{"id":45141467,"url":"https://github.com/biomass-dev/biomass","last_synced_at":"2026-02-20T00:37:59.571Z","repository":{"id":37282679,"uuid":"215932388","full_name":"biomass-dev/biomass","owner":"biomass-dev","description":"A Python Framework for Modeling and Analysis of Signaling Systems","archived":false,"fork":false,"pushed_at":"2026-01-19T21:26:39.000Z","size":27273,"stargazers_count":30,"open_issues_count":1,"forks_count":13,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-01-27T05:56:07.139Z","etag":null,"topics":["biochemical-networks","computational-biology","dynamical-systems","kinetic-modeling","modeling","network-analysis","ode","optimization","ordinary-differential-equations","parameter-estimation","python","simulation","systems-biology","systems-biology-simulation"],"latest_commit_sha":null,"homepage":"http://biomass-core.rtfd.io","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/biomass-dev.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","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":"2019-10-18T03:16:39.000Z","updated_at":"2025-09-19T14:28:37.000Z","dependencies_parsed_at":"2024-01-29T21:55:12.420Z","dependency_job_id":"28de99b6-0b73-4a60-affe-7ba64574e53b","html_url":"https://github.com/biomass-dev/biomass","commit_stats":{"total_commits":950,"total_committers":11,"mean_commits":86.36363636363636,"dds":0.3810526315789474,"last_synced_commit":"2ad16db84085b28f69ac41c439ec5e2660ac9120"},"previous_names":[],"tags_count":36,"template":false,"template_full_name":null,"purl":"pkg:github/biomass-dev/biomass","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomass-dev%2Fbiomass","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomass-dev%2Fbiomass/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomass-dev%2Fbiomass/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomass-dev%2Fbiomass/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biomass-dev","download_url":"https://codeload.github.com/biomass-dev/biomass/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biomass-dev%2Fbiomass/sbom","scorecard":{"id":239253,"data":{"date":"2025-08-11","repo":{"name":"github.com/biomass-dev/biomass","commit":"f4654b7d3dfc1a5534f533501ddeca70e8889aaa"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":4.4,"checks":[{"name":"Maintained","score":0,"reason":"0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"Code-Review","score":1,"reason":"Found 4/25 approved changesets -- score normalized to 1","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Dangerous-Workflow","score":10,"reason":"no dangerous workflow patterns detected","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Info: jobLevel 'actions' permission set to 'read': .github/workflows/codeql.yml:16","Info: jobLevel 'contents' permission set to 'read': .github/workflows/codeql.yml:17","Warn: no topLevel permission defined: .github/workflows/build.yml:1","Warn: no topLevel permission defined: .github/workflows/codeql.yml:1","Warn: no topLevel permission defined: .github/workflows/pypi-publish.yml:1","Info: no jobLevel write permissions found"],"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"Pinned-Dependencies","score":0,"reason":"dependency not pinned by hash detected -- score normalized to 0","details":["Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/build.yml:17: update your workflow using https://app.stepsecurity.io/secureworkflow/biomass-dev/biomass/build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/build.yml:19: update your workflow using https://app.stepsecurity.io/secureworkflow/biomass-dev/biomass/build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/codeql.yml:27: update your workflow using https://app.stepsecurity.io/secureworkflow/biomass-dev/biomass/codeql.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/codeql.yml:30: update your workflow using https://app.stepsecurity.io/secureworkflow/biomass-dev/biomass/codeql.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/codeql.yml:36: update your workflow using https://app.stepsecurity.io/secureworkflow/biomass-dev/biomass/codeql.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/codeql.yml:39: update your workflow using https://app.stepsecurity.io/secureworkflow/biomass-dev/biomass/codeql.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pypi-publish.yml:12: update your workflow using https://app.stepsecurity.io/secureworkflow/biomass-dev/biomass/pypi-publish.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/pypi-publish.yml:13: update your workflow using https://app.stepsecurity.io/secureworkflow/biomass-dev/biomass/pypi-publish.yml/master?enable=pin","Warn: pipCommand not pinned by hash: .github/workflows/build.yml:26","Warn: pipCommand not pinned by hash: .github/workflows/build.yml:27","Warn: pipCommand not pinned by hash: .github/workflows/build.yml:28","Warn: pipCommand not pinned by hash: .github/workflows/pypi-publish.yml:16","Warn: pipCommand not pinned by hash: .github/workflows/pypi-publish.yml:17","Info:   0 out of   8 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   5 pipCommand dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"Vulnerabilities","score":10,"reason":"0 existing vulnerabilities detected","details":null,"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"CII-Best-Practices","score":2,"reason":"badge detected: InProgress","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Info: FSF or OSI recognized license: Apache License 2.0: LICENSE:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"Branch-Protection","score":-1,"reason":"internal error: error during branchesHandler.setup: internal error: githubv4.Query: Resource not accessible by integration","details":null,"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}},{"name":"SAST","score":7,"reason":"SAST tool detected but not run on all commits","details":["Info: SAST configuration detected: CodeQL","Warn: 4 commits out of 30 are checked with a SAST tool"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}}]},"last_synced_at":"2025-08-17T06:21:55.933Z","repository_id":37282679,"created_at":"2025-08-17T06:21:55.934Z","updated_at":"2025-08-17T06:21:55.934Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29637461,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-19T22:32:43.237Z","status":"ssl_error","status_checked_at":"2026-02-19T22:32:38.330Z","response_time":117,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":["biochemical-networks","computational-biology","dynamical-systems","kinetic-modeling","modeling","network-analysis","ode","optimization","ordinary-differential-equations","parameter-estimation","python","simulation","systems-biology","systems-biology-simulation"],"created_at":"2026-02-20T00:37:58.098Z","updated_at":"2026-02-20T00:37:58.641Z","avatar_url":"https://github.com/biomass-dev.png","language":"Python","readme":null,"funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiomass-dev%2Fbiomass","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiomass-dev%2Fbiomass","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiomass-dev%2Fbiomass/lists"}