{"query":"BioReason","filters":{"category":null,"platform":null,"track":null,"safety":null,"include_blocked":false,"min_stars":0},"total":1,"skills":[{"rank":1,"match_type":"exact","match_score":99,"raw_match_score":1001.2,"semantic_relevance":100,"slug":"bowang-lab-bioreason","name":"BioReason","description":"BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model  |  NeurIPS '25","tagline":"BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model  |  NeurIPS '25","category":"geo-science","tags":["bioinformatics","analysis","geo-science","computational-biology","dna","foundation-models","grpo","large-language-models","reasoning","jupyter notebook"],"author":{"name":"bowang-lab","verified":false,"url":"https://github.com/bowang-lab"},"attribution":{"status":"community_indexed","statusLabel":"Community indexed","shortLabel":"COMMUNITY INDEXED","sourceLabel":"GitHub star discovery","sourceDetail":"bowang-lab/BioReason","creatorName":"bowang-lab","creatorUrl":"https://github.com/bowang-lab","sourceUrl":"https://github.com/bowang-lab/BioReason","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/bowang-lab-bioreason#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. 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Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/bowang-lab-bioreason/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/bowang-lab-bioreason"},"trust":{"score":78,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"395 GitHub stars","repoActivity":"395 stars, 55 forks","lastPushed":"3mo since push","license":"Apache-2.0","repository":"https://github.com/bowang-lab/BioReason","install":"npx skills add bowang-lab/BioReason","installSafety":"standard package or runtime install path","permissionSurface":"no high-risk permission surface in public metadata","documentation":"Usable metadata, review docs","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":["geo-science","bioinformatics","analysis","computational-biology","dna","foundation-models"],"known_risks":["Quality score needs review","Documentation summary is thin"]},"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":["Documentation summary is thin","Quality score needs review"]},"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":71,"label":"Strong"},"supply":{"track":"Data, BI, and analytics","scenario":"Data analysis","maintenance":"3mo 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","Documentation summary is thin","Quality score needs review","Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"],"agent_contract":{"task_input":"Use BioReason in an agent workflow","recommended_action":"Require human approval before installing into a real workspace.","install_policy":"review","minimum_review_before_use":["Trust: 78/100 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":"bowang-lab-bioreason (BioReason)","install_command":"npx skills add bowang-lab/BioReason","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":"bowang-lab-bioreason","task":"Use BioReason 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/bowang-lab-bioreason","api":"https://www.openagentskill.com/api/agent/skills/bowang-lab-bioreason","audit":"https://www.openagentskill.com/skills/bowang-lab-bioreason/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=bowang-lab-bioreason&task=Use%20BioReason%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20BioReason%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20BioReason%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/bowang-lab-bioreason/install","manifest":"https://www.openagentskill.com/api/registry/manifest/bowang-lab-bioreason"}},"platforms":["Jupyter Notebook","Bioinformatics"],"use_cases":[{"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":"data-analysis","title":"Data analysis","url":"https://www.openagentskill.com/use-cases/data-analysis"},{"slug":"github-automation","title":"GitHub automation","url":"https://www.openagentskill.com/use-cases/github-automation"}],"install":"npx skills add bowang-lab/BioReason","install_targets":[{"id":"openagentskill-cli","label":"CLI","title":"OpenAgentSkill CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz install bowang-lab-bioreason","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 \"BioReason\" agent skill from https://github.com/bowang-lab/BioReason. 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: BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model | NeurIPS '25 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\":\"bowang-lab-bioreason\",\"task\":\"Install BioReason\",\"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 \"BioReason\" as a Claude Code skill from https://github.com/bowang-lab/BioReason. 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: BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model | NeurIPS '25 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\":\"bowang-lab-bioreason\",\"task\":\"Install BioReason\",\"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 \"BioReason\" from https://github.com/bowang-lab/BioReason 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: BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model | NeurIPS '25 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\":\"bowang-lab-bioreason\",\"task\":\"Install BioReason\",\"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/bowang-lab/BioReason","github_repo":"bowang-lab/BioReason","version":"1.0.0","license":"Apache-2.0","updated_at":"2026-08-18T17:22:21.819119+00:00","canonical_key":"bowang-lab/bioreason","recommendation_reasons":["Matches task terms: bioreason","Install handoff is available","Repository freshness signal is available","Registry match score 99"],"urls":{"web":"https://www.openagentskill.com/skills/bowang-lab-bioreason","api":"https://www.openagentskill.com/api/agent/skills/bowang-lab-bioreason","install_api":"https://www.openagentskill.com/api/skills/bowang-lab-bioreason/install","audit":"https://www.openagentskill.com/skills/bowang-lab-bioreason/audit","repository":"https://github.com/bowang-lab/BioReason"}}],"meta":{"endpoint":"/api/skills/search","canonical_agent_endpoint":"/api/agent/resolve","lookup_intent":true,"exact_match_found":true,"match_counts":{"exact":1,"near":0,"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":"2026-08-22T23:01:19.362Z"}}