{"id":26573254,"url":"https://github.com/linsalrob/pyfba","last_synced_at":"2025-03-23T00:39:57.936Z","repository":{"id":51118920,"uuid":"46241465","full_name":"linsalrob/PyFBA","owner":"linsalrob","description":"A python implementation of flux balance analysis to model microbial metabolism","archived":false,"fork":false,"pushed_at":"2023-02-25T21:54:29.000Z","size":11849,"stargazers_count":25,"open_issues_count":8,"forks_count":14,"subscribers_count":6,"default_branch":"master","last_synced_at":"2024-10-10T09:35:04.424Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://linsalrob.github.io/PyFBA/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/linsalrob.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.md","codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2015-11-15T23:51:34.000Z","updated_at":"2024-07-04T08:40:51.000Z","dependencies_parsed_at":"2022-09-17T07:10:29.716Z","dependency_job_id":"42d33b20-1af6-4b5f-9773-cdbf0e9d22bb","html_url":"https://github.com/linsalrob/PyFBA","commit_stats":{"total_commits":779,"total_committers":2,"mean_commits":389.5,"dds":0.08215661103979466,"last_synced_commit":"3723e95e6f96481c4fc470a004dc88da3617f3c3"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2FPyFBA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2FPyFBA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2FPyFBA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2FPyFBA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/linsalrob","download_url":"https://codeload.github.com/linsalrob/PyFBA/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245040190,"owners_count":20551299,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":[],"created_at":"2025-03-23T00:39:57.202Z","updated_at":"2025-03-23T00:39:57.927Z","avatar_url":"https://github.com/linsalrob.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Edwards Lab](https://img.shields.io/badge/Bioinformatics-EdwardsLab-03A9F4)](https://edwards.sdsu.edu/research)\n[![DOI](https://www.zenodo.org/badge/46241465.svg)](https://www.zenodo.org/badge/latestdoi/46241465)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n![GitHub language count](https://img.shields.io/github/languages/count/linsalrob/PyFBA)\n[![PyPi](https://img.shields.io/pypi/pyversions/pyfba.svg?style=flat-square\u0026label=PyPi%20Versions)](https://pypi.org/project/PyFBA/)\n[![BioConda Install](https://img.shields.io/conda/dn/bioconda/pyfba.svg?style=flat-square\u0026label=BioConda%20install)](https://anaconda.org/bioconda/pyfba)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/pyfba/badges/version.svg)](https://anaconda.org/bioconda/pyfba)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/pyfba/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda)\n\n\n# PyFBA\nA python implementation of flux balance analysis to model microbial metabolism. [Read more ...](http://linsalrob.github.io/PyFBA/)\n\n## About PyFBA\n\nPyFBA is a Python flux-balance-analysis package that allows you to build models from genomes, gapfill models, and run\nflux-balance-analysis on that model. The aim of PyFBA is to provide an extensible, python-based platform for\nFBA work.\n\nPyFBA is being developed by Daniel Cuevas, Taylor O'Connell, and Rob Edwards in [Rob's bioinformatics\ngroup](http://edwards.flinders.edu.au/) initially at [San Diego State University](http://www.sdsu.edu/) and now at \n[Flinders University](http://www.flinders.edu.au/). Amazing help was also provided by the developers of the ModelSEED, \nin particular  Janaka Edirisinghe, Chris Henry, Ross Overbeek and others at [Argonne National Labs](http://www.theseed.org/).\n\nYou can [read more about PyFBA](http://linsalrob.github.io/PyFBA/) on our github.io pages.\n\n## Installing PyFBA\n\nPyFBA is available in [bioconda](https://bioconda.github.io/) and we recommend installing it that way. It's what we \nuse!\n\n```commandline\nconda create -n pyfba -c bioconda pyfba\nconda activate pyfba\npyfba -v\npyfba help\n```\n\nThere are other options described in the [installation documents](INSTALLATION.md), but just use conda!\n\n## Getting Started with PyFBA\n\nOnce you have installed PyFBA, you will most likely want to build a model from a genome, gap fill that\nmodel, and test it for growth on different media. We have [detailed instructions](GETTING_STARTED.md) that walk you through the step-by-step\nprocedures that you need to use to run flux balance analysis on your own genome.\n\n### Citing PyFBA\n\nPlease use the command:\n\n```commandline\npyfba citations\n```\n\nto get the citations for PyFBA. They are available in _plain text_ and _bibtex_ format, please let us know if you would like\nother formats!\n\n### Copyright and License\n\nPyFBA is copyright Daniel Cuevas, Taylor O'Connell, and Rob Edwards, and is released under the MIT license.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Fpyfba","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flinsalrob%2Fpyfba","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Fpyfba/lists"}