{"id":19221749,"url":"https://github.com/matthiaskoenig/dfba","last_synced_at":"2026-03-05T14:01:43.453Z","repository":{"id":68691986,"uuid":"71236313","full_name":"matthiaskoenig/dfba","owner":"matthiaskoenig","description":"Encoding Dynamic Flux Balance Analysis in SBML","archived":false,"fork":false,"pushed_at":"2020-09-16T20:59:49.000Z","size":89802,"stargazers_count":11,"open_issues_count":9,"forks_count":1,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-02-23T09:43:12.368Z","etag":null,"topics":["dfba","sbml","simulation"],"latest_commit_sha":null,"homepage":"","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/matthiaskoenig.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-10-18T10:20:51.000Z","updated_at":"2023-05-29T12:04:55.000Z","dependencies_parsed_at":"2023-04-13T12:33:52.907Z","dependency_job_id":null,"html_url":"https://github.com/matthiaskoenig/dfba","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/matthiaskoenig/dfba","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthiaskoenig%2Fdfba","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthiaskoenig%2Fdfba/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthiaskoenig%2Fdfba/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthiaskoenig%2Fdfba/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/matthiaskoenig","download_url":"https://codeload.github.com/matthiaskoenig/dfba/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/matthiaskoenig%2Fdfba/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30130030,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-05T12:40:50.676Z","status":"ssl_error","status_checked_at":"2026-03-05T12:39:32.209Z","response_time":93,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: 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":["dfba","sbml","simulation"],"created_at":"2024-11-09T14:44:09.936Z","updated_at":"2026-03-05T14:01:43.435Z","avatar_url":"https://github.com/matthiaskoenig.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Dynamic Flux Balance Analysis in SBML\n[![DOI](https://www.zenodo.org/badge/71236313.svg)](https://www.zenodo.org/badge/latestdoi/71236313)\n[![GitHub version](https://badge.fury.io/gh/matthiaskoenig%2Fdfba.svg)](https://badge.fury.io/gh/matthiaskoenig%2Fdfba)\n[![License (LGPL version 3)](https://img.shields.io/badge/license-LGPLv3.0-blue.svg?style=flat-square)](http://opensource.org/licenses/LGPL-3.0)\n\n\u003cb\u003e\u003ca href=\"https://orcid.org/0000-0003-1725-179X\" title=\"orcid id\"\u003e\u003cimg src=\"./docs/images/logos/orcid.png\" height=\"15\"/\u003e\u003c/a\u003e Matthias König,\n Leandro Watanabe, Chris Myers\n\u003c/b\u003e\n\nThis repository provides guidelines and rules for the encoding of dynamic flux balance analysis (DFBA) models in SBML. The latest guidelines and rules are available from this repository at [latest schema](./schema/DFBA_models_in_SBML.md). \n\nAs part of this project DFBA implementations based on these guidelines have been implemented in \n[iBioSim](http://www.async.ece.utah.edu/ibiosim) and [sbmlutils](https://github.com/matthiaskoenig/sbmlutils/).\n \n\n\u003ca href=\"http://www.async.ece.utah.edu/ibiosim\" title=\"iBioSim\" target=\"_blank\"\u003e\u003cimg src=\"./docs/images/logos/ibiosim.png\" height=\"35\"/\u003e\u003c/a\u003e\u0026nbsp;\n\u003ca href=\"https://github.com/matthiaskoenig/sbmlutils/\" title=\"sbmlutils\" target=\"_blank\"\u003e\u003cimg src=\"./docs/images/logos/sbmlutils.jpg\" height=\"35\"/\u003e\u003c/a\u003e\u0026nbsp;\n\nThis repository contains the following content\n* [`./docs/`](./docs/): documentation, presentation, tutorial\n* [`./schema/`](./schema/): guidelines for encoding DFBA in SBML\n* [`./models/`](./models/): examples models with simulation results, cytoscape visualizations, jupyter notebooks\n* [`./README.md`](./README.md): this document\n\nDetailed instructions on how to run the example models are provided [below](#running-example-models).\n\n## Standardization\nThis effort builds on existing standards, i.e., [SBML](http://sbml.org), [SED-ML](http://sed-ml.org), and the [COMBINE archive](http://co.mbine.org/documents/archive).\n\n\u003ca href=\"http://sbml.org\" title=\"SBML\" target=\"_blank\"\u003e\u003cimg src=\"./docs/images/logos/sbml.png\" height=\"35\"/\u003e\u003c/a\u003e\u0026nbsp;\n\u003ca href=\"http://sed-ml.org\" title=\"SED-ML\" target=\"_blank\"\u003e\u003cimg src=\"./docs/images/logos/sedml.png\" height=\"35\"/\u003e\u003c/a\u003e\u0026nbsp;\n\u003ca href=\"http://co.mbine.org/documents/archive\" title=\"CombineArchive\" target=\"_blank\"\u003e\u003cimg src=\"./docs/images/logos/omex.png\" height=\"35\"/\u003e\u003c/a\u003e\u0026nbsp;\n\n##  How to cite\nIf you use these schema and guidelines and/or the provided examples, or want to reference the information within,  \nplease cite corresponding manuscript and this repository via its DOI\n\n[![DOI](https://www.zenodo.org/badge/71236313.svg)](https://www.zenodo.org/badge/latestdoi/71236313)\n\nThe latest manuscript is available from\n[https://www.overleaf.com/6382003zbbpfy#/21488847/](https://www.overleaf.com/6382003zbbpfy#/21488847/).\n\n  \n## License\n* Source Code: [LGPLv3](http://opensource.org/licenses/LGPL-3.0)\n* Documentation: [CC BY-SA 4.0](http://creativecommons.org/licenses/by-sa/4.0/)\n\n## Funding\nMatthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany) \nwithin the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054).\n\n\u003ca href=\"http://www.lisym.org/\" alt=\"LiSyM\" target=\"_blank\"\u003e\u003cimg src=\"./docs/images/logos/lisym.png\" height=\"35\"\u003e\u003c/a\u003e \u0026nbsp;\u0026nbsp;\n\u003ca href=\"http://www.bmbf.de/\" alt=\"BMBF\" target=\"_blank\"\u003e\u003cimg src=\"./docs/images/logos/bmbf.png\" height=\"35\"\u003e\u003c/a\u003e \u0026nbsp;\u0026nbsp;\n\nThe development of iBioSim is supported by the National Science Foundation under Grants CCF-1218095 and CCF-1748200. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.\n\n\u003ca href=\"http://www.lisym.org/\" alt=\"NSF\" target=\"_blank\"\u003e\u003cimg src=\"./docs/images/logos/nsf.jpg\" height=\"50\"\u003e\u003c/a\u003e \n\n# Example models\nModel examples encoded in the proposed dynamic FBA scheme in the [`./models/`](./models/) folder. \nExample models contain\n* SBML model(s) according to guidelines and rules\n* SED-ML file encoding example simulation experiments\n* Simulation results for [iBioSim](http://www.async.ece.utah.edu/ibiosim) and [sbmlutils](https://github.com/matthiaskoenig/sbmlutils/)\n* Jupyter notebooks\n* Cytoscape visualization\n\nThe model examples are provided as COMBINE archives for exchange.\n\n\n## sbmlutils \n\u003ca href=\"https://github.com/matthiaskoenig/sbmlutils/\" title=\"sbmlutils\"\u003e\u003cimg src=\"./docs/images/logos/sbmlutils.jpg\" height=\"35\"/\u003e\u003c/a\u003e \n\nExample jupyter notebooks reproducing the results are available for the individual DFBA models. \nInstallation instructions and the entry point is available at [`./models/index.ipynb`](./models/index.ipynb)\n\n* [`./models/toy_wholecell/toy_wholecell.ipynb`](./models/toy_wholecell/toy_wholecell.ipynb)\n* [`./models/toy_atp/toy_atp.ipynb`](./models/toy_atp/toy_atp.ipynb)\n* [`./models/diauxic_growth/diauxic_growth.ipynb`](./models/diauxic_growth/diauxic_growth.ipynb)\n* [`./models/ecoli/ecoli.ipynb`](./models/ecoli/ecoli.ipynb)\n\n## iBioSim\n\u003ca href=\"http://www.async.ece.utah.edu/ibiosim\" title=\"iBioSim\"\u003e\u003cimg src=\"./docs/images/logos/ibiosim.png\" height=\"35\"/\u003e\u003c/a\u003e\n\nTo use iBioSim, you can follow the instructions available [here](./models/iBioSim_Tutorial.md).\n\n## Tool reproducibility\nThe numerical identity of the results was checked with results available in the\nfollowing notebook  \n[`./models/compare.ipynb`](./models/compare.ipynb)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmatthiaskoenig%2Fdfba","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmatthiaskoenig%2Fdfba","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmatthiaskoenig%2Fdfba/lists"}