research Viewpoint

Have a look at the COMMONS research discussion forum

This is PMAS's COMMONS Lab daily Open Notebook.

2025-02-12

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

