{"task":"Use arboreto","agent":"codex","constraints":{"max_risk":"medium","needs_install_command":true,"min_stars":0},"feedback":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","outcome_api":"https://www.openagentskill.com/api/agent/outcome","method":"POST","selected_skill_slug":"k-dense-ai-arboreto","selected_skill_name":"arboreto","alternative_skill_slugs":[],"expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"report_after":["After trying the selected skill, report whether it solved the task.","Mark blocked_by_risk when audit, license, credentials, shell, or network risk prevents safe use.","Mark setup_required when the skill looks relevant but needs missing keys, data, or manual configuration.","Mark not_relevant when the selected skill does not match the task after inspection.","Include output_quality, error_type, workspace, human_review_required, evidence_url, and time_to_useful_ms when available."],"json_example":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","skill_slug":"k-dense-ai-arboreto","task":"Use arboreto","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":"Solved the task in a sandbox workflow."},"cli_example":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz outcome \"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5\" --skill \"k-dense-ai-arboreto\" --task \"Use arboreto\" --agent \"codex\" --outcome success"},"agent_feedback_loop":{"version":"openagentskill-agent-feedback-loop-v3","status":"active","purpose":"Report the result of one resolved skill run so Trust Score v5 and future Resolve rankings learn from real use.","event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","selected_skill_slug":"k-dense-ai-arboreto","selected_skill_name":"arboreto","endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","idempotency":"Retrying the same event_id updates the previous outcome.","dry_run":{"supported":true,"instruction":"Set dry_run=true to validate a payload before wiring a new agent integration."},"expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"error_types":["install_failed","runtime_error","not_relevant","permission_blocked","risk_blocked","setup_required","low_quality_output","missing_dependency","timeout","other"],"workspaces":["sandbox","local","ci","production","unknown"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url"],"payload_template":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","skill_slug":"k-dense-ai-arboreto","task":"Use arboreto","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":"Solved the task in a sandbox workflow."},"cli_example":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz outcome \"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5\" --skill \"k-dense-ai-arboreto\" --task \"Use arboreto\" --agent \"codex\" --outcome success","ranking_inputs_updated":["Trust Score v5 outcome confidence","Resolve ranking outcome evidence","Skill detail outcome signal block","Outcome leaderboard"]},"install_receipt":{"version":"openagentskill-install-receipt-v1","receipt_id":"receipt_b6065127-0846-44b9-9eab-79b9bb0182b5","resolve_event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","generated_at":"2026-08-22T15:18:50.934Z","task":"Use arboreto","agent":"codex","constraints":{"max_risk":"medium","needs_install_command":true,"min_stars":0},"urls":{"web":"https://www.openagentskill.com/resolve?task=Use+arboreto&agent=codex&max_risk=medium","json":"https://www.openagentskill.com/api/agent/receipt?task=Use+arboreto&agent=codex&max_risk=medium","text":"https://www.openagentskill.com/api/agent/receipt?task=Use+arboreto&agent=codex&max_risk=medium&format=text","resolve_json":"https://www.openagentskill.com/api/agent/resolve?task=Use+arboreto&agent=codex&max_risk=medium","resolve_text":"https://www.openagentskill.com/api/agent/resolve?task=Use+arboreto&agent=codex&max_risk=medium&format=text"},"selected_skill":{"slug":"k-dense-ai-arboreto","name":"arboreto","description":"Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.","category":"data-analysis","url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto","api_url":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto","audit_url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","eval_url":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium","install_api_url":"https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","target":"codex","label":"Codex install prompt","kind":"agent-prompt","value":"Install the \"arboreto\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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.","ready":true,"policy":"review","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"blocked":false},"decision":{"recommendation":"Review the audit page, then allow agent install in a sandboxed workflow.","why_selected":["Matches task terms: arboreto","Strong GitHub adoption: 33,974 stars","Install handoff is available","Repository freshness signal is available","Registry match score 30","Primary pick for GitHub automation","77/100 Trust Score","0/100 Agent Proven Score"],"suited_tasks":["GitHub automation workflows","Claude Code teams","teams that value GitHub adoption signals","Inspect repository metadata","Compare code changes","Write concise engineering summaries","Search sources","Extract claims"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"]},"trust":{"score":77,"label":"Review then install","version":"trust-score-v5","base_score":85,"outcome_confidence":0,"outcome_signal":"No agent outcome data yet","outcome_total":0,"outcome_success_rate":null,"decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Ask for approval or run a sandbox-only trial before installing.","reasoning":["77/100 Trust Score v5","85/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is available","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human 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"]},"outcome_loop":{"version":"openagentskill-agent-outcome-v3","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]}},"agent_proven":{"score":0,"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,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"installAttempts":0,"installSuccessRate":null,"riskBlocked":0,"setupRequired":0,"avgOutputQuality":null,"productionOutcomes":0}},"risk":{"level":"Safe to try","safety_tier":"Reviewed","safety_score":79,"audit_score":91,"notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","Safe-to-try audit","79/100 agent safety score"],"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","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","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"],"minimum_review_before_use":["Trust: 85/100 Strong shortlist","Audit: 91/100 Safe to try","Safety: 79/100 Review before install","Review repository, license, install command, and permission surface before production use."]},"alternatives":[],"outcome_feedback":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","skill_slug":"k-dense-ai-arboreto","task":"Use arboreto","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":"Solved the task in a sandbox workflow."},"dry_run_payload":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","skill_slug":"k-dense-ai-arboreto","task":"Use arboreto","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":"Solved the task in a sandbox workflow.","dry_run":true},"cli_example":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz outcome \"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5\" --skill \"k-dense-ai-arboreto\" --task \"Use arboreto\" --agent \"codex\" --outcome success","instruction":"After one narrow sandbox run, report success, failed, not_relevant, blocked_by_risk, or setup_required so Trust Score v5 and future agent rankings learn from real usage."},"next_steps":["Read the audit page: https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","Fetch the pre-install eval: https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium","Do not auto-install yet. Ask for human review before running: npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","Run one narrow task with no production secrets or irreversible side effects.","Report the result to https://www.openagentskill.com/api/agent/outcome using event_id resolve_b6065127-0846-44b9-9eab-79b9bb0182b5."],"stable_fields":["receipt_id","selected_skill","install","trust","risk","alternatives","outcome_feedback","next_steps"],"freshness_policy":"Re-resolve before production use or after 24 hours to refresh trust, audit, and outcome signals."},"recommendation":{"task":"Use arboreto","agent":"codex","best_skill":{"slug":"k-dense-ai-arboreto","name":"arboreto","description":"Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.","category":"data-analysis","url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto","api_url":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto","audit_url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","eval_url":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","target":"codex","label":"Codex install prompt","kind":"agent-prompt","value":"Install the \"arboreto\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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.","install_api":"https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install","ready":true,"review_required":true,"auto_install_allowed":false,"policy":"review"},"why_recommended":["Matches task terms: arboreto","Strong GitHub adoption: 33,974 stars","Install handoff is available","Repository freshness signal is available","Registry match score 30","Primary pick for GitHub automation","77/100 OpenAgentSkill Trust Score v5","91/100 audit score"],"trust_score_v5":{"score":77,"base_score":85,"outcome_confidence":0,"tier":"strong","label":"Review then install","version":"trust-score-v5","install_policy":"human_review_before_install","decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Ask for approval or run a sandbox-only trial before installing.","reasoning":["77/100 Trust Score v5","85/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is available","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human 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"]},"evidence":{"stars":"34K GitHub stars","repoActivity":"34K stars, 3.3K forks","lastPushed":"2d since push","license":"BSD-3-Clause license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","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","agentProvenScore":0,"outcomeConfidence":"0%","installPolicy":"human_review_before_install"},"agent_compatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"risk":{"level":"medium","label":"Review before production","notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"outcomes":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Ask for approval or run a sandbox-only trial before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v3","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]},"agent_contract":{"suited_tasks":["data-analysis","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","trust_score":77,"trust_version":"trust-score-v5","risk_level":"medium","do_not_use_when":["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"],"before_install":["Read the audit page and machine-readable metadata.","Confirm the install command, license, and permission surface fit the workspace.","Get explicit human approval or choose an alternative before installing."],"after_run":["Report the outcome to /api/agent/outcome using the resolve event id.","Include output_quality, workspace, human_review_required, and evidence_url when available.","Re-resolve before broad production rollout."]},"best_for":["data-analysis","agent-skill"],"do_not_use_for":["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"],"known_risks":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":85,"tier":"strong","label":"Strong shortlist","summary":"Good trust signals with a few areas worth checking before rollout."}}},"trust_score_v4":{"score":85,"tier":"strong","label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"34K GitHub stars","repoActivity":"34K stars, 3.3K forks","lastPushed":"2d since push","license":"BSD-3-Clause license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","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"},"agent_compatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"risk":{"level":"medium","label":"Review before production","notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"outcomes":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["data-analysis","agent-skill"],"do_not_use_for":["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"],"known_risks":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"trust_score_v3":{"score":85,"tier":"strong","label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"34K GitHub stars","repoActivity":"34K stars, 3.3K forks","lastPushed":"2d since push","license":"BSD-3-Clause license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","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"},"agent_compatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"risk":{"level":"medium","label":"Review before production","notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]}},"trust_score_v2":{"score":85,"tier":"strong","label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"34K GitHub stars","repoActivity":"34K stars, 3.3K forks","lastPushed":"2d since push","license":"BSD-3-Clause license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","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"},"agent_compatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"risk":{"level":"medium","label":"Review before production","notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]}},"risk":{"level":"Safe to try","safety_tier":"Reviewed","safety":"79/100 Review before install","trust":"85/100 Strong shortlist","notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"safety_gate":{"tier":"reviewed","label":"Reviewed","badge":"REVIEWED","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow.","reasons":["Safe-to-try audit","79/100 agent safety score"]},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"k-dense-ai-arboreto","name":"arboreto","description":"Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.","category":"data-analysis","url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","github_repo":"K-Dense-AI/scientific-agent-skills"},"suited_tasks":["GitHub automation workflows","Claude Code teams","teams that value GitHub adoption signals","Inspect repository metadata","Compare code changes","Write concise engineering summaries","Search sources","Extract claims"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz install k-dense-ai-arboreto"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"arboreto\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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 \"arboreto\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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 \"arboreto\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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/k-dense-ai-arboreto/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-arboreto"},"trust":{"score":85,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"34K GitHub stars","repoActivity":"34K stars, 3.3K forks","lastPushed":"2d since push","license":"BSD-3-Clause license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","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":["data-analysis","agent-skill"],"known_risks":["Quality score needs review","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":91,"risk_level":"safe_to_try","risk_label":"Safe to try","warnings":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"safety_gate":{"tier":"reviewed","label":"Reviewed","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow."},"quality":{"score":92,"label":"Excellent"},"supply":{"track":"Coding and developer agents","scenario":"GitHub automation","maintenance":"2d since push","risk":"Safe to try"},"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","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","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 arboreto","recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow.","install_policy":"review","minimum_review_before_use":["Trust: 85/100 Strong shortlist","Audit: 91/100 Safe to try","Safety: 79/100 Review before install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"k-dense-ai-arboreto (arboreto)","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","risk_summary":"Safe to try; Reviewed; 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":"k-dense-ai-arboreto","task":"Use arboreto","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/k-dense-ai-arboreto","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto","audit":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20arboreto&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20arboreto&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install","manifest":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-arboreto"}},"agent_contract":{"version":"openagentskill-resolve-contract-v2","input_task":"Use arboreto","recommended_skill_slug":"k-dense-ai-arboreto","recommended_skill_name":"arboreto","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","install_policy":"review","auto_install_allowed":false,"human_review_required":true,"audit_url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","eval_url":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium","skill_api_url":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto","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","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","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"],"minimum_review_before_use":["Trust: 85/100 Strong shortlist","Audit: 91/100 Safe to try","Safety: 79/100 Review before install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"k-dense-ai-arboreto (arboreto)","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","risk_summary":"Safe to try; Reviewed; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"supply_asset":{"track":{"slug":"coding","label":"Coding and developer agents","shortLabel":"Coding","description":"Code review, repo analysis, testing, CI, GitHub, DevOps, and developer workflow skills."},"scenario":{"label":"GitHub automation","description":"I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.","useCases":[{"slug":"github-automation","title":"GitHub automation"},{"slug":"research-agents","title":"Research agents"},{"slug":"finance-quant","title":"Finance and quant"}]},"maintenance":{"status":"fresh","label":"2d since push","daysSincePush":2,"lastPushedAt":"2026-08-20T13:03:17+00:00"},"github_quality":{"stars":33974,"starsLabel":"34K","forks":3307,"license":"BSD-3-Clause license","qualityScore":92,"trustScore":85,"auditScore":91},"coverage_tags":["Coding","GitHub automation","data-analysis","agent-skill"]},"alternatives":[],"decision_packet":{"version":"openagentskill-agent-decision-packet-v1","task":"Use arboreto","agent":"codex","selected_skill":{"slug":"k-dense-ai-arboreto","name":"arboreto","url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto","api_url":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto","audit_url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},"suited_tasks":["GitHub automation workflows","Claude Code teams","teams that value GitHub adoption signals","Inspect repository metadata","Compare code changes","Write concise engineering summaries","Search sources","Extract claims"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","target":"codex","label":"Codex install prompt","policy":"review","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true},"trust":{"score":77,"label":"Review then install","version":"trust-score-v5","base_score":85,"outcome_confidence":0,"decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Ask for approval or run a sandbox-only trial before installing.","reasoning":["77/100 Trust Score v5","85/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is available","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human 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"]},"dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":100,"status":"pass","detail":"34K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":97,"status":"pass","detail":"34K stars, 3.3K forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"status":"pass","detail":"2d since push"},{"id":"license","label":"License clarity","score":86,"status":"pass","detail":"BSD-3-Clause license"},{"id":"documentation","label":"README/SKILL.md completeness","score":52,"status":"warn","detail":"Public metadata needs stronger README/SKILL.md context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":90,"status":"pass","detail":"no major dependency risk hints in public metadata"},{"id":"installability","label":"Install availability","score":92,"status":"pass","detail":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto"},{"id":"install_safety","label":"Install command safety","score":92,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":100,"status":"pass","detail":"no high-risk permission surface in public metadata"},{"id":"repository","label":"Repository evidence","score":86,"status":"pass","detail":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},{"id":"review_status","label":"Review status","score":88,"status":"pass","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"status":"info","detail":"No agent outcome data yet"}]},"risk":{"level":"Safe to try","audit_label":"Safe to try","safety":"79/100 Review before install","trust":"85/100 Strong shortlist","safety_tier":"Reviewed","notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"],"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","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","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"],"minimum_review_before_use":["Trust: 85/100 Strong shortlist","Audit: 91/100 Safe to try","Safety: 79/100 Review before install","Review repository, license, install command, and permission surface before production use."]},"alternatives":[],"outcome_feedback":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","skill_slug":"k-dense-ai-arboreto","task":"Use arboreto","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":"Solved the task in a sandbox workflow."},"cli_example":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz outcome \"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5\" --skill \"k-dense-ai-arboreto\" --task \"Use arboreto\" --agent \"codex\" --outcome success"},"next_agent_action":"Ask for human approval or choose a safer alternative before installing.","stable_fields":["decision_packet.selected_skill","decision_packet.install","decision_packet.risk.do_not_use_when","decision_packet.alternatives","decision_packet.outcome_feedback","decision_packet.trust.decision"]},"agent_instruction":"Use arboreto for: Use arboreto\nReview audit: https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit\nAsk for human approval before installing: npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto\nIf the audit or policy warnings are unacceptable, choose one of the alternatives."},"recommendation_lanes":{"best_match":{"rank":1,"match_score":30,"raw_match_score":99.7,"semantic_relevance":30,"skill":{"slug":"k-dense-ai-arboreto","name":"arboreto","description":"Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.","category":"data-analysis","github_stars":33974,"created_at":"2026-08-20T13:23:14.06357+00:00","updated_at":"2026-08-20T13:03:17+00:00","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","github_repo":"K-Dense-AI/scientific-agent-skills"},"recommendation_reasons":["Matches task terms: arboreto","Strong GitHub adoption: 33,974 stars","Install handoff is available","Repository freshness signal is available","Registry match score 30"],"supply_profile":{"track":{"slug":"coding","label":"Coding and developer agents","shortLabel":"Coding","description":"Code review, repo analysis, testing, CI, GitHub, DevOps, and developer workflow skills."},"scenario":{"label":"GitHub automation","description":"I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.","useCases":[{"slug":"github-automation","title":"GitHub automation"},{"slug":"research-agents","title":"Research agents"},{"slug":"finance-quant","title":"Finance and quant"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":33974,"starsLabel":"34K","forks":3307,"license":"BSD-3-Clause license","qualityScore":92,"trustScore":85,"auditScore":91},"maintenance":{"status":"fresh","label":"2d since push","daysSincePush":2,"lastPushedAt":"2026-08-20T13:03:17+00:00"},"risk":{"level":"safe_to_try","label":"Safe to try","requiresReview":true,"notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"coverageTags":["Coding","GitHub automation","data-analysis","agent-skill"]},"quality":{"score":92,"tier":"excellent","label":"Excellent","summary":"High-confidence pick with strong adoption and healthy maintenance signals.","signals":[{"label":"GitHub stars","value":"34K","tone":"positive"},{"label":"Freshness","value":"2d ago","tone":"positive"},{"label":"Install ready","value":"Yes","tone":"positive"},{"label":"License","value":"BSD-3-Clause license","tone":"neutral"}],"warnings":[]},"trust":{"version":"trust-score-v4","score":85,"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":100,"weight":0.13,"status":"pass","detail":"34K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":97,"weight":0.08,"status":"pass","detail":"34K stars, 3.3K forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"2d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"BSD-3-Clause license"},{"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 K-Dense-AI/scientific-agent-skills --skill arboreto"},{"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/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},{"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":"pass","label":"GitHub adoption","detail":"34K GitHub stars"},{"status":"pass","label":"Stars/forks activity","detail":"34K stars, 3.3K forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"2d since push"},{"status":"pass","label":"License clarity","detail":"BSD-3-Clause license"},{"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 K-Dense-AI/scientific-agent-skills --skill arboreto"},{"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/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},{"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","Large GitHub adoption signal","Install command has no obvious high-risk pattern"],"warnings":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"],"evidence":{"stars":"34K GitHub stars","repoActivity":"34K stars, 3.3K forks","lastPushed":"2d since push","license":"BSD-3-Clause license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","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"},"installReadiness":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","2d since push"]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Human review or sandbox validation is required before automatic installation."},"bestFor":["data-analysis","agent-skill"],"doNotUseFor":["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"],"knownRisks":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"trust_v5":{"version":"trust-score-v5","score":77,"base_score":85,"outcome_confidence":0,"tier":"strong","label":"Review then install","summary":"Good shortlist signal, but the agent should review audit notes, install policy, and outcome evidence before running it.","recommendedAction":"Use as the primary candidate after human or sandbox review.","decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Ask for approval or run a sandbox-only trial before installing.","reasoning":["77/100 Trust Score v5","85/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is available","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human 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"]},"dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":100,"weight":0.13,"status":"pass","detail":"34K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":97,"weight":0.08,"status":"pass","detail":"34K stars, 3.3K forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"2d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"BSD-3-Clause license"},{"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 K-Dense-AI/scientific-agent-skills --skill arboreto"},{"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/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},{"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":"pass","label":"GitHub adoption","detail":"34K GitHub stars"},{"status":"pass","label":"Stars/forks activity","detail":"34K stars, 3.3K forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"2d since push"},{"status":"pass","label":"License clarity","detail":"BSD-3-Clause license"},{"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 K-Dense-AI/scientific-agent-skills --skill arboreto"},{"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/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},{"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","Large GitHub adoption signal","Install command has no obvious high-risk pattern","Outcome loop is ready but needs first real agent run"],"warnings":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","No real agent outcome reports yet","Human review required before unattended installation"],"evidence":{"stars":"34K GitHub stars","repoActivity":"34K stars, 3.3K forks","lastPushed":"2d since push","license":"BSD-3-Clause license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","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","agentProvenScore":0,"outcomeConfidence":"0%","installPolicy":"human_review_before_install"},"installReadiness":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","2d since push","Trust Score v5 requires review or sandbox-only use before install."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Ask for approval or run a sandbox-only trial before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v3","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]},"agent_contract":{"suited_tasks":["data-analysis","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","trust_score":77,"trust_version":"trust-score-v5","risk_level":"medium","do_not_use_when":["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"],"before_install":["Read the audit page and machine-readable metadata.","Confirm the install command, license, and permission surface fit the workspace.","Get explicit human approval or choose an alternative before installing."],"after_run":["Report the outcome to /api/agent/outcome using the resolve event id.","Include output_quality, workspace, human_review_required, and evidence_url when available.","Re-resolve before broad production rollout."]},"bestFor":["data-analysis","agent-skill"],"doNotUseFor":["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"],"knownRisks":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":85,"tier":"strong","label":"Strong shortlist","summary":"Good trust signals with a few areas worth checking before rollout."}}},"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":{"audit_score":91,"risk_level":"safe_to_try","risk_label":"Safe to try","warnings":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"safety":{"score":79,"level":"review_before_install","label":"Review before install","safety_tier":{"tier":"reviewed","label":"Reviewed","badge":"REVIEWED","summary":"Good audit and safety signals with no high-risk permission hints in public metadata.","recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow.","auto_install_policy":"review","reasons":["Safe-to-try audit","79/100 agent safety score"]},"auto_install_allowed":false,"human_review_required":true,"blocked":false,"audit_risk":"safe_to_try","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","badge":"REVIEWED","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow.","reasons":["Safe-to-try audit","79/100 agent safety score"]},"decision":{"readiness_score":100,"readiness_label":"Production-ready","headline":"Primary pick for GitHub automation","role":"Primary pick","best_for":["GitHub automation workflows","Claude Code teams","teams that value GitHub adoption signals"],"risks":["No OpenAgentSkill engagement data yet"],"next_steps":["Install it in a sandbox agent and run one GitHub automation task end to end.","Compare output quality, latency, and failure behavior against at least one alternative.","Promote it into production only after reviewing repository permissions, license, and maintenance signals."]},"install_plan":{"target":"codex","label":"Codex install prompt","command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","value":"Install the \"arboreto\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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.","kind":"agent-prompt","steps":["Review arboreto trust and audit signals before installing.","Send the install prompt to the target agent.","Install in a sandbox or low-risk workspace first.","Pin the repository source and re-check the audit before production use."],"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 k-dense-ai-arboreto","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 \"arboreto\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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 \"arboreto\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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 \"arboreto\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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"}]},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"k-dense-ai-arboreto","name":"arboreto","description":"Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.","category":"data-analysis","url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","github_repo":"K-Dense-AI/scientific-agent-skills"},"suited_tasks":["GitHub automation workflows","Claude Code teams","teams that value GitHub adoption signals","Inspect repository metadata","Compare code changes","Write concise engineering summaries","Search sources","Extract claims"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz install k-dense-ai-arboreto"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"arboreto\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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 \"arboreto\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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 \"arboreto\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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/k-dense-ai-arboreto/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-arboreto"},"trust":{"score":85,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"34K GitHub stars","repoActivity":"34K stars, 3.3K forks","lastPushed":"2d since push","license":"BSD-3-Clause license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","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":["data-analysis","agent-skill"],"known_risks":["Quality score needs review","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":91,"risk_level":"safe_to_try","risk_label":"Safe to try","warnings":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"safety_gate":{"tier":"reviewed","label":"Reviewed","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow."},"quality":{"score":92,"label":"Excellent"},"supply":{"track":"Coding and developer agents","scenario":"GitHub automation","maintenance":"2d since push","risk":"Safe to try"},"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","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","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 arboreto","recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow.","install_policy":"review","minimum_review_before_use":["Trust: 85/100 Strong shortlist","Audit: 91/100 Safe to try","Safety: 79/100 Review before install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"k-dense-ai-arboreto (arboreto)","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","risk_summary":"Safe to try; Reviewed; 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":"k-dense-ai-arboreto","task":"Use arboreto","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/k-dense-ai-arboreto","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto","audit":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20arboreto&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20arboreto&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install","manifest":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-arboreto"}},"use_cases":[{"slug":"github-automation","title":"GitHub automation","url":"https://www.openagentskill.com/use-cases/github-automation"},{"slug":"research-agents","title":"Research agents","url":"https://www.openagentskill.com/use-cases/research-agents"},{"slug":"finance-quant","title":"Finance and quant","url":"https://www.openagentskill.com/use-cases/finance-quant"}],"urls":{"web":"https://www.openagentskill.com/skills/k-dense-ai-arboreto","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto","install_api":"https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install","audit":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium","badge":"https://www.openagentskill.com/api/badge/k-dense-ai-arboreto?metric=audit","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"}},"safer_alternative":null,"popular_alternative":null,"new_contender":null,"no_skill_option":{"recommended":true,"label":"Build without a third-party skill","reason":"Use a native agent workflow when the third-party permission or maintenance surface is not acceptable.","action":"Use the agent’s built-in tools for one narrow run, then reconsider a skill only if the workflow repeats."}},"selected":{"rank":1,"match_score":30,"raw_match_score":99.7,"semantic_relevance":30,"skill":{"slug":"k-dense-ai-arboreto","name":"arboreto","description":"Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.","category":"data-analysis","github_stars":33974,"created_at":"2026-08-20T13:23:14.06357+00:00","updated_at":"2026-08-20T13:03:17+00:00","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","github_repo":"K-Dense-AI/scientific-agent-skills"},"recommendation_reasons":["Matches task terms: arboreto","Strong GitHub adoption: 33,974 stars","Install handoff is available","Repository freshness signal is available","Registry match score 30"],"supply_profile":{"track":{"slug":"coding","label":"Coding and developer agents","shortLabel":"Coding","description":"Code review, repo analysis, testing, CI, GitHub, DevOps, and developer workflow skills."},"scenario":{"label":"GitHub automation","description":"I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.","useCases":[{"slug":"github-automation","title":"GitHub automation"},{"slug":"research-agents","title":"Research agents"},{"slug":"finance-quant","title":"Finance and quant"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":33974,"starsLabel":"34K","forks":3307,"license":"BSD-3-Clause license","qualityScore":92,"trustScore":85,"auditScore":91},"maintenance":{"status":"fresh","label":"2d since push","daysSincePush":2,"lastPushedAt":"2026-08-20T13:03:17+00:00"},"risk":{"level":"safe_to_try","label":"Safe to try","requiresReview":true,"notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"coverageTags":["Coding","GitHub automation","data-analysis","agent-skill"]},"quality":{"score":92,"tier":"excellent","label":"Excellent","summary":"High-confidence pick with strong adoption and healthy maintenance signals.","signals":[{"label":"GitHub stars","value":"34K","tone":"positive"},{"label":"Freshness","value":"2d ago","tone":"positive"},{"label":"Install ready","value":"Yes","tone":"positive"},{"label":"License","value":"BSD-3-Clause license","tone":"neutral"}],"warnings":[]},"trust":{"version":"trust-score-v4","score":85,"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":100,"weight":0.13,"status":"pass","detail":"34K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":97,"weight":0.08,"status":"pass","detail":"34K stars, 3.3K forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"2d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"BSD-3-Clause license"},{"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 K-Dense-AI/scientific-agent-skills --skill arboreto"},{"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/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},{"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":"pass","label":"GitHub adoption","detail":"34K GitHub stars"},{"status":"pass","label":"Stars/forks activity","detail":"34K stars, 3.3K forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"2d since push"},{"status":"pass","label":"License clarity","detail":"BSD-3-Clause license"},{"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 K-Dense-AI/scientific-agent-skills --skill arboreto"},{"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/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},{"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","Large GitHub adoption signal","Install command has no obvious high-risk pattern"],"warnings":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"],"evidence":{"stars":"34K GitHub stars","repoActivity":"34K stars, 3.3K forks","lastPushed":"2d since push","license":"BSD-3-Clause license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","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"},"installReadiness":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","2d since push"]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Human review or sandbox validation is required before automatic installation."},"bestFor":["data-analysis","agent-skill"],"doNotUseFor":["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"],"knownRisks":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"trust_v5":{"version":"trust-score-v5","score":77,"base_score":85,"outcome_confidence":0,"tier":"strong","label":"Review then install","summary":"Good shortlist signal, but the agent should review audit notes, install policy, and outcome evidence before running it.","recommendedAction":"Use as the primary candidate after human or sandbox review.","decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Ask for approval or run a sandbox-only trial before installing.","reasoning":["77/100 Trust Score v5","85/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is available","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human 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"]},"dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":100,"weight":0.13,"status":"pass","detail":"34K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":97,"weight":0.08,"status":"pass","detail":"34K stars, 3.3K forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"2d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"BSD-3-Clause license"},{"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 K-Dense-AI/scientific-agent-skills --skill arboreto"},{"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/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},{"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":"pass","label":"GitHub adoption","detail":"34K GitHub stars"},{"status":"pass","label":"Stars/forks activity","detail":"34K stars, 3.3K forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"2d since push"},{"status":"pass","label":"License clarity","detail":"BSD-3-Clause license"},{"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 K-Dense-AI/scientific-agent-skills --skill arboreto"},{"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/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},{"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","Large GitHub adoption signal","Install command has no obvious high-risk pattern","Outcome loop is ready but needs first real agent run"],"warnings":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","No real agent outcome reports yet","Human review required before unattended installation"],"evidence":{"stars":"34K GitHub stars","repoActivity":"34K stars, 3.3K forks","lastPushed":"2d since push","license":"BSD-3-Clause license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","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","agentProvenScore":0,"outcomeConfidence":"0%","installPolicy":"human_review_before_install"},"installReadiness":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","2d since push","Trust Score v5 requires review or sandbox-only use before install."]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Ask for approval or run a sandbox-only trial before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v3","required_after_install":true,"endpoint":"/api/agent/outcome","method":"POST","event_id_source":"feedback.event_id, install_receipt.resolve_event_id, or decision_packet.outcome_feedback.event_id","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"required_fields":["event_id","skill_slug","task"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url","time_to_useful_ms"],"ranking_inputs_updated":["Trust Score v5 outcome confidence","Agent Proven Score","Resolve ranking task-fit evidence","Skill detail machine-readable metadata","Outcome leaderboard"]},"agent_contract":{"suited_tasks":["data-analysis","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","trust_score":77,"trust_version":"trust-score-v5","risk_level":"medium","do_not_use_when":["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"],"before_install":["Read the audit page and machine-readable metadata.","Confirm the install command, license, and permission surface fit the workspace.","Get explicit human approval or choose an alternative before installing."],"after_run":["Report the outcome to /api/agent/outcome using the resolve event id.","Include output_quality, workspace, human_review_required, and evidence_url when available.","Re-resolve before broad production rollout."]},"bestFor":["data-analysis","agent-skill"],"doNotUseFor":["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"],"knownRisks":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":85,"tier":"strong","label":"Strong shortlist","summary":"Good trust signals with a few areas worth checking before rollout."}}},"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":{"audit_score":91,"risk_level":"safe_to_try","risk_label":"Safe to try","warnings":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"safety":{"score":79,"level":"review_before_install","label":"Review before install","safety_tier":{"tier":"reviewed","label":"Reviewed","badge":"REVIEWED","summary":"Good audit and safety signals with no high-risk permission hints in public metadata.","recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow.","auto_install_policy":"review","reasons":["Safe-to-try audit","79/100 agent safety score"]},"auto_install_allowed":false,"human_review_required":true,"blocked":false,"audit_risk":"safe_to_try","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","badge":"REVIEWED","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow.","reasons":["Safe-to-try audit","79/100 agent safety score"]},"decision":{"readiness_score":100,"readiness_label":"Production-ready","headline":"Primary pick for GitHub automation","role":"Primary pick","best_for":["GitHub automation workflows","Claude Code teams","teams that value GitHub adoption signals"],"risks":["No OpenAgentSkill engagement data yet"],"next_steps":["Install it in a sandbox agent and run one GitHub automation task end to end.","Compare output quality, latency, and failure behavior against at least one alternative.","Promote it into production only after reviewing repository permissions, license, and maintenance signals."]},"install_plan":{"target":"codex","label":"Codex install prompt","command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","value":"Install the \"arboreto\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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.","kind":"agent-prompt","steps":["Review arboreto trust and audit signals before installing.","Send the install prompt to the target agent.","Install in a sandbox or low-risk workspace first.","Pin the repository source and re-check the audit before production use."],"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 k-dense-ai-arboreto","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 \"arboreto\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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 \"arboreto\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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 \"arboreto\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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"}]},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"k-dense-ai-arboreto","name":"arboreto","description":"Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.","category":"data-analysis","url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","github_repo":"K-Dense-AI/scientific-agent-skills"},"suited_tasks":["GitHub automation workflows","Claude Code teams","teams that value GitHub adoption signals","Inspect repository metadata","Compare code changes","Write concise engineering summaries","Search sources","Extract claims"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz install k-dense-ai-arboreto"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"arboreto\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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 \"arboreto\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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 \"arboreto\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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/k-dense-ai-arboreto/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-arboreto"},"trust":{"score":85,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"34K GitHub stars","repoActivity":"34K stars, 3.3K forks","lastPushed":"2d since push","license":"BSD-3-Clause license","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","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":["data-analysis","agent-skill"],"known_risks":["Quality score needs review","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":91,"risk_level":"safe_to_try","risk_label":"Safe to try","warnings":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"safety_gate":{"tier":"reviewed","label":"Reviewed","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow."},"quality":{"score":92,"label":"Excellent"},"supply":{"track":"Coding and developer agents","scenario":"GitHub automation","maintenance":"2d since push","risk":"Safe to try"},"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","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","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 arboreto","recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow.","install_policy":"review","minimum_review_before_use":["Trust: 85/100 Strong shortlist","Audit: 91/100 Safe to try","Safety: 79/100 Review before install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"k-dense-ai-arboreto (arboreto)","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","risk_summary":"Safe to try; Reviewed; 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":"k-dense-ai-arboreto","task":"Use arboreto","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/k-dense-ai-arboreto","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto","audit":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20arboreto&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20arboreto&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install","manifest":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-arboreto"}},"use_cases":[{"slug":"github-automation","title":"GitHub automation","url":"https://www.openagentskill.com/use-cases/github-automation"},{"slug":"research-agents","title":"Research agents","url":"https://www.openagentskill.com/use-cases/research-agents"},{"slug":"finance-quant","title":"Finance and quant","url":"https://www.openagentskill.com/use-cases/finance-quant"}],"urls":{"web":"https://www.openagentskill.com/skills/k-dense-ai-arboreto","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto","install_api":"https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install","audit":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium","badge":"https://www.openagentskill.com/api/badge/k-dense-ai-arboreto?metric=audit","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"}},"alternatives":[],"blocked_candidates":[],"agent_workflow":{"mode":"resolve_review_install","recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow.","selected_skill":{"slug":"k-dense-ai-arboreto","name":"arboreto","url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},"install":{"target":"codex","label":"Codex install prompt","kind":"agent-prompt","command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","value":"Install the \"arboreto\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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.","api":"https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install"},"copy_paste_prompt":"Task: Use arboreto\nUse arboreto from https://www.openagentskill.com/skills/k-dense-ai-arboreto.\nReview the audit first: https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit\nReview the eval first: https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium\nInstall handoff: https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install\nInstall command: npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto\nIf audit or policy warnings look unsafe for this workspace, use one of the alternatives instead.","api_sequence":[{"step":1,"label":"Resolve task","method":"GET","url":"https://www.openagentskill.com/api/agent/resolve?task=Use%20arboreto&agent=codex&max_risk=medium"},{"step":2,"label":"Fetch pre-install eval","method":"GET","url":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium"},{"step":3,"label":"Fetch selected skill profile","method":"GET","url":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto"},{"step":4,"label":"Fetch install handoff","method":"GET","url":"https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install"},{"step":5,"label":"Review audit","method":"GET","url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit"},{"step":6,"label":"Report outcome","method":"POST","url":"https://www.openagentskill.com/api/agent/outcome","body":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","skill_slug":"k-dense-ai-arboreto","task":"Use arboreto","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":"Solved the task in a sandbox workflow."}}],"review_checklist":["Safety tier: Reviewed","Safety score: 79/100 Review before install","Audit score: 91/100 Safe to try","Trust score: 77/100 Review then install","Readiness: 100/100 Production-ready","Quality score needs review","Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"],"fallback_strategy":[],"expected_agent_output":{"selected_skill":"slug and name","install_command":"command or agent prompt used","risk_summary":"audit, trust, and policy notes","next_step":"what the agent will do after install","outcome_event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5"}},"agent_handoff":{"version":"openagentskill-agent-handoff-v1","mode":"resolve_compare_review_install","task":"Use arboreto","agent":"codex","selected_skill":{"slug":"k-dense-ai-arboreto","name":"arboreto","url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto","api_url":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto","audit_url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","eval_url":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},"install_plan":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","target":"codex","label":"Codex install prompt","kind":"agent-prompt","value":"Install the \"arboreto\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto. 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: Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets. 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\":\"k-dense-ai-arboreto\",\"task\":\"Install arboreto\",\"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.","install_api":"https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install","auto_install_allowed":false,"human_review_required":true,"policy":"review"},"api_sequence":[{"step":1,"label":"Resolve task","method":"GET","url":"https://www.openagentskill.com/api/agent/resolve?task=Use%20arboreto&agent=codex&max_risk=medium"},{"step":2,"label":"Fetch pre-install eval","method":"GET","url":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium"},{"step":3,"label":"Fetch selected skill profile","method":"GET","url":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto"},{"step":4,"label":"Fetch install handoff","method":"GET","url":"https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install"},{"step":5,"label":"Review audit","method":"GET","url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit"},{"step":6,"label":"Report outcome","method":"POST","url":"https://www.openagentskill.com/api/agent/outcome","body":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","skill_slug":"k-dense-ai-arboreto","task":"Use arboreto","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":"Solved the task in a sandbox workflow."}}],"platform_templates":[{"id":"codex","name":"Codex","surface":"Coding agent / local workspace","copy_prompt":"Task: Use arboreto\nSelected skill: arboreto (k-dense-ai-arboreto)\nSkill URL: https://www.openagentskill.com/skills/k-dense-ai-arboreto\nAudit URL: https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit\nEval URL: https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium\nInstall handoff: https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install\nInstall command: npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto\nInstall policy: Human review is required before install.\nOutcome feedback: use install_receipt.outcome_feedback.event_id or feedback.event_id from the Resolve API and report the result to /api/agent/outcome after one narrow run. Include outcome, install_used, task_success, output_quality, workspace, error_type, and human_review_required when known.\n\nBefore installing:\n1. Read the audit and eval result.\n2. Report risk notes and files or commands that will be touched.\n3. Install only in a sandbox or low-risk workspace first.\n4. If risk is unacceptable, use an alternative.\n\nAlternatives:\n- No safer alternative returned by the resolver.\n\nExpected Codex output:\n- selected_skill\n- install_command\n- risk_summary\n- outcome_event_id\n- alternatives\n- files_or_commands_to_touch\n- next_action"},{"id":"claude-code","name":"Claude Code","surface":"Claude Code skill workflow","copy_prompt":"Task: Use arboreto\nSelected skill: arboreto (k-dense-ai-arboreto)\nSkill URL: https://www.openagentskill.com/skills/k-dense-ai-arboreto\nAudit URL: https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit\nEval URL: https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium\nInstall handoff: https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install\nInstall command: npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto\nInstall policy: Human review is required before install.\nOutcome feedback: use install_receipt.outcome_feedback.event_id or feedback.event_id from the Resolve API and report the result to /api/agent/outcome after one narrow run. Include outcome, install_used, task_success, output_quality, workspace, error_type, and human_review_required when known.\n\nBefore installing:\n1. Read the audit and eval result.\n2. Report risk notes and files or commands that will be touched.\n3. Install only in a sandbox or low-risk workspace first.\n4. If risk is unacceptable, use an alternative.\n\nAlternatives:\n- No safer alternative returned by the resolver.\n\nExpected Claude Code output:\n- selected_skill\n- skill_files_or_instructions\n- install_prompt\n- risk_summary\n- outcome_event_id\n- activation_steps\n- fallback_skill"},{"id":"cursor","name":"Cursor","surface":"Cursor rules / agent instructions","copy_prompt":"Task: Use arboreto\nSelected skill: arboreto (k-dense-ai-arboreto)\nSkill URL: https://www.openagentskill.com/skills/k-dense-ai-arboreto\nAudit URL: https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit\nEval URL: https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-arboreto&task=Use%20arboreto&max_risk=medium\nInstall handoff: https://www.openagentskill.com/api/skills/k-dense-ai-arboreto/install\nInstall command: npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto\nInstall policy: Human review is required before install.\nOutcome feedback: use install_receipt.outcome_feedback.event_id or feedback.event_id from the Resolve API and report the result to /api/agent/outcome after one narrow run. Include outcome, install_used, task_success, output_quality, workspace, error_type, and human_review_required when known.\n\nBefore installing:\n1. Read the audit and eval result.\n2. Report risk notes and files or commands that will be touched.\n3. Install only in a sandbox or low-risk workspace first.\n4. If risk is unacceptable, use an alternative.\n\nAlternatives:\n- No safer alternative returned by the resolver.\n\nExpected Cursor output:\n- selected_skill\n- cursor_rule_or_prompt\n- install_command\n- risk_summary\n- outcome_event_id\n- when_to_use\n- when_not_to_use"}],"review_checklist":["Safety tier: Reviewed","Safety score: 79/100 Review before install","Audit score: 91/100 Safe to try","Trust score: 77/100 Review then install","Readiness: 100/100 Production-ready","Quality score needs review","Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"],"expected_output":{"selected_skill":"slug and name","install_command":"command or agent prompt used","risk_summary":"audit, trust, and policy notes","next_step":"what the agent will do after install","outcome_event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5"},"feedback":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","outcome_api":"https://www.openagentskill.com/api/agent/outcome","cli_example":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz outcome \"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5\" --skill \"k-dense-ai-arboreto\" --task \"Use arboreto\" --agent \"codex\" --outcome success","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"]},"blocked_actions":["Do not install when safety_gate.blocked is true.","Do not install when the audit or eval reports unacceptable workspace risk.","Do not execute shell commands, access secrets, or call external services without user approval.","Do not keep the skill as an always-on instruction if it only fits a narrow task."]},"policy_decision":{"status":"human_review_required","summary":"Review the audit page, then allow agent install in a sandboxed workflow."},"agent_decision":{"input_task":"Use arboreto","recommended_skill":{"slug":"k-dense-ai-arboreto","name":"arboreto","url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto","audit_url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto","safety_tier":"Reviewed","auto_install_policy":"review"},"alternative_skills":[],"install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","install_target":"Codex install prompt","why_recommended":["Matches task terms: arboreto","Strong GitHub adoption: 33,974 stars","Install handoff is available","Repository freshness signal is available","Registry match score 30","Primary pick for GitHub automation"],"risk_summary":{"level":"Safe to try","safety_tier":"Reviewed","safety":"79/100 Review before install","trust":"85/100 Strong shortlist","notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"safety_gate":{"tier":"reviewed","label":"Reviewed","auto_install_policy":"review","action":"Review the audit page, then allow agent install in a sandboxed workflow."},"feedback":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","outcome_api":"https://www.openagentskill.com/api/agent/outcome","cli_example":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz outcome \"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5\" --skill \"k-dense-ai-arboreto\" --task \"Use arboreto\" --agent \"codex\" --outcome success","contract":{"version":"openagentskill-agent-feedback-loop-v3","status":"active","purpose":"Report the result of one resolved skill run so Trust Score v5 and future Resolve rankings learn from real use.","event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","selected_skill_slug":"k-dense-ai-arboreto","selected_skill_name":"arboreto","endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","idempotency":"Retrying the same event_id updates the previous outcome.","dry_run":{"supported":true,"instruction":"Set dry_run=true to validate a payload before wiring a new agent integration."},"expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"error_types":["install_failed","runtime_error","not_relevant","permission_blocked","risk_blocked","setup_required","low_quality_output","missing_dependency","timeout","other"],"workspaces":["sandbox","local","ci","production","unknown"],"quality_fields":["task_success","output_quality","error_type","human_review_required","used_in_production","workspace","evidence_url"],"payload_template":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","skill_slug":"k-dense-ai-arboreto","task":"Use arboreto","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":"Solved the task in a sandbox workflow."},"cli_example":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz outcome \"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5\" --skill \"k-dense-ai-arboreto\" --task \"Use arboreto\" --agent \"codex\" --outcome success","ranking_inputs_updated":["Trust Score v5 outcome confidence","Resolve ranking outcome evidence","Skill detail outcome signal block","Outcome leaderboard"]}},"agent_next_steps":["Read the audit URL before installing.","Ask for human approval before installing.","Use install command: npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","After one narrow task, report the outcome with: npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz outcome \"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5\" --skill \"k-dense-ai-arboreto\" --task \"Use arboreto\" --agent \"codex\" --outcome success","Summarize output, warnings, files touched, and whether setup or human review was required."]},"decision_packet":{"version":"openagentskill-agent-decision-packet-v1","task":"Use arboreto","agent":"codex","selected_skill":{"slug":"k-dense-ai-arboreto","name":"arboreto","url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto","api_url":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-arboreto","audit_url":"https://www.openagentskill.com/skills/k-dense-ai-arboreto/audit","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},"suited_tasks":["GitHub automation workflows","Claude Code teams","teams that value GitHub adoption signals","Inspect repository metadata","Compare code changes","Write concise engineering summaries","Search sources","Extract claims"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto","target":"codex","label":"Codex install prompt","policy":"review","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true},"trust":{"score":77,"label":"Review then install","version":"trust-score-v5","base_score":85,"outcome_confidence":0,"decision":{"install_policy":"human_review_before_install","auto_install_allowed":false,"human_review_required":true,"sandbox_first":true,"agent_action":"Ask for approval or run a sandbox-only trial before installing.","reasoning":["77/100 Trust Score v5","85/100 Trust Score v4 baseline","Needs more real agent outcomes before unattended install","Install path is available","Review before production"],"review_required_when":["The workspace contains production secrets, payments, private customer data, or irreversible actions.","The install command requests shell, network, credential, database, or broad filesystem access.","Outcome evidence is missing, recently failed, or required human 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"]},"dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":100,"status":"pass","detail":"34K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":97,"status":"pass","detail":"34K stars, 3.3K forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"status":"pass","detail":"2d since push"},{"id":"license","label":"License clarity","score":86,"status":"pass","detail":"BSD-3-Clause license"},{"id":"documentation","label":"README/SKILL.md completeness","score":52,"status":"warn","detail":"Public metadata needs stronger README/SKILL.md context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":90,"status":"pass","detail":"no major dependency risk hints in public metadata"},{"id":"installability","label":"Install availability","score":92,"status":"pass","detail":"npx skills add K-Dense-AI/scientific-agent-skills --skill arboreto"},{"id":"install_safety","label":"Install command safety","score":92,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":100,"status":"pass","detail":"no high-risk permission surface in public metadata"},{"id":"repository","label":"Repository evidence","score":86,"status":"pass","detail":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/arboreto"},{"id":"review_status","label":"Review status","score":88,"status":"pass","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"status":"info","detail":"No agent outcome data yet"}]},"risk":{"level":"Safe to try","audit_label":"Safe to try","safety":"79/100 Review before install","trust":"85/100 Strong shortlist","safety_tier":"Reviewed","notes":["Quality score needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"],"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","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","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"],"minimum_review_before_use":["Trust: 85/100 Strong shortlist","Audit: 91/100 Safe to try","Safety: 79/100 Review before install","Review repository, license, install command, and permission surface before production use."]},"alternatives":[],"outcome_feedback":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5","skill_slug":"k-dense-ai-arboreto","task":"Use arboreto","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":"Solved the task in a sandbox workflow."},"cli_example":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.2.1/openagentskill-0.2.1.tgz outcome \"resolve_b6065127-0846-44b9-9eab-79b9bb0182b5\" --skill \"k-dense-ai-arboreto\" --task \"Use arboreto\" --agent \"codex\" --outcome success"},"next_agent_action":"Ask for human approval or choose a safer alternative before installing.","stable_fields":["decision_packet.selected_skill","decision_packet.install","decision_packet.risk.do_not_use_when","decision_packet.alternatives","decision_packet.outcome_feedback","decision_packet.trust.decision"]},"benchmark":{"endpoint":"https://www.openagentskill.com/api/agent/evals","note":"Use the evals endpoint to regression-test recommendation quality before changing ranking logic."},"meta":{"endpoint":"/api/agent/resolve","api_version":"2.0","generated_at":"2026-08-22T15:18:50.934Z","total_skills_searched":799,"total_candidates":1,"candidate_pool":{"sort":"quality","size":799,"note":"Resolver searches the highest-quality candidate pool for low-latency agent use. Browse /skills for the full public index."},"contract":{"best_skill":"recommendation.best_skill","install":"recommendation.install","why":"recommendation.why_recommended","risk":"recommendation.risk","alternatives":"recommendation.alternatives","agent_handoff":"agent_handoff.platform_templates + agent_handoff.review_checklist","decision_packet":"decision_packet","install_receipt":"install_receipt","recommendation_lanes":"recommendation_lanes"}}}