{"id":423434,"name":"ratesb_python: A Python Package for Analyzing Rate Laws in Biological Models","description":"ratesb_python: A Python Package for Analyzing Rate Laws in Biological Models - Published in JOSS (2025)","url":"https://github.com/sys-bio/ratesb_python","last_synced_at":"2025-10-10T14:30:17.854Z","repository":{"id":186969678,"uuid":"673459956","full_name":"sys-bio/ratesb_python","owner":"sys-bio","description":"Analysis of rate laws in reaction networks.","archived":false,"fork":false,"pushed_at":"2025-09-22T21:31:45.000Z","size":28080,"stargazers_count":1,"open_issues_count":8,"forks_count":2,"subscribers_count":8,"default_branch":"main","last_synced_at":"2025-09-29T10:09:40.589Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/sys-bio.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-08-01T17:12:20.000Z","updated_at":"2025-09-22T21:28:52.000Z","dependencies_parsed_at":"2024-02-09T08:28:54.399Z","dependency_job_id":"828bc28c-17d5-4151-98f1-510d61d8dbf5","html_url":"https://github.com/sys-bio/ratesb_python","commit_stats":null,"previous_names":["sys-bio/ratesb-python","sys-bio/ratesb_python"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/sys-bio/ratesb_python","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sys-bio","download_url":"https://codeload.github.com/sys-bio/ratesb_python/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279004191,"owners_count":26083688,"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":"2025-10-10T02:00:06.843Z","response_time":62,"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"}},"owner":{"login":"sys-bio","name":"UW Sauro Lab","uuid":"5590646","kind":"organization","description":"","email":"hsauro@u.washington.edu","website":"www.sys-bio.org","location":"Seattle","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/5590646?v=4","repositories_count":91,"last_synced_at":"2023-08-10T01:54:11.480Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/sys-bio","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-06T22:48:33.198Z","updated_at":"2023-08-10T01:54:13.864Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sys-bio","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sys-bio/repositories"},"packages":[{"id":8169977,"name":"ratesb-python","ecosystem":"pypi","description":"rate law analysis for systems biology","homepage":"https://github.com/sys-bio/ratesb_python","licenses":"MIT License\n        \n        Copyright (c) 2023 UW Sauro Lab\n        \n        Permission is hereby granted, free of charge, to any person obtaining a copy\n        of this software and associated documentation files (the \"Software\"), to deal\n        in the Software without restriction, including without limitation the rights\n        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell\n        copies of the Software, and to permit persons to whom the Software is\n        furnished to do so, subject to the following conditions:\n        \n        The above copyright notice and this permission notice shall be included in all\n        copies or substantial portions of the Software.\n        \n        THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\n        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\n        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\n        SOFTWARE.\n        ","normalized_licenses":["Other"],"repository_url":"https://github.com/sys-bio/ratesb_python","keywords_array":[],"namespace":null,"versions_count":10,"first_release_published_at":"2023-08-31T18:07:04.000Z","latest_release_published_at":"2025-06-01T20:24:02.000Z","latest_release_number":"0.2.8","last_synced_at":"2025-09-29T10:16:43.710Z","created_at":"2023-08-31T18:22:26.285Z","updated_at":"2025-09-29T10:54:33.648Z","registry_url":"https://pypi.org/project/ratesb-python/","install_command":"pip install ratesb-python --index-url https://pypi.org/simple","documentation_url":"https://ratesb-python.readthedocs.io/","metadata":{"funding":null,"documentation":null,"classifiers":["Operating System :: OS Independent","Programming Language :: Python :: 3"],"normalized_name":"ratesb-python","project_status":null},"repo_metadata":{"id":186969678,"uuid":"673459956","full_name":"sys-bio/ratesb_python","owner":"sys-bio","description":"Analysis of rate laws in reaction networks.","archived":false,"fork":false,"pushed_at":"2025-09-22T06:51:51.000Z","size":28073,"stargazers_count":1,"open_issues_count":9,"forks_count":2,"subscribers_count":8,"default_branch":"main","last_synced_at":"2025-09-22T08:42:46.413Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/sys-bio.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-08-01T17:12:20.000Z","updated_at":"2025-09-22T06:51:55.000Z","dependencies_parsed_at":"2024-02-09T08:28:54.399Z","dependency_job_id":"828bc28c-17d5-4151-98f1-510d61d8dbf5","html_url":"https://github.com/sys-bio/ratesb_python","commit_stats":null,"previous_names":["sys-bio/ratesb-python","sys-bio/ratesb_python"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/sys-bio/ratesb_python","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sys-bio","download_url":"https://codeload.github.com/sys-bio/ratesb_python/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":277496295,"owners_count":25827931,"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":"2025-09-29T02:00:09.175Z","response_time":84,"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"},"owner_record":{"login":"sys-bio","name":"UW Sauro Lab","uuid":"5590646","kind":"organization","description":"","email":"hsauro@u.washington.edu","website":"www.sys-bio.org","location":"Seattle","twitter":null,"company":null,"icon_url":"https://avatars.githubusercontent.com/u/5590646?v=4","repositories_count":91,"last_synced_at":"2023-08-10T01:54:11.480Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/sys-bio","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-06T22:48:33.198Z","updated_at":"2023-08-10T01:54:13.864Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sys-bio","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sys-bio/repositories"},"tags":[]},"repo_metadata_updated_at":"2025-09-29T10:54:33.648Z","dependent_packages_count":0,"downloads":32,"downloads_period":"last-month","dependent_repos_count":0,"rankings":{"downloads":null,"dependent_repos_count":69.77214682758274,"dependent_packages_count":7.485922955348075,"stargazers_count":39.11522860433672,"forks_count":30.200010015524064,"docker_downloads_count":null,"average":36.6433271006979},"purl":"pkg:pypi/ratesb-python","advisories":[],"docker_usage_url":"https://docker.ecosyste.ms/usage/pypi/ratesb-python","docker_dependents_count":null,"docker_downloads_count":null,"usage_url":"https://repos.ecosyste.ms/usage/pypi/ratesb-python","dependent_repositories_url":"https://repos.ecosyste.ms/api/v1/usage/pypi/ratesb-python/dependencies","status":null,"funding_links":[],"critical":null,"issue_metadata":{"last_synced_at":"2025-09-23T23:11:24.405Z","issues_count":16,"pull_requests_count":1,"avg_time_to_close_issue":3785030.875,"avg_time_to_close_pull_request":7259521.0,"issues_closed_count":8,"pull_requests_closed_count":1,"pull_request_authors_count":1,"issue_authors_count":3,"avg_comments_per_issue":0.8125,"avg_comments_per_pull_request":2.0,"merged_pull_requests_count":0,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":11,"past_year_pull_requests_count":1,"past_year_avg_time_to_close_issue":3966631.4285714286,"past_year_avg_time_to_close_pull_request":7259521.0,"past_year_issues_closed_count":7,"past_year_pull_requests_closed_count":1,"past_year_pull_request_authors_count":1,"past_year_issue_authors_count":2,"past_year_avg_comments_per_issue":1.0909090909090908,"past_year_avg_comments_per_pull_request":2.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":0,"issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python/issues","maintainers":[{"login":"longxf21","count":5,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/longxf21"}],"active_maintainers":[]},"versions_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/ratesb-python/versions","version_numbers_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/ratesb-python/version_numbers","dependent_packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/ratesb-python/dependent_packages","related_packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages/ratesb-python/related_packages","maintainers":[{"uuid":"flx000327","login":"flx000327","name":null,"email":null,"url":null,"packages_count":2,"html_url":"https://pypi.org/user/flx000327/","role":null,"created_at":"2023-08-31T18:23:36.941Z","updated_at":"2023-08-31T18:23:36.941Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers/flx000327/packages"}],"registry":{"name":"pypi.org","url":"https://pypi.org","ecosystem":"pypi","default":true,"packages_count":737766,"maintainers_count":313452,"namespaces_count":0,"keywords_count":244029,"github":"pypi","metadata":{"funded_packages_count":52179},"icon_url":"https://github.com/pypi.png","created_at":"2022-04-04T15:19:23.364Z","updated_at":"2025-10-10T05:47:48.012Z","packages_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/packages","maintainers_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/maintainers","namespaces_url":"https://packages.ecosyste.ms/api/v1/registries/pypi.org/namespaces"}}],"commits":{"id":11401024,"full_name":"sys-bio/ratesb_python","default_branch":"master","committers":[{"name":"Aldrich Fan","email":"fanaldrich@gmail.com","login":null,"count":64},{"name":"Aldrich Fan","email":"longxf@uw.edu","login":null,"count":3},{"name":"Longxuan Fan","email":"flxnb@amazon.com","login":null,"count":3},{"name":"github-actions[bot]","email":"github-actions[bot]@users.noreply.github.com","login":null,"count":2},{"name":"longxf","email":"104124300+longxf21@users.noreply.github.com","login":null,"count":2},{"name":"Joseph Hellerstein","email":"joseph-hellerstein@users.noreply.github.com","login":null,"count":1}],"total_commits":75,"total_committers":6,"total_bot_commits":2,"total_bot_committers":1,"mean_commits":12.5,"dds":0.1466666666666666,"past_year_committers":[{"name":"Aldrich Fan","email":"fanaldrich@gmail.com","login":null,"count":23},{"name":"Longxuan Fan","email":"flxnb@amazon.com","login":null,"count":3},{"name":"github-actions[bot]","email":"github-actions[bot]@users.noreply.github.com","login":null,"count":2}],"past_year_total_commits":28,"past_year_total_committers":3,"past_year_total_bot_commits":2,"past_year_total_bot_committers":1,"past_year_mean_commits":9.333333333333334,"past_year_dds":0.1785714285714286,"last_synced_at":"2025-09-29T10:58:15.736Z","last_synced_commit":"befce5caca28c03746d9cfbc668d298081ca8f54","created_at":"2025-09-29T10:54:27.281Z","updated_at":"2025-09-29T10:58:11.940Z","commits_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python/commits","host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-10-10T00:00:09.217Z","repositories_count":6036804,"commits_count":920841832,"contributors_count":35722587,"owners_count":1097940,"icon_url":"https://github.com/github.png","host_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://commits.ecosyste.ms/api/v1/hosts/GitHub/repositories"}},"issues_stats":{"full_name":"sys-bio/ratesb_python","html_url":"https://github.com/sys-bio/ratesb_python","last_synced_at":"2025-09-23T23:11:24.405Z","status":null,"issues_count":16,"pull_requests_count":1,"avg_time_to_close_issue":3785030.875,"avg_time_to_close_pull_request":7259521.0,"issues_closed_count":8,"pull_requests_closed_count":1,"pull_request_authors_count":1,"issue_authors_count":3,"avg_comments_per_issue":0.8125,"avg_comments_per_pull_request":2.0,"merged_pull_requests_count":0,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":11,"past_year_pull_requests_count":1,"past_year_avg_time_to_close_issue":3966631.4285714286,"past_year_avg_time_to_close_pull_request":7259521.0,"past_year_issues_closed_count":7,"past_year_pull_requests_closed_count":1,"past_year_pull_request_authors_count":1,"past_year_issue_authors_count":2,"past_year_avg_comments_per_issue":1.0909090909090908,"past_year_avg_comments_per_pull_request":2.0,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":0,"created_at":"2025-08-29T17:13:59.161Z","updated_at":"2025-09-23T23:11:24.407Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/sys-bio%2Fratesb_python/issues","issue_labels_count":{"enhancement":2},"pull_request_labels_count":{},"issue_author_associations_count":{"NONE":11,"COLLABORATOR":5},"pull_request_author_associations_count":{"NONE":1},"issue_authors":{"ayush9pandey":7,"longxf21":5,"dilawar":4},"pull_request_authors":{"RMeli":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-10-10T00:00:07.881Z","repositories_count":10968509,"issues_count":33895624,"pull_requests_count":110053665,"authors_count":11032635,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"NONE":11},"past_year_pull_request_author_associations_count":{"NONE":1},"past_year_issue_authors":{"ayush9pandey":7,"dilawar":4},"past_year_pull_request_authors":{"RMeli":1},"maintainers":[{"login":"longxf21","count":5,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/longxf21"}],"active_maintainers":[]},"events":{"total":{"IssuesEvent":23,"WatchEvent":1,"MemberEvent":1,"IssueCommentEvent":31,"PushEvent":23,"PullRequestEvent":1,"ForkEvent":1},"last_year":{"IssuesEvent":23,"WatchEvent":1,"MemberEvent":1,"IssueCommentEvent":31,"PushEvent":23,"PullRequestEvent":1,"ForkEvent":1}},"keywords":[],"dependencies":[{"ecosystem":"pypi","filepath":"pyproject.toml","sha":null,"kind":"manifest","created_at":"2023-08-31T11:40:46.367Z","updated_at":"2023-08-31T11:40:46.367Z","repository_link":"https://github.com/sys-bio/ratesb_python/blob/main/pyproject.toml","dependencies":[]},{"ecosystem":"actions","filepath":".github/workflows/python_tests.yml","sha":null,"kind":"manifest","created_at":"2024-02-09T08:28:54.260Z","updated_at":"2024-02-09T08:28:54.260Z","repository_link":"https://github.com/sys-bio/ratesb_python/blob/main/.github/workflows/python_tests.yml","dependencies":[{"id":16127972836,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":16127972837,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"docker","filepath":".devcontainer/Dockerfile","sha":null,"kind":"manifest","created_at":"2024-02-09T08:28:54.308Z","updated_at":"2024-02-09T08:28:54.308Z","repository_link":"https://github.com/sys-bio/ratesb_python/blob/main/.devcontainer/Dockerfile","dependencies":[{"id":16127972838,"package_name":"python","ecosystem":"docker","requirements":"3.9-slim","direct":true,"kind":"build","optional":false}]}],"score":7.485491608030754,"created_at":"2025-10-10T14:30:06.388Z","updated_at":"2025-10-10T14:30:19.156Z","avatar_url":"https://github.com/sys-bio.png","language":"Python","category":null,"sub_category":null,"monthly_downloads":32,"funding_links":[],"readme_doi_urls":["https://doi.org/10.1186/s12859-023-05380-3"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/423434","html_url":"https://science.ecosyste.ms/projects/423434"}