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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","flux-balance-analysis","metabolic-engineering","metabolic-pathways"],"created_at":"2026-01-16T10:20:56.919Z","updated_at":"2026-01-16T10:20:57.570Z","avatar_url":"https://github.com/brsynth.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# StrainDesign\n\n[![Github Version](https://img.shields.io/github/v/release/brsynth/straindesign?display_name=tag\u0026sort=semver)](version) [![Conda Version](https://img.shields.io/conda/vn/bioconda/straindesign.svg)](https://anaconda.org/bioconda/straindesign)  \n[![GitHub Super-Linter](https://github.com/brsynth/straindesign/workflows/Tests/badge.svg)](https://github.com/marketplace/actions/super-linter) [![Coverage](https://img.shields.io/coveralls/github/brsynth/straindesign)](coveralls)  \n[![License](https://img.shields.io/github/license/brsynth/straindesign)](license) [![DOI](https://zenodo.org/badge/436924636.svg)](https://zenodo.org/badge/latestdoi/436924636) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Gitter](https://badges.gitter.im/BioRetroSynth/SynBioCAD.svg)](https://gitter.im/BioRetroSynth/SynBioCAD?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge)  \n\n## Description\n\n*straindesign* provides a cli interface to predict gene knockout targets with an heterologous pathway.\nIntegrate an hard fork from [cameo](https://github.com/biosustain/cameo) (v0.13.6) named `cameobrs` to add features.\n\n## Installation\n\n```sh\nconda install -c bioconda straindesign\n```\n\n## Usage\n\n### Define the best combination of genes deletion to optimize a target\n\n```sh\npython -m straindesign simulate-deletion \\\n    [input files]\n    --input-model-file \u003cSBML file\u003e\n    --input-pathway-file \u003cSBML file\u003e\n    --input-medium-file \u003cCSV/TSV file\u003e\n    [parameters]\n    --biomass-rxn-id \u003cid reaction, str\u003e\n    --target-rxn-id \u003cid reaction, str\u003e\n    --substrate-rxn-id \u003cid reaction, str\u003e\n    [output file]\n    --output-file \u003cCSV/TSV file\u003e\n```\n\n### Delete genes in a model\n\n```sh\npython -m straindesign reduce-model \\\n    [input files]\n    --input-model-file \u003cSBML file\u003e\n    --input-straindesign-file \u003cCSV file\u003e\n    and/or\n    --input-gene-str \u003cid gene, str\u003e\n    [parameters]\n    --parameter-strategy-str \u003cyield-max, gene-max, gene-min\u003e\n    [output file]\n    --output-file-sbml \u003cSBML file\u003e\n```\n\nYou can provide a list of genes to delete in the model or the file produced by the command `simulate-deletion`.\nIf this file is provided, the combination of genes is choosen among three strategies:\n\n* yield-max: genes are sorted by the best yield\n* gene-max: the combination of the maximum number of genes\n* gene-min: the combination of the minimum number of genes\n\n### Produce a pareto plot\n\n```sh\npython -m straindesign analyzing-model \\\n    [input files]\n    --input-model-file \u003cSBML file\u003e\n    --input-medium-file \u003cCSV/TSV file\u003e\n    --input-pathway-file \u003cSBML file\u003e\n    [parameters]\n    --biomass-rxn-id \u003cid reaction, str\u003e\n    --target-rxn-id \u003cid reaction, str\u003e\n    --substrate-rxn-id \u003cid reaction, str\u003e\n    [output file]\n    --output-pareto-png \u003cPNG file\u003e\n```\nYou 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.  \nThe `substrate-rxn-id` argument lets you to choose the main carbon source.\n\n## Tests\n\nRequires:\n* *pytest*\n* *pytest-benchmark*\n\n```sh\npython -m pytest\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Fstraindesign","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrsynth%2Fstraindesign","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrsynth%2Fstraindesign/lists"}