{"id":"cmuxiqskv0xm2ad071gram6d7","slug":"cobrapy","publicId":"776ad32c-93fc-4ebf-99bf-ddd8b4877269","name":"cobrapy","description":"Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes, gap filling, and SBML model validation for systems biology and metabolic engineering.","version":"1.5","author":"k-dense-ai","license":"GPL-2.0 license","compatibility":"Requires Python 3.9+ and cobra; examples tested with Python 3.12 and cobra 0.32.1. GLPK installs via swiglpk; commercial solvers need separate installation/licensing. Remote model downloads need network access; bundled textbook examples run offline.","status":"completed","overallGrade":"B","scannerVersion":11,"fileCount":3,"hasSkillMd":true,"hasScripts":false,"hasReferences":true,"hasEvals":false,"hasAssets":false,"sourceType":"github","sourceUrl":"https://github.com/k-dense-ai/scientific-agent-skills/tree/main/skills/cobrapy","createdAt":"2026-10-07T02:59:07.183Z","completedAt":"2026-10-07T02:59:07.181Z","visibility":"public","publishedAt":"2026-09-10T21:06:22.289Z","category":"","frameworks":[],"badgeStatus":"conditional","downloadCount":0,"verdictRationale":{"summary":"Skill has warnings: 1 warning in security or structure checks.","verdict":"warn","scanners":[{"source":"vettd","weight":1,"verdict":"warn"},{"source":"cisco","weight":0.8,"verdict":"pass"}],"consensus":"warn","warnTriggers":["References external URL — review for indirect prompt injection risk"],"policyVersion":"consensus-v1","hardFailTriggers":[]},"verdictPolicyVersion":"consensus-v1","skillId":"cmtw0p08zbbv8ad07w5v5smkq","findings":[{"id":"cmuxiqskv0xm3ad07g05406px","source":"vettd","category":"security","label":"References external URL — review for indirect prompt injection risk","detail":"External URL(s) detected in SKILL.md — referenced content can change after audit","severity":"medium","ruleId":"VTD-0088","owaspLlmCategory":null,"intent":null,"chainId":null,"fingerprint":"42638a8b7e9fc5df27449992eaebc724","filepath":"SKILL.md"}],"scannerRuns":[{"source":"cisco","status":"success","verdict":null,"grade":"A","findingCount":0,"criticalCount":0,"highCount":0},{"source":"vettd","status":"success","verdict":null,"grade":"B","findingCount":1,"criticalCount":0,"highCount":0}],"user":{"name":"Kris Mondlane","image":"https://avatars.githubusercontent.com/u/237055?v=4"},"repository":{"owner":"k-dense-ai","name":"scientific-agent-skills"},"freshness":{"status":"verified_unchanged","reason":null,"retryable":false,"renamedTo":null,"lastCheckedAt":"2026-10-22T06:19:40.309Z","lastVerifiedAt":"2026-10-22T06:19:40.309Z","lastChangeDetectedAt":"2026-10-08T09:30:35.585Z","scannedHash":"eb30956411b8b0a4d00c89665bad802b3cbdfcdb","latestUpstreamHash":"eb30956411b8b0a4d00c89665bad802b3cbdfcdb","nextCheckDueAt":"2026-10-23T04:08:48.299Z"},"signalCategories":[{"category":"safety","label":"Safety","form":"graded","verdict":null,"rows":[]},{"category":"reliability","label":"Reliability & Quality","form":"graded","verdict":null,"rows":[]},{"category":"performance","label":"Performance","form":"measured","verdict":{"form":"measured","magnitudes":[{"ruleId":"performance/static-context-tokens","label":"Static context tokens","value":2582,"unit":null,"method":"tiktoken/cl100k_base/skill-md-body"}]},"rows":[{"origin":"signal","id":"cmuxiqtet0xmxad079zdjx5cj","subjectType":"skill_audit","subjectId":"cmuxiqskv0xm2ad071gram6d7","relatedType":"","relatedId":"","dataCategory":"performance","sourceClass":"scan","source":"vettd","ruleId":"performance/static-context-tokens","severity":null,"label":"Static context tokens","detail":null,"valueNum":2582,"valueText":null,"unit":null,"method":"tiktoken/cl100k_base/skill-md-body","derivation":null,"confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T02:59:05.000Z","payload":null},{"origin":"signal","id":"cmuxiqu9t0xuhad07ze9fublk","subjectType":"skill_audit","subjectId":"cmuxiqskv0xm2ad071gram6d7","relatedType":"","relatedId":"","dataCategory":"performance","sourceClass":"scan","source":"vettd","ruleId":"performance/progressive-disclosure","severity":null,"label":"Progressive disclosure","detail":null,"valueNum":null,"valueText":"present","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T02:59:05.000Z","payload":null}]},{"category":"cost","label":"Cost","form":"measured","verdict":null,"rows":[]},{"category":"compatibility","label":"Compatibility","form":"unjudged","verdict":{"form":"unjudged"},"rows":[{"origin":"signal","id":"cmuxiqthg0xndad073y6ss10r","subjectType":"skill_audit","subjectId":"cmuxiqskv0xm2ad071gram6d7","relatedType":"","relatedId":"","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-environment-assumptions","severity":null,"label":"Declared environment assumptions","detail":null,"valueNum":null,"valueText":"Requires Python 3.9+ and cobra; examples tested with Python 3.12 and cobra 0.32.1. GLPK installs via swiglpk; commercial solvers need separate installation/licensing. Remote model downloads need network access; bundled textbook examples run offline.","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T02:59:05.000Z","payload":null},{"origin":"signal","id":"cmuxiqtkx0xomad07b4tk1d6h","subjectType":"skill_audit","subjectId":"cmuxiqskv0xm2ad071gram6d7","relatedType":"declared_tool","relatedId":"Bash","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-required-tools","severity":null,"label":"Declared required tool","detail":null,"valueNum":null,"valueText":"Bash","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T02:59:05.000Z","payload":null},{"origin":"signal","id":"cmuxiqtqa0xpwad07boa2bdt0","subjectType":"skill_audit","subjectId":"cmuxiqskv0xm2ad071gram6d7","relatedType":"declared_tool","relatedId":"Write","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-required-tools","severity":null,"label":"Declared required tool","detail":null,"valueNum":null,"valueText":"Write","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T02:59:05.000Z","payload":null},{"origin":"signal","id":"cmuxiqtps0xpcad07vu8o1z7f","subjectType":"skill_audit","subjectId":"cmuxiqskv0xm2ad071gram6d7","relatedType":"declared_tool","relatedId":"Read","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-required-tools","severity":null,"label":"Declared required tool","detail":null,"valueNum":null,"valueText":"Read","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T02:59:05.000Z","payload":null},{"origin":"signal","id":"cmuxiqtnc0xp0ad07jm3fpkqp","subjectType":"skill_audit","subjectId":"cmuxiqskv0xm2ad071gram6d7","relatedType":"declared_tool","relatedId":"Edit","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-required-tools","severity":null,"label":"Declared required tool","detail":null,"valueNum":null,"valueText":"Edit","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T02:59:05.000Z","payload":null},{"origin":"signal","id":"cmuxiqtvu0xrcad07o9b7a10w","subjectType":"skill_audit","subjectId":"cmuxiqskv0xm2ad071gram6d7","relatedType":"","relatedId":"","dataCategory":"compatibility","sourceClass":"scan","source":"vettd","ruleId":"compatibility/declared-name","severity":null,"label":"Declared skill name","detail":null,"valueNum":null,"valueText":"cobrapy","unit":null,"method":null,"derivation":"read","confidence":null,"sampleSize":null,"synthetic":false,"firstParty":true,"observedAt":"2026-10-07T02:59:05.000Z","payload":null}]},{"category":"sentiment","label":"Popularity","form":"unjudged","verdict":null,"rows":[]},{"category":"characteristics","label":"Characteristics","form":"unjudged","verdict":null,"rows":[]}],"signalCount":28,"publisherSupplied":["name","description","author","version","license"]}