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Reviewed with permission notes; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"opencobra-cobrapy","task":"Use Cobrapy in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/opencobra-cobrapy","api":"https://www.openagentskill.com/api/agent/skills/opencobra-cobrapy","audit":"https://www.openagentskill.com/skills/opencobra-cobrapy/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=opencobra-cobrapy&task=Use%20Cobrapy%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20Cobrapy%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20Cobrapy%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/opencobra-cobrapy/install","manifest":"https://www.openagentskill.com/api/registry/manifest/opencobra-cobrapy"}},"platforms":["Python","Bioinformatics"],"use_cases":[{"slug":"design-creative","title":"Design and creative","url":"https://www.openagentskill.com/use-cases/design-creative"},{"slug":"browser-automation","title":"Browser automation","url":"https://www.openagentskill.com/use-cases/browser-automation"},{"slug":"research-agents","title":"Research agents","url":"https://www.openagentskill.com/use-cases/research-agents"},{"slug":"github-automation","title":"GitHub automation","url":"https://www.openagentskill.com/use-cases/github-automation"}],"install":"npx skills add opencobra/cobrapy","install_targets":[{"id":"openagentskill-cli","label":"CLI","title":"OpenAgentSkill CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add opencobra-cobrapy","description":"Resolve policy, run the source installer safely, and report a verified install receipt.","copyLabel":"Copy command"},{"id":"codex","label":"Codex","title":"Codex install prompt","kind":"agent-prompt","value":"Install the \"Cobrapy\" agent skill from https://github.com/opencobra/cobrapy. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: COBRApy is a package for constraint-based modeling of metabolic networks. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"opencobra-cobrapy\",\"task\":\"Install Cobrapy\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Give Codex a repo-aware install prompt when the skill is not available through a local CLI.","copyLabel":"Copy prompt"},{"id":"claude-code","label":"Claude Code","title":"Claude Code skill prompt","kind":"agent-prompt","value":"Add \"Cobrapy\" as a Claude Code skill from https://github.com/opencobra/cobrapy. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: COBRApy is a package for constraint-based modeling of metabolic networks. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"opencobra-cobrapy\",\"task\":\"Install Cobrapy\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this prompt to ask Claude Code to add the skill and explain the local activation steps.","copyLabel":"Copy prompt"},{"id":"cursor","label":"Cursor","title":"Cursor rule prompt","kind":"agent-prompt","value":"Turn \"Cobrapy\" from https://github.com/opencobra/cobrapy into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: COBRApy is a package for constraint-based modeling of metabolic networks. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"opencobra-cobrapy\",\"task\":\"Install Cobrapy\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this when installing as Cursor project rules or reusable agent instructions.","copyLabel":"Copy prompt"}],"repository":"https://github.com/opencobra/cobrapy","github_repo":"opencobra/cobrapy","version":"1.0.0","license":"GPL-2.0","updated_at":"2026-09-01T11:59:28.941454+00:00","canonical_key":"opencobra/cobrapy","recommendation_reasons":["Matches task terms: cobrapy","Useful GitHub adoption: 568 stars","Install handoff is available","Repository freshness signal is available","Registry match score 99"],"urls":{"web":"https://www.openagentskill.com/skills/opencobra-cobrapy","api":"https://www.openagentskill.com/api/agent/skills/opencobra-cobrapy","install_api":"https://www.openagentskill.com/api/skills/opencobra-cobrapy/install","audit":"https://www.openagentskill.com/skills/opencobra-cobrapy/audit","repository":"https://github.com/opencobra/cobrapy"}},{"rank":2,"match_type":"near","match_score":31,"raw_match_score":314,"semantic_relevance":84,"ranking_signals":{"retrieval":296,"semantic":84,"quality":9,"projectPopularity":9,"verifiedOutcomes":0,"verifiedSource":0},"slug":"alterlab-ieu-alterlab-cobrapy","name":"alterlab-cobrapy","description":"Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite.","tagline":"Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phen","category":"design-creative","tags":["agent-skill"],"author":{"name":"AlterLab-IEU","verified":false,"url":"https://github.com/AlterLab-IEU"},"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"recursive skill source sync","sourceDetail":"AlterLab-IEU/AlterLab-Academic-Skills","creatorName":"AlterLab-IEU","creatorUrl":"https://github.com/AlterLab-IEU","sourceUrl":"https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/alterlab-ieu-alterlab-cobrapy#claim-this-skill","claimCta":"Claim this skill","trustNote":"This listing was indexed from public sources and is not marked official until a maintainer claim is approved.","publicNote":"Attribution links to the public repository or creator profile. Creators can claim the listing to update ownership signals."},"stats":{"stars":63,"forks":13,"verified_installs":0,"install_attempts":0,"successful_runs":0,"total_outcomes":0,"downloads":0,"rating":0,"review_count":0,"quality_score":36.04},"quality":{"score":65,"tier":"promising","label":"Promising","summary":"Useful candidate, but compare it with alternatives before adopting.","signals":[{"label":"GitHub stars","value":"63","tone":"neutral"},{"label":"Freshness","value":"1d ago","tone":"positive"},{"label":"Install ready","value":"Yes","tone":"positive"},{"label":"License","value":"GPL-2.0","tone":"neutral"}],"warnings":[]},"trust":{"version":"trust-score-v4","score":76,"tier":"strong","label":"Strong shortlist","summary":"Good trust signals with a few areas worth checking before rollout.","recommendedAction":"Test in a sandbox workflow and compare its install path with close alternatives.","dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":48,"weight":0.13,"status":"warn","detail":"63 GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":48,"weight":0.08,"status":"warn","detail":"63 stars, 13 forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"1d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"GPL-2.0"},{"id":"documentation","label":"README/SKILL.md completeness","score":52,"weight":0.14,"status":"warn","detail":"Public metadata needs stronger README/SKILL.md context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":90,"weight":0.12,"status":"pass","detail":"no major dependency risk hints in public metadata"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cobrapy"},{"id":"install_safety","label":"Install command safety","score":92,"weight":0.1,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":100,"weight":0.07,"status":"pass","detail":"no high-risk permission surface in public metadata"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy"},{"id":"review_status","label":"Review status","score":88,"weight":0.05,"status":"pass","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"weight":0.13,"status":"info","detail":"No agent outcome data yet"}],"checks":[{"status":"warn","label":"GitHub adoption","detail":"63 GitHub stars"},{"status":"warn","label":"Stars/forks activity","detail":"63 stars, 13 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"1d since push"},{"status":"pass","label":"License clarity","detail":"GPL-2.0"},{"status":"warn","label":"README/SKILL.md completeness","detail":"Public metadata needs stronger README/SKILL.md context"},{"status":"pass","label":"Dependency/runtime risk","detail":"no major dependency risk hints in public metadata"},{"status":"pass","label":"Install availability","detail":"npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cobrapy"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"pass","label":"Permission surface","detail":"no high-risk permission surface in public metadata"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy"},{"status":"pass","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"info","label":"OpenAgentSkill usage","detail":"No local usage activity yet"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Install command has no obvious high-risk pattern"],"warnings":["Quality score needs review","GitHub adoption: 63 GitHub stars","Stars/forks activity: 63 stars, 13 forks; 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issue activity unavailable in current metadata","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"safety":{"score":68,"level":"review_before_install","label":"Review before install","safety_tier":{"tier":"reviewed","label":"Reviewed with permission notes","badge":"REVIEWED","summary":"Usable candidate, but the agent should surface permission and audit notes before installation.","recommended_action":"Require human approval before installing into a real workspace.","auto_install_policy":"review","reasons":["Quality score needs review","68/100 agent safety score"]},"auto_install_allowed":false,"human_review_required":true,"blocked":false,"audit_risk":"needs_review","permission_hints":[{"id":"network","label":"Network access","reason":"Skill likely fetches remote pages, APIs, repositories, or external services.","severity":"medium"}],"policy_warnings":["Quality score needs review"],"constraints_applied":{"max_risk":"medium","needs_install_command":true,"min_stars":0}},"safety_gate":{"tier":"reviewed","label":"Reviewed with permission notes","badge":"REVIEWED","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Require human approval before installing into a real workspace.","reasons":["Quality score needs review","68/100 agent safety score"]},"supply_profile":{"track":{"slug":"design","label":"Design and creative production","shortLabel":"Design","description":"Design assets, images, video, audio, multimodal media, presentation, and creative production skills."},"scenario":{"label":"Design and creative","description":"I need my agent to produce design assets, UI directions, presentations, or creative media workflows.","useCases":[{"slug":"design-creative","title":"Design and creative"},{"slug":"browser-automation","title":"Browser automation"},{"slug":"research-agents","title":"Research agents"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cobrapy","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":63,"starsLabel":"63","forks":13,"license":"GPL-2.0","qualityScore":65,"trustScore":76,"auditScore":80},"maintenance":{"status":"fresh","label":"1d since push","daysSincePush":1,"lastPushedAt":"2026-09-04T13:48:46+00:00"},"risk":{"level":"needs_review","label":"Needs review","requiresReview":true,"notes":["Quality score needs review","GitHub adoption: 63 GitHub stars","Stars/forks activity: 63 stars, 13 forks; 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Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. 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Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"alterlab-ieu-alterlab-cobrapy\",\"task\":\"Install alterlab-cobrapy\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"alterlab-cobrapy\" as a Claude Code skill from https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"alterlab-ieu-alterlab-cobrapy\",\"task\":\"Install alterlab-cobrapy\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"alterlab-cobrapy\" from https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"alterlab-ieu-alterlab-cobrapy\",\"task\":\"Install alterlab-cobrapy\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/alterlab-ieu-alterlab-cobrapy/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/alterlab-ieu-alterlab-cobrapy"},"trust":{"score":76,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"63 GitHub stars","repoActivity":"63 stars, 13 forks","lastPushed":"1d since push","license":"GPL-2.0","repository":"https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy","install":"npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cobrapy","installSafety":"standard package or runtime install path","permissionSurface":"no high-risk permission surface in public metadata","documentation":"Thin public metadata","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["design-creative","agent-skill"],"known_risks":["Quality score needs review","GitHub adoption: 63 GitHub stars","Stars/forks activity: 63 stars, 13 forks; issue activity unavailable in current metadata","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":80,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Quality score needs review","GitHub adoption: 63 GitHub stars","Stars/forks activity: 63 stars, 13 forks; issue activity unavailable in current metadata","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"safety_gate":{"tier":"reviewed","label":"Reviewed with permission notes","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Require human approval before installing into a real workspace."},"quality":{"score":65,"label":"Promising"},"supply":{"track":"Design and creative production","scenario":"Design and creative","maintenance":"1d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","high-compliance environments without internal security review","No OpenAgentSkill engagement data yet","Quality score needs review","GitHub adoption: 63 GitHub stars","Stars/forks activity: 63 stars, 13 forks; issue activity unavailable in current metadata","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","Production credentials, payments, or irreversible account changes without explicit human review"],"agent_contract":{"task_input":"Use alterlab-cobrapy in an agent workflow","recommended_action":"Require human approval before installing into a real workspace.","install_policy":"review","minimum_review_before_use":["Trust: 76/100 Strong shortlist","Audit: 80/100 Needs review","Safety: 68/100 Review before install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"alterlab-ieu-alterlab-cobrapy (alterlab-cobrapy)","install_command":"npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cobrapy","risk_summary":"Needs review; Reviewed with permission notes; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"alterlab-ieu-alterlab-cobrapy","task":"Use alterlab-cobrapy in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/alterlab-ieu-alterlab-cobrapy","api":"https://www.openagentskill.com/api/agent/skills/alterlab-ieu-alterlab-cobrapy","audit":"https://www.openagentskill.com/skills/alterlab-ieu-alterlab-cobrapy/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=alterlab-ieu-alterlab-cobrapy&task=Use%20alterlab-cobrapy%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20alterlab-cobrapy%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20alterlab-cobrapy%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/alterlab-ieu-alterlab-cobrapy/install","manifest":"https://www.openagentskill.com/api/registry/manifest/alterlab-ieu-alterlab-cobrapy"}},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"alterlab-ieu-alterlab-cobrapy","name":"alterlab-cobrapy","description":"Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite.","category":"design-creative","url":"https://www.openagentskill.com/skills/alterlab-ieu-alterlab-cobrapy","repository":"https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy","github_repo":"AlterLab-IEU/AlterLab-Academic-Skills"},"suited_tasks":["Design and creative workflows","Claude Code teams","builders willing to evaluate younger projects","Inspect visual requirements","Generate reusable assets","Package output for review","Navigate pages","Click and type safely"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cobrapy","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add alterlab-ieu-alterlab-cobrapy"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"alterlab-cobrapy\" agent skill from https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"alterlab-ieu-alterlab-cobrapy\",\"task\":\"Install alterlab-cobrapy\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"alterlab-cobrapy\" as a Claude Code skill from https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"alterlab-ieu-alterlab-cobrapy\",\"task\":\"Install alterlab-cobrapy\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"alterlab-cobrapy\" from https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"alterlab-ieu-alterlab-cobrapy\",\"task\":\"Install alterlab-cobrapy\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/alterlab-ieu-alterlab-cobrapy/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/alterlab-ieu-alterlab-cobrapy"},"trust":{"score":76,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"63 GitHub stars","repoActivity":"63 stars, 13 forks","lastPushed":"1d since push","license":"GPL-2.0","repository":"https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy","install":"npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cobrapy","installSafety":"standard package or runtime install path","permissionSurface":"no high-risk permission surface in public metadata","documentation":"Thin public metadata","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["design-creative","agent-skill"],"known_risks":["Quality score needs review","GitHub adoption: 63 GitHub stars","Stars/forks activity: 63 stars, 13 forks; issue activity unavailable in current metadata","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":80,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Quality score needs review","GitHub adoption: 63 GitHub stars","Stars/forks activity: 63 stars, 13 forks; issue activity unavailable in current metadata","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"safety_gate":{"tier":"reviewed","label":"Reviewed with permission notes","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Require human approval before installing into a real workspace."},"quality":{"score":65,"label":"Promising"},"supply":{"track":"Design and creative production","scenario":"Design and creative","maintenance":"1d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","high-compliance environments without internal security review","No OpenAgentSkill engagement data yet","Quality score needs review","GitHub adoption: 63 GitHub stars","Stars/forks activity: 63 stars, 13 forks; issue activity unavailable in current metadata","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","Production credentials, payments, or irreversible account changes without explicit human review"],"agent_contract":{"task_input":"Use alterlab-cobrapy in an agent workflow","recommended_action":"Require human approval before installing into a real workspace.","install_policy":"review","minimum_review_before_use":["Trust: 76/100 Strong shortlist","Audit: 80/100 Needs review","Safety: 68/100 Review before install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"alterlab-ieu-alterlab-cobrapy (alterlab-cobrapy)","install_command":"npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cobrapy","risk_summary":"Needs review; Reviewed with permission notes; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"alterlab-ieu-alterlab-cobrapy","task":"Use alterlab-cobrapy in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/alterlab-ieu-alterlab-cobrapy","api":"https://www.openagentskill.com/api/agent/skills/alterlab-ieu-alterlab-cobrapy","audit":"https://www.openagentskill.com/skills/alterlab-ieu-alterlab-cobrapy/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=alterlab-ieu-alterlab-cobrapy&task=Use%20alterlab-cobrapy%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20alterlab-cobrapy%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20alterlab-cobrapy%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/alterlab-ieu-alterlab-cobrapy/install","manifest":"https://www.openagentskill.com/api/registry/manifest/alterlab-ieu-alterlab-cobrapy"}},"platforms":["Claude Code"],"use_cases":[{"slug":"design-creative","title":"Design and creative","url":"https://www.openagentskill.com/use-cases/design-creative"},{"slug":"browser-automation","title":"Browser automation","url":"https://www.openagentskill.com/use-cases/browser-automation"},{"slug":"research-agents","title":"Research agents","url":"https://www.openagentskill.com/use-cases/research-agents"},{"slug":"marketing-growth","title":"Marketing and growth","url":"https://www.openagentskill.com/use-cases/marketing-growth"}],"install":"npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-cobrapy","install_targets":[{"id":"openagentskill-cli","label":"CLI","title":"OpenAgentSkill CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add alterlab-ieu-alterlab-cobrapy","description":"Resolve policy, run the source installer safely, and report a verified install receipt.","copyLabel":"Copy command"},{"id":"codex","label":"Codex","title":"Codex install prompt","kind":"agent-prompt","value":"Install the \"alterlab-cobrapy\" agent skill from https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"alterlab-ieu-alterlab-cobrapy\",\"task\":\"Install alterlab-cobrapy\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Give Codex a repo-aware install prompt when the skill is not available through a local CLI.","copyLabel":"Copy prompt"},{"id":"claude-code","label":"Claude Code","title":"Claude Code skill prompt","kind":"agent-prompt","value":"Add \"alterlab-cobrapy\" as a Claude Code skill from https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"alterlab-ieu-alterlab-cobrapy\",\"task\":\"Install alterlab-cobrapy\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this prompt to ask Claude Code to add the skill and explain the local activation steps.","copyLabel":"Copy prompt"},{"id":"cursor","label":"Cursor","title":"Cursor rule prompt","kind":"agent-prompt","value":"Turn \"alterlab-cobrapy\" from https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phenotypes, or running systems-biology and metabolic-engineering analyses on SBML genome-scale models. Part of the AlterLab Academic Skills suite. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"alterlab-ieu-alterlab-cobrapy\",\"task\":\"Install alterlab-cobrapy\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this when installing as Cursor project rules or reusable agent instructions.","copyLabel":"Copy prompt"}],"repository":"https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy","github_repo":"AlterLab-IEU/AlterLab-Academic-Skills","version":"1.0.0","license":"GPL-2.0","updated_at":"2026-09-05T00:48:30.285644+00:00","canonical_key":"alterlab-ieu/alterlab-academic-skills#skills/bioinformatics/alterlab-cobrapy","recommendation_reasons":["Matches task terms: cobrapy","Install handoff is available","Repository freshness signal is available","Registry match score 31"],"urls":{"web":"https://www.openagentskill.com/skills/alterlab-ieu-alterlab-cobrapy","api":"https://www.openagentskill.com/api/agent/skills/alterlab-ieu-alterlab-cobrapy","install_api":"https://www.openagentskill.com/api/skills/alterlab-ieu-alterlab-cobrapy/install","audit":"https://www.openagentskill.com/skills/alterlab-ieu-alterlab-cobrapy/audit","repository":"https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/bioinformatics/alterlab-cobrapy"}}],"meta":{"endpoint":"/api/skills/search","canonical_agent_endpoint":"/api/agent/resolve","ranking_model":"hybrid-v2-task-fit-quality-outcomes","shortlist_policy":"Return one best match plus up to four distinct alternatives; suppress unrelated direct-name matches.","lookup_intent":true,"exact_match_found":true,"match_counts":{"exact":1,"near":1,"related":0},"no_match_message":null,"safety_policy":"Blocked candidates are excluded by default. Pass include_blocked=true only for manual audit workflows.","agent_friendly":true,"api_version":"1.0","generated_at":"2026-09-06T07:01:11.651Z"}}