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description: " A place with the background and the *how to* of the *microbetag* tool"
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# About 

![microbetag logo](_static/img/fig_abstract_white.png)

<div style="display: flex; gap: 10px;">
   <a href="https://apps.cytoscape.org/apps/mgg" class="btn-green"> CytoscapeApp </a>
   <a href="https://github.com/hariszaf/microbetag" class="btn-purple"> View it on GitHub </a>
   <a href="https://matrix.to/#/#microbetagcommunity:matrix.org" class="btn-blue"> Join us on Matrix </a>
</div>



Microbial interactions play a fundamental role in deciphering the underlying mechanisms that govern ecosystem functioning.
Co-occurrence networks have been widely used for inferring microbial associations or/and interactions from metagenomic data.
However, spurious associations and tool - dependence confine the network inference.
The integration of previous evidence or/and knowledge can increase or decrease the confidence level of the retrieved associations.
This way, associations can be further investigated, and more reliable conclusions can be drawn.


*`microbetag`* implements data integration techniques to annotate both the nodes (taxa) and the edges (predicted associations) of such a network 
to enhance microbial co-occurrence network analysis for amplicon data. 
Have a look at the [**modules**](modules/modules.md) tab to get an overview of the methods used.

<!-- It retrieves the KEGG modules that have been assigned to each of the species found related. 
Based on the **pathway complementarity** concept, pathways found in both taxa of an association are further explored to check whether the processes of each of the two taxa are complementary denoting a  positive interaction. 
Likewise, if the same processes are found to occur in both taxa, a negative interaction will be derived.

On top of that, *microbetag* integrates phenotypic information thanks to resources such as [FAPROTAX](https://github.com/knights-lab/BugBase); 
a series of environmental variables (pH optima, oxygen tolerance etc.) are assembled in each node of the network.
Their comparison in each pair of correlated taxa evaluates their corresponding association further.  -->


![microbetagDB content stats](_static/img/content-stats.png)



## A software suite

`microbetag` is a software suite with different software modules to use based on the tasks you are going for.

The most common use is through its graphical interface, a Cytoscape app called `MGG`.
[Cytoscape](https://cytoscape.org) is a well-established, widely used software for network data integration, analysis, and visualization.

<!-- `microbetag` is available as a [Cytoscape App](https://apps.cytoscape.org/apps/mgg) -->
To use `MGG` you need to first make sure you have Cytoscape installed on your machine; if not you can do this from the [Cytoscape Install page](https://cytoscape.org/download.html)
Then, there are two ways to install MGG in Cytoscape: 
Either from through the Cytoscape app store on a browser or from within Cytoscape.
In the first case, you need to **first launching Cytoscape**, and then visit the [MGG Cytoscape Appstore page](https://apps.cytoscape.org/apps/mgg). By clicking the `Install` button `MGG` will be automatically added on your Cytoscape.
Alternatively, to install `MGG` from within Cytoscape, you may click `Apps > App Store > Show App Store`, then search for "microbetag" in the pop-up box and follow this will guide you to the MGG page.

Once MGG is installed, you are ready to use `microbetag` either on the fly, by providing an OTUs/ASVs (amplicon data) and optionally a network, if you already have one, or locally, if you want to apply the annotations on your own bins/MAGs. In the last case, you will also have to install [Docker](https://www.docker.com) or [Singularity](https://sylabs.io) and pull the `microbetag` image that allows you to do so (see [Additional tutorials](advanced_use/tutorials.md) for more).

```{important}
**HOW TO USE AND INTERPRET MICROBETAG's FINDINGS**

For a thorough description of the app, please check the [Cytoscape App](basic_usage/mgg_totorials.md) tab.
```

In addition, `microbetag`'s annotations are also available through its [Application Programming Interface (API)](api.md). 
This way, one may have direct access to the `microbetagDB` and may export annotations for species or pairs of species of interest, without the need of a network. 


<!-- 
## Dependencies

To run *microbetag* you need to have [Docker](https://www.docker.com/) on your computing environment. 
As described from IBM, Docker is an open source containerization platform. 
It enables developers to package applications into containers—standardized executable components combining application source code with the operating system libraries and dependencies required to run that code in any environment.

You can install Docker in Linux, MaxOS or Windows systems by following the instructions you will finde [here](https://docs.docker.com/get-docker/).


### Get

Once Docker is available, to get *microbetag* you need to *pull* it from DockerHub. 
To do this, you need to run: 

```bash=
docker push hariszaf/microbetag
```

This way, the latest version of *microbetag* will be pulled. 
You may specify which version of *microbetag* you wish to pull by running instead:

```bash=
docker push hariszaf/microbetag:tagname
```
where `tagname` is the name of the specific version. 

 -->


## Contact

For hints on how to use microbetag, ideas for new features and bug reports find us on out [Matrix space](https://matrix.to/#/#microbetagcommunity:matrix.org).
If you do not have a Matrix account, it's only two clicks away! 
For more information, you may check [here](https://matrix.org/docs/chat_basics/matrix-for-im/).


## Cite us
Zafeiropoulos, H., Michail Delopoulos, E. I., Erega, A., Schneider, A., Geirnaert, A., Morris, J., & Faust, K. (2024). 
[microbetag: simplifying microbial network interpretation through annotation, enrichment tests and metabolic complementarity analysis]( https://doi.org/10.1101/2024.10.01.616208). bioRxiv, 2024-10.

## Funding

This project was funded by an [EMBO Scientific Exchange Grants](https://www.embo.org/funding/fellowships-grants-and-career-support/scientific-exchange-grants/) 
and the [3D’omics](https://www.3domics.eu) Horizon 2020 project (101000309).

<!-- https://www.embo.org/documents/news/facts_figures/EMBO_facts_figures_2021.pdf -->

## License

*microbetag* is under [GNU General Public License v3.0](https://opensource.org/license/gpl-3-0). For third-party components separate licenses apply. The MGG CytoscapeApp is under [Apache License, Version 2.0](https://opensource.org/license/apache-2-0).