https://github.com/brsynth/straindesign

Library to perform metabolic engineering tasks
https://github.com/brsynth/straindesign

bioinformatics flux-balance-analysis metabolic-engineering metabolic-pathways

Last synced: 5 months ago
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Library to perform metabolic engineering tasks

• Host: GitHub
• URL: https://github.com/brsynth/straindesign
• Owner: brsynth
• License: mit
• Created: 2021-12-10T09:38:27.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2024-04-29T21:15:37.000Z (about 2 years ago)
• Last Synced: 2025-09-09T20:14:09.136Z (9 months ago)
• Topics: bioinformatics, flux-balance-analysis, metabolic-engineering, metabolic-pathways
• Language: Python
• Homepage:
• Size: 10.4 MB
• Stars: 5
• Watchers: 1
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE
  • Zenodo: .zenodo.json

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README

          
# StrainDesign

[![Github Version](https://img.shields.io/github/v/release/brsynth/straindesign?display_name=tag&sort=semver)](version) [![Conda Version](https://img.shields.io/conda/vn/bioconda/straindesign.svg)](https://anaconda.org/bioconda/straindesign)  

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## Description

*straindesign* provides a cli interface to predict gene knockout targets with an heterologous pathway.

Integrate an hard fork from [cameo](https://github.com/biosustain/cameo) (v0.13.6) named `cameobrs` to add features.

## Installation

```sh

conda install -c bioconda straindesign

```

## Usage

### Define the best combination of genes deletion to optimize a target

```sh

python -m straindesign simulate-deletion \

    [input files]

    --input-model-file 

    --input-pathway-file 

    --input-medium-file 

    [parameters]

    --biomass-rxn-id 

    --target-rxn-id 

    --substrate-rxn-id 

    [output file]

    --output-file 

```

### Delete genes in a model

```sh

python -m straindesign reduce-model \

    [input files]

    --input-model-file 

    --input-straindesign-file 

    and/or

    --input-gene-str 

    [parameters]

    --parameter-strategy-str 

    [output file]

    --output-file-sbml 

```

You can provide a list of genes to delete in the model or the file produced by the command `simulate-deletion`.

If this file is provided, the combination of genes is choosen among three strategies:

* yield-max: genes are sorted by the best yield

* gene-max: the combination of the maximum number of genes

* gene-min: the combination of the minimum number of genes

### Produce a pareto plot

```sh

python -m straindesign analyzing-model \

    [input files]

    --input-model-file 

    --input-medium-file 

    --input-pathway-file 

    [parameters]

    --biomass-rxn-id 

    --target-rxn-id 

    --substrate-rxn-id 

    [output file]

    --output-pareto-png 

```

You can provide an heterologous pathway to implement the metabolic pathway producing the targeted compound represented by the `target-rxn-id`, the reaction which produces this compound.  

The `substrate-rxn-id` argument lets you to choose the main carbon source.

## Tests

Requires:

* *pytest*

* *pytest-benchmark*

```sh

python -m pytest

```