{"id":22308543,"url":"https://github.com/sysbiochalmers/sybil-sbml","last_synced_at":"2025-07-29T06:30:41.966Z","repository":{"id":39406179,"uuid":"460453949","full_name":"SysBioChalmers/sybil-SBML","owner":"SysBioChalmers","description":"SBML (Systems Biology Markup Language) integration in sybil","archived":false,"fork":false,"pushed_at":"2023-08-01T19:31:34.000Z","size":322,"stargazers_count":4,"open_issues_count":3,"forks_count":0,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-04-05T08:51:15.332Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/SysBioChalmers.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2022-02-17T13:46:48.000Z","updated_at":"2024-02-23T02:09:42.000Z","dependencies_parsed_at":"2022-08-11T08:40:10.389Z","dependency_job_id":null,"html_url":"https://github.com/SysBioChalmers/sybil-SBML","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/SysBioChalmers/sybil-SBML","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2Fsybil-SBML","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2Fsybil-SBML/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2Fsybil-SBML/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2Fsybil-SBML/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioChalmers","download_url":"https://codeload.github.com/SysBioChalmers/sybil-SBML/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2Fsybil-SBML/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267639569,"owners_count":24119780,"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","status":"online","status_checked_at":"2025-07-29T02:00:12.549Z","response_time":2574,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":[],"created_at":"2024-12-03T20:14:19.481Z","updated_at":"2025-07-29T06:30:41.365Z","avatar_url":"https://github.com/SysBioChalmers.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# sybil-SBML\n\nThis SBML (Systems Biology Markup Language) integration provides SBML support for [sybil](https://github.com/SysBioChalmers/sybil).\n\nIf you're facing any problems, please open an [issue](issues/new) or a [discussion](/discusions/new).\n\n### Installation\n\n\u003e The guide below has worked with R 4.1.2 on Linux Mint 21, which is based on Ubuntu 22.04 LTS.\n\nStart by installing the dependencies. Follow the [installation instructions from libSBML](https://github.com/sbmlteam/libsbml#installation). Below is a shortcut of the instructions adapted to Ubuntu, thus might require some tweaking for your system.\n\nStart by fetching the latest libSBML and R interface from the official location:\n```bash\nwget https://sourceforge.net/projects/sbml/files/libsbml/5.18.0/stable/Linux/64-bit/libSBML-5.18.0-Linux-x64.deb\nwget https://sourceforge.net/projects/sbml/files/libsbml/5.18.0/stable/R%20interface/libSBML_5.18.0.tar.gz\n```\n\nThen install libSBML as a system library:\n```bash\nsudo apt install ./libSBML-5.18.0-Linux-x64.deb \n```\n\nIf the previous step failed, it might be that some libSBML dependencies (such as lixbml2) might need for the previous step to work:\n```bash\nsudo yum install libxml2-devel\n```\n\nFinally, proceed to install the R interface to libSBML (will take a while):\n```bash\nR CMD INSTALL libSBML_5.18.0.tar.gz\n```\n\nFor various reasons, `sybil-SBML` is temporarily not available on CRAN anymore. Until then, it needs to be installed straight from this GitHub repository:\n\nUse the following commands in the R console to install this package:\n```R\ninstall.packages(\"remotes\")\nremotes::install_github(\"SysBioChalmers/sybil-SBML\")\n```\n\nIf the above fails because of failing to load `libsbml.so`, try adding the path to this file before starting R:\n```bash\nLD_LIBRARY_PATH=/usr/lib64 R\n```\nIf the fix worked, make this permanent by changing this variable in your `.bashrc` file.\n\nRemove the installation files::\n```bash\nrm libSBML-5.18.0-Linux-x64.deb libSBML_5.18.0.tar.gz \n```\n\n\n_Note_: This repository was previously hosted at https://gitlab.cs.uni-duesseldorf.de/general/ccb/sybilSBML .","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fsybil-sbml","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsysbiochalmers%2Fsybil-sbml","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fsybil-sbml/lists"}