https://github.com/cdanielmachado/designmc

Designing microbial communities
https://github.com/cdanielmachado/designmc

design genome-scale-models metabolism microbial-communities

Last synced: 5 months ago
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Designing microbial communities

• Host: GitHub
• URL: https://github.com/cdanielmachado/designmc
• Owner: cdanielmachado
• License: apache-2.0
• Created: 2020-01-09T11:35:13.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2022-12-26T21:00:35.000Z (over 3 years ago)
• Last Synced: 2026-01-09T08:38:40.823Z (5 months ago)
• Topics: design, genome-scale-models, metabolism, microbial-communities
• Language: Python
• Size: 114 KB
• Stars: 6
• Watchers: 1
• Forks: 4
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
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![DesignMC](logo_300px.png)

Designing microbial communities using genome-scale metabolic models.

### Installation

Can be easily installed using **pip**:

```

pip install designmc

```

### Usage

**DesignMC** is a tool for designing synthetic microbial communities with a desired phenotypic trait (i.e. design target) using genome-scale metabolic models. The minimum required input is a list of single-species models, one design target (secreted metabolite), and a definition of the growth medium:

```

designmc models/*.xml -t trp__L -m M9 -d mediadb.tsv

```

> **Please note** that this tool is still under development. It currently only supports models using [BiGG](http://bigg.ucsd.edu/) notation, such as those created with [CarveMe](https://github.com/cdanielmachado/carveme). The only design strategy currently available is random sampling. 

 

You can control the maximum number of species per community (example: `-s 5` or `--species 5 `) and the maximum number of combinations to simulate (`-n 100` or `--iters 100`).

For more options and details please check the help menu:

```

designmc -h

```

### Credits

Daniel Machado,

European Molecular Biology Laboratory (EMBL),

2020

![](data:image/jpeg;base64,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)