{"slug":"k-dense-ai-biopython","name":"biopython","description":"Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.","long_description":"---\nname: biopython\ndescription: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.\nallowed-tools: Read Write Edit Bash\ncompatibility: Requires Python 3.10+, NumPy, and Biopython. Entrez and web BLAST examples require network access; local BLAST/MUSCLE examples require those command-line tools installed separately.\nlicense: Biopython License Agreement\nmetadata:\n  version: \"1.2\"\n  skill-author: K-Dense Inc.\n  openclaw:\n    envVars:\n    - name: NCBI_EMAIL\n      required: false\n      description: Email for NCBI Entrez identification (required by NCBI policy for Entrez calls).\n    - name: NCBI_API_KEY\n      required: false\n      description: NCBI API key to raise Entrez rate limits.\n---\n\n# Biopython: Computational Molecular Biology in Python\n\n## Overview\n\nBiopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks. The current version is **Biopython 1.87** (released 30 March 2026). It supports **Python 3.10-3.14** and PyPy3.10, and requires NumPy. Biopython 1.87 also addresses **CVE-2025-68463** in `Bio.Entrez.Parser` when parsing untrusted files, so prefer 1.87+ for workflows that parse externally supplied Entrez XML.\n\n## When to Use This Skill\n\nUse this skill when:\n\n- Working with biological sequences (DNA, RNA, or protein)\n- Reading, writing, or converting biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, etc.)\n- Accessing NCBI databases (GenBank, PubMed, Protein, Gene, etc.) via Entrez\n- Running BLAST searches or parsing BLAST results\n- Performing sequence alignments (pairwise or multiple sequence alignments)\n- Analyzing protein structures from PDB files\n- Creating, manipulating, or visualizing phylogenetic trees\n- Finding sequence motifs or analyzing motif patterns\n- Calculating sequence statistics (GC content, molecular weight, melting temperature, etc.)\n- Performing structural bioinformatics tasks\n- Working with population genetics data\n- Any other computational molecular biology task\n\n## Core Capabilities\n\nBiopython is organized into modular sub-packages, each addressing specific bioinformatics domains:\n\n1. **Sequence Handling** - Bio.Seq and Bio.SeqIO for sequence manipulation and file I/O\n2. **Alignment Analysis** - Bio.Align and Bio.AlignIO for pairwise and multiple sequence alignments\n3. **Database Access** - Bio.Entrez for programmatic access to NCBI databases\n4. **BLAST Operations** - Bio.Blast for running and parsing BLAST searches\n5. **Structural Bioinformatics** - Bio.PDB for working with 3D protein structures\n6. **Phylogenetics** - Bio.Phylo for phylogenetic tree manipulation and visualization\n7. **Advanced Features** - Motifs, population genetics, sequence utilities, and more\n\n## Installation and Setup\n\nInstall the current stable Biopython release with an explicit version pin for reproducibility:\n\n```bash\nuv pip install \"biopython==1.87\"\n```\n\nFor NCBI database access, always set your email address (required by NCBI). For reusable software, set a stable `Entrez.tool` value and register the tool/email with NCBI. For higher rate limits (10 req/s instead of 3 req/s), read only `NCBI_API_KEY` from the environment — do not hardcode keys or load unrelated environment variables:\n\n```python\nimport os\nfrom Bio import Entrez\n\nEntrez.email = \"your.email@example.com\"  # required — use your real email\nEntrez.tool = \"your_tool_name\"  # optional but recommended for reusable software\n\n# Optional: register at https://www.ncbi.nlm.nih.gov/account/settings/\nif api_key := os.environ.get(\"NCBI_API_KEY\"):\n    Entrez.api_key = api_key\n```\n\n## Using This Skill\n\nThis skill provides comprehensive documentation organized by functionality area. When working on a task, consult the relevant reference documentation:\n\n### 1. Sequence Handling (Bio.Seq & Bio.SeqIO)\n\n**Reference:** `references/sequence_io.md`\n\nUse for:\n- Creating and manipulating biological sequences\n- Reading and writing sequence files (FASTA, GenBank, FASTQ, etc.)\n- Converting between file formats\n- Extracting sequences from large files\n- Sequence translation, transcription, and reverse complement\n- Working with SeqRecord objects\n\n**Quick example:**\n```python\nfrom Bio import SeqIO\n\n# Read sequences from FASTA file\nfor record in SeqIO.parse(\"sequences.fasta\", \"fasta\"):\n    print(f\"{record.id}: {len(record.seq)} bp\")\n\n# Convert GenBank to FASTA\nSeqIO.convert(\"input.gb\", \"genbank\", \"output.fasta\", \"fasta\")\n```\n\n### 2. Alignment Analysis (Bio.Align & Bio.AlignIO)\n\n**Reference:** `references/alignment.md`\n\nUse for:\n- Pairwise sequence alignment (global and local)\n- Reading and writing multiple sequence alignments\n- Using substitution matrices (BLOSUM, PAM)\n- Calculating alignment statistics\n- Customizing alignment parameters\n\n**Quick example:**\n```python\nfrom Bio import Align\n\n# Pairwise alignment\naligner = Align.PairwiseAligner()\naligner.mode = 'global'\nalignments = aligner.align(\"ACCGGT\", \"ACGGT\")\nprint(alignments[0])\n```\n\n### 3. Database Access (Bio.Entrez)\n\n**Reference:** `references/databases.md`\n\nUse for:\n- Searching NCBI databases (PubMed, GenBank, Protein, Gene, etc.)\n- Downloading sequences and records\n- Fetching publication information\n- Finding related records across databases\n- Batch downloading with proper rate limiting\n\n**Quick example:**\n```python\nfrom Bio import Entrez\nEntrez.email = \"your.email@example.com\"\n\n# Search PubMed\nhandle = Entrez.esearch(db=\"pubmed\", term=\"biopython\", retmax=10)\nresults = Entrez.read(handle)\nhandle.close()\nprint(f\"Found {results['Count']} results\")\n```\n\n### 4. BLAST Operations (Bio.Blast)\n\n**Reference:** `references/blast.md`\n\nUse for:\n- Running BLAST searches via NCBI web services\n- Running local BLAST searches\n- Parsing BLAST XML output\n- Filtering results by E-value or identity\n- Extracting hit sequences\n\n**Quick example:**\n```python\nfrom Bio.Blast import NCBIWWW, NCBIXML\n\n# Run BLAST search\nresult_handle = NCBIWWW.qblast(\"blastn\", \"nt\", \"ATCGATCGATCG\")\nblast_record = NCBIXML.read(result_handle)\n\n# Display top hits\nfor alignment in blast_record.alignments[:5]:\n    print(f\"{alignment.title}: E-value={alignment.hsps[0].expect}\")\n```\n\n### 5. Structural Bioinformatics (Bio.PDB)\n\n**Reference:** `references/structure.md`\n\nUse for:\n- Parsing PDB and mmCIF structure files\n- Navigating protein structure hierarchy (SMCRA: Structure/Model/Chain/Residue/Atom)\n- Calculating distances, angles, and dihedrals\n- Secondary structure assignment (DSSP)\n- Structure superimposition and RMSD calculation\n- Extracting sequences from structures\n\n**Quick example:**\n```python\nfrom Bio.PDB import PDBParser\n\n# Parse structure\nparser = PDBParser(QUIET=True)\nstructure = parser.get_structure(\"1crn\", \"1crn.pdb\")\n\n# Calculate distance between alpha carbons\nchain = structure[0][\"A\"]\ndistance = chain[10][\"CA\"] - chain[20][\"CA\"]\nprint(f\"Distance: {distance:.2f} Å\")\n```\n\n### 6. Phylogenetics (Bio.Phylo)\n\n**Reference:** `references/phylogenetics.md`\n\nUse for:\n- Reading and writing phylogenetic trees (Newick, NEXUS, phyloXML)\n- Building trees from distance matrices or alignments\n- Tree manipulation (pruning, rerooting, ladderizing)\n- Calculating phylogenetic distances\n- Creating consensus trees\n- Visualizing trees\n\n**Quick example:**\n```python\nfrom Bio import Phylo\n\n# Read and visualize tree\ntree = Phylo.read(\"tree.nwk\", \"newick\")\nPhylo.draw_ascii(tree)\n\n# Calculate distance\ndistance = tree.distance(\"Species_A\", \"Species_B\")\nprint(f\"Distance: {distance:.3f}\")\n```\n\n### 7. Advanced Features\n\n**Reference:** `references/advanced.md`\n\nUse for:\n- **Sequence motifs** (Bio.motifs) - Finding and analyzing motif patterns\n- **Population genetics** (Bio.PopGen) - GenePop files, Fst calculations, Hardy-Weinberg tests\n- **Sequence utilities** (Bio.SeqUtils) - GC content, melting temperature, molecular weight, protein analysis\n- **Restriction analysis** (Bio.Restriction) - Finding restriction enzyme sites\n- **Clustering** (Bio.Cluster) - K-means and hierarchical clustering\n- **Genome diagrams** (GenomeDiagram) - Visualizing genomic features\n\n**Quick example:**\n```python\nfrom Bio.SeqUtils import gc_fraction, molecular_weight\nfrom Bio.Seq import Seq\n\nseq = Seq(\"ATCGATCGATCG\")\nprint(f\"GC content: {gc_fraction(seq):.2%}\")\nprint(f\"Molecular weight: {molecular_weight(seq, seq_type='DNA'):.2f} g/mol\")\n```\n\n## General Workflow Guidelines\n\n### Reading Documentation\n\nWhen a user asks about a specific Biopython task:\n\n1. **Identify the relevant module** based on the task description\n2. **Read the appropriate reference file** using the Read tool\n3. **Extract relevant code patterns** and adapt them to the user's specific needs\n4. **Combine multiple modules** when the task requires it\n\nExample search patterns for reference files:\n```bash\n# Find information about specific functions\nrg -n \"SeqIO.parse\" references/sequence_io.md\n\n# Find examples of specific tasks\nrg -n \"BLAST\" references/blast.md\n\n# Find information about specific concepts\nrg -n \"alignment\" references/alignment.md\n```\n\n### Writing Biopython Code\n\nFollow these principles when writing Biopython code:\n\n1. **Import modules explicitly**\n   ```python\n   from Bio import SeqIO, Entrez\n   from Bio.Seq import Seq\n   ```\n\n2. **Set Entrez email** when using NCBI databases; load only `NCBI_API_KEY` from the environment if present\n   ```python\n   import os\n   from Bio import Entrez\n\n   Entrez.email = \"your.email@example.com\"\n   Entrez.tool = \"your_tool_name\"\n   if api_key := os.environ.get(\"NCBI_API_KEY\"):\n       Entrez.api_key = api_key\n   ```\n\n3. **Use appropriate file formats** - Check which format best suits the task\n   ```python\n   # Common formats: \"fasta\", \"genbank\", \"fastq\", \"clustal\", \"phylip\"\n   ```\n\n4. **Handle files properly** - Close handles after use or use context managers\n   ```python\n   with open(\"file.fasta\") as handle:\n       records = SeqIO.parse(handle, \"fasta\")\n   ```\n\n5. **Use iterators for large files** - Avoid loading everything into memory\n   ```python\n   for record in SeqIO.parse(\"large_file.fasta\", \"fasta\"):\n       # Process one record at a time\n   ```\n\n6. **Handle errors gracefully** - Network operations and file parsing can fail\n   ```python\n   from urllib.error import HTTPError\n\n   try:\n       handle = Entrez.efetch(db=\"nucleotide\", id=accession)\n   except HTTPError as e:\n       print(f\"Error: {e}\")\n   ```\n\n## Common Patterns\n\n### Pattern 1: Fetch Sequence from GenBank\n\n```python\nfrom Bio import Entrez, SeqIO\n\nEntrez.email = \"your.email@example.com\"\n\n# Fetch sequence\nhandle = Entrez.efetch(db=\"nucleotide\", id=\"EU490707\", rettype=\"gb\", retmode=\"text\")\nrecord = SeqIO.read(handle, \"genbank\")\nhandle.close()\n\nprint(f\"Description: {record.description}\")\nprint(f\"Sequence length: {len(record.seq)}\")\n```\n\n### Pattern 2: Sequence Analysis Pipeline\n\n```python\nfrom Bio import SeqIO\nfrom Bio.SeqUtils import gc_fraction\n\nfor record in SeqIO.parse(\"sequences.fasta\", \"fasta\"):\n    # Calculate statistics\n    gc = gc_fraction(record.seq)\n    length = len(record.seq)\n\n    # Find ORFs, translate, etc.\n    protein = record.seq.translate()\n\n    print(f\"{record.id}: {length} bp, GC={gc:.2%}\")\n```\n\n### Pattern 3: BLAST and Fetch Top Hits\n\n```python\nfrom Bio.Blast import NCBIWWW, NCBIXML\nfrom Bio import Entrez, SeqIO\n\nEntrez.email = \"your.email@example.com\"\n\n# Run BLAST\nresult_handle = NCBIWWW.qblast(\"blastn\", \"nt\", sequence)\nblast_record = NCBIXML.read(result_handle)\n\n# Get top hit accessions\naccessions = [aln.accession for aln in blast_record.alignments[:5]]\n\n# Fetch sequences\nfor acc in accessions:\n    handle = Entrez.efetch(db=\"nucleotide\", id=acc, rettype=\"fasta\", retmode=\"text\")\n    record = SeqIO.read(handle, \"fasta\")\n ","tagline":"Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for","category":"design-creative","tags":["agent-skill"],"author":"K-Dense-AI","verified":false,"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"recursive skill source sync","sourceDetail":"K-Dense-AI/scientific-agent-skills","creatorName":"K-Dense-AI","creatorUrl":"https://github.com/K-Dense-AI","sourceUrl":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/k-dense-ai-biopython#claim-this-skill","claimCta":"Claim this skill","trustNote":"This listing was indexed from public sources and is not marked official until a maintainer claim is approved.","publicNote":"Attribution links to the public repository or creator profile. 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The referenced file appears to be missing.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":69,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection."}}},"trust_score_v5":{"version":"trust-score-v5","score":61,"base_score":69,"outcome_confidence":0,"tier":"review","label":"Sandbox only","summary":"Useful candidate with missing or mixed trust signals. 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The referenced file appears to be missing.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution","No real agent outcome reports yet","Human review required before unattended installation"],"evidence":{"stars":"38K GitHub stars","repoActivity":"38K stars, 3.6K forks","lastPushed":"6d since push","license":"Biopython License Agreement","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","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 biopython","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","6d 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":["SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"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":"Compare alternatives before installing."},"outcome_loop":{"version":"openagentskill-agent-outcome-v4","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","source_version"],"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":["design-creative","agent-skill"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython","trust_score":61,"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":["design-creative","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":["SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":69,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection."}}},"trust_score_v4":{"version":"trust-score-v4","score":69,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection.","recommendedAction":"Inspect the repository, license, and recent activity before connecting it to agent workflows.","dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":100,"weight":0.13,"status":"pass","detail":"38K GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":97,"weight":0.08,"status":"pass","detail":"38K stars, 3.6K forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"6d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"Biopython License Agreement"},{"id":"documentation","label":"README/SKILL.md completeness","score":86,"weight":0.14,"status":"pass","detail":"Metadata includes enough usage and workflow context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":28,"weight":0.12,"status":"fail","detail":"command execution surface, credential or environment access"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython"},{"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":18,"weight":0.07,"status":"fail","detail":"secrets or environment access, shell or command execution"},{"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/biopython"},{"id":"review_status","label":"Review status","score":66,"weight":0.05,"status":"info","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":"38K GitHub stars"},{"status":"pass","label":"Stars/forks activity","detail":"38K stars, 3.6K forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"6d since push"},{"status":"pass","label":"License clarity","detail":"Biopython License Agreement"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"fail","label":"Dependency/runtime risk","detail":"command execution surface, credential or environment access"},{"status":"pass","label":"Install availability","detail":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"fail","label":"Permission surface","detail":"secrets or environment access, shell or command execution"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython"},{"status":"info","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":"pass","label":"OpenAgentSkill usage","detail":"4 views, 0 install copies"},{"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":["SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"],"evidence":{"stars":"38K GitHub stars","repoActivity":"38K stars, 3.6K forks","lastPushed":"6d since push","license":"Biopython License Agreement","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"installReadiness":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython","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","6d since push"]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"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":["design-creative","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":["SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"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"]},"outcome_stats":null,"safety":{"score":38,"level":"avoid_auto_install","label":"Avoid automatic install","safety_tier":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","summary":"Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","auto_install_policy":"review","reasons":["Metadata combines secrets access with shell or command execution","High-risk permission hints: Shell or command execution, Secrets or environment access","38/100 agent safety score"]},"auto_install_allowed":false,"human_review_required":true,"blocked":false,"audit_risk":"needs_review","permission_hints":[{"id":"shell","label":"Shell or command execution","reason":"Skill metadata references terminal, CLI, shell, subprocess, or command execution workflows.","severity":"high"},{"id":"network","label":"Network access","reason":"Skill likely fetches remote pages, APIs, repositories, or external services.","severity":"medium"},{"id":"filesystem","label":"Filesystem access","reason":"Skill may read or write project files, documents, generated artifacts, or local workspace state.","severity":"medium"},{"id":"secrets","label":"Secrets or environment access","reason":"Skill metadata references credentials, tokens, environment variables, or secret-bearing workflows.","severity":"high"},{"id":"database","label":"Database access","reason":"Skill may inspect schemas, query databases, or work with persistent stores.","severity":"medium"}],"policy_warnings":["High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review"],"constraints_applied":{"max_risk":"medium","needs_install_command":true,"min_stars":0}},"safety_gate":{"tier":"experimental","label":"Experimental","badge":"EXPERIMENTAL","auto_install_policy":"review","auto_install_allowed":false,"blocked":false,"human_review_required":true,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","reasons":["Metadata combines secrets access with shell or command execution","High-risk permission hints: Shell or command execution, Secrets or environment access","38/100 agent safety score"]},"eval":{"version":"openagentskill-skill-eval-v1","status":"failed","score":72,"risk_level":"high","decision":{"recommendation":"do_not_auto_install","reason":"Permission surface: secrets or environment access, shell or command execution","auto_install_allowed":false,"policy":"block","human_review_required":true},"blockers":["Permission surface: secrets or environment access, shell or command execution"],"warnings":["Trust score: Potentially useful, but at least one trust signal needs human inspection.","Audit score: Needs review","Agent safety gate: Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","The NCBI_EMAIL environment variable is listed as optional in metadata, while the documentation correctly states that NCBI policy requires an email for Entrez. The example hardcodes a placeholder instead of reading from the environment, which may cause failed Entrez calls.","The skill does not include an explicit license/attribution notice beyond the repository license declaration. If the content is derived from Biopython documentation, upstream copyright and license notices should be preserved.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"],"validation_plan":["Inspect repository, README/SKILL.md, license, and recent commits before production use.","Install in an isolated workspace or sandbox with no production secrets available.","Run the smallest representative task and record files touched, commands run, network access, and outputs.","Compare the selected skill against at least one alternative when the eval status is review or failed.","Promote only after the agent reports a successful verification result and unresolved warnings are accepted."],"checks":[{"id":"task_fit","label":"Task fit","status":"pass","score":84,"required_for_auto_install":true,"detail":"Task wording matches this skill metadata.","evidence":["Evaluate biopython before installing it in an agent workflow","design-creative","Workflow automation workflows; Claude Code teams; teams that value GitHub adoption signals"]},{"id":"install_path","label":"Install path","status":"pass","score":92,"required_for_auto_install":true,"detail":"Install handoff is available.","evidence":["npx skills add K-Dense-AI/scientific-agent-skills --skill biopython"]},{"id":"install_safety","label":"Install command safety","status":"pass","score":92,"required_for_auto_install":true,"detail":"standard package or runtime install path","evidence":["npx skills add K-Dense-AI/scientific-agent-skills --skill biopython"]},{"id":"trust_score","label":"Trust score","status":"warn","score":69,"required_for_auto_install":true,"detail":"Potentially useful, but at least one trust signal needs human inspection.","evidence":["Manual review","38K GitHub stars","Biopython License Agreement"]},{"id":"audit_score","label":"Audit score","status":"warn","score":82,"required_for_auto_install":true,"detail":"Needs review","evidence":["Dependency or permission surface needs review"]},{"id":"agent_safety_gate","label":"Agent safety gate","status":"warn","score":38,"required_for_auto_install":true,"detail":"Sparse or mixed signals. Useful for discovery, but not for autonomous installation.","evidence":["Test manually in an isolated workspace and compare against safer alternatives.","Metadata combines secrets access with shell or command execution"]},{"id":"readme_skillmd_completeness","label":"README/SKILL.md completeness","status":"pass","score":86,"required_for_auto_install":false,"detail":"Metadata includes enough usage and workflow context","evidence":["Strong README/SKILL.md context"]},{"id":"license_clarity","label":"License clarity","status":"pass","score":86,"required_for_auto_install":true,"detail":"Biopython License Agreement","evidence":["Biopython License Agreement"]},{"id":"recent_maintenance","label":"Recent maintenance","status":"pass","score":100,"required_for_auto_install":false,"detail":"6d since push","evidence":["6d since push"]},{"id":"permission_surface","label":"Permission surface","status":"fail","score":18,"required_for_auto_install":true,"detail":"secrets or environment access, shell or command execution","evidence":["Shell or command execution: high","Network access: medium","Filesystem access: medium"]},{"id":"alternatives","label":"Alternatives available","status":"info","score":55,"required_for_auto_install":false,"detail":"No close alternatives were found in the current shortlist.","evidence":[]}],"endpoints":{"web":"https://www.openagentskill.com/skills/k-dense-ai-biopython/evals","api":"/api/agent/evals?slug=k-dense-ai-biopython","text":"/api/agent/evals?slug=k-dense-ai-biopython&format=text"}},"agent_readable_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"k-dense-ai-biopython","name":"biopython","description":"Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.","category":"design-creative","url":"https://www.openagentskill.com/skills/k-dense-ai-biopython","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython","github_repo":"K-Dense-AI/scientific-agent-skills"},"suited_tasks":["Workflow automation workflows","Claude Code teams","teams that value GitHub adoption signals","Move data between tools","Transform files","Trigger repeatable actions","Read uploaded files","Extract structured fields"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add k-dense-ai-biopython"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"biopython\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython. 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: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices. 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-biopython\",\"task\":\"Install biopython\",\"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 \"biopython\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython. 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: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices. 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-biopython\",\"task\":\"Install biopython\",\"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 \"biopython\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython 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: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices. 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-biopython\",\"task\":\"Install biopython\",\"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-biopython/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-biopython"},"trust":{"score":69,"label":"Manual review","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"38K GitHub stars","repoActivity":"38K stars, 3.6K forks","lastPushed":"6d since push","license":"Biopython License Agreement","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["design-creative","agent-skill"],"known_risks":["SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"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":82,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","The NCBI_EMAIL environment variable is listed as optional in metadata, while the documentation correctly states that NCBI policy requires an email for Entrez. The example hardcodes a placeholder instead of reading from the environment, which may cause failed Entrez calls.","The skill does not include an explicit license/attribution notice beyond the repository license declaration. If the content is derived from Biopython documentation, upstream copyright and license notices should be preserved.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"safety_gate":{"tier":"experimental","label":"Experimental","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives."},"quality":{"score":92,"label":"Excellent"},"supply":{"track":"Design and creative production","scenario":"Multimodal media","maintenance":"6d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","The NCBI_EMAIL environment variable is listed as optional in metadata, while the documentation correctly states that NCBI policy requires an email for Entrez. The example hardcodes a placeholder instead of reading from the environment, which may cause failed Entrez calls.","The skill does not include an explicit license/attribution notice beyond the repository license declaration. If the content is derived from Biopython documentation, upstream copyright and license notices should be preserved."],"agent_contract":{"task_input":"Use biopython in an agent workflow","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","install_policy":"review","minimum_review_before_use":["Trust: 69/100 Manual review","Audit: 82/100 Needs review","Safety: 38/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"k-dense-ai-biopython (biopython)","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython","risk_summary":"Needs review; Experimental; 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-biopython","task":"Use biopython in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/k-dense-ai-biopython","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-biopython","audit":"https://www.openagentskill.com/skills/k-dense-ai-biopython/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-biopython&task=Use%20biopython%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20biopython%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20biopython%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/k-dense-ai-biopython/install","manifest":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-biopython"}},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"k-dense-ai-biopython","name":"biopython","description":"Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.","category":"design-creative","url":"https://www.openagentskill.com/skills/k-dense-ai-biopython","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython","github_repo":"K-Dense-AI/scientific-agent-skills"},"suited_tasks":["Workflow automation workflows","Claude Code teams","teams that value GitHub adoption signals","Move data between tools","Transform files","Trigger repeatable actions","Read uploaded files","Extract structured fields"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add k-dense-ai-biopython"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"biopython\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython. 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: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices. 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-biopython\",\"task\":\"Install biopython\",\"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 \"biopython\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython. 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: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices. 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-biopython\",\"task\":\"Install biopython\",\"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 \"biopython\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython 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: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices. 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-biopython\",\"task\":\"Install biopython\",\"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-biopython/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-biopython"},"trust":{"score":69,"label":"Manual review","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"38K GitHub stars","repoActivity":"38K stars, 3.6K forks","lastPushed":"6d since push","license":"Biopython License Agreement","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython","install":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["design-creative","agent-skill"],"known_risks":["SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"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":82,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","The NCBI_EMAIL environment variable is listed as optional in metadata, while the documentation correctly states that NCBI policy requires an email for Entrez. The example hardcodes a placeholder instead of reading from the environment, which may cause failed Entrez calls.","The skill does not include an explicit license/attribution notice beyond the repository license declaration. If the content is derived from Biopython documentation, upstream copyright and license notices should be preserved.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"safety_gate":{"tier":"experimental","label":"Experimental","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Test manually in an isolated workspace and compare against safer alternatives."},"quality":{"score":92,"label":"Excellent"},"supply":{"track":"Design and creative production","scenario":"Multimodal media","maintenance":"6d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","The NCBI_EMAIL environment variable is listed as optional in metadata, while the documentation correctly states that NCBI policy requires an email for Entrez. The example hardcodes a placeholder instead of reading from the environment, which may cause failed Entrez calls.","The skill does not include an explicit license/attribution notice beyond the repository license declaration. If the content is derived from Biopython documentation, upstream copyright and license notices should be preserved."],"agent_contract":{"task_input":"Use biopython in an agent workflow","recommended_action":"Test manually in an isolated workspace and compare against safer alternatives.","install_policy":"review","minimum_review_before_use":["Trust: 69/100 Manual review","Audit: 82/100 Needs review","Safety: 38/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"k-dense-ai-biopython (biopython)","install_command":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython","risk_summary":"Needs review; Experimental; 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-biopython","task":"Use biopython in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/k-dense-ai-biopython","api":"https://www.openagentskill.com/api/agent/skills/k-dense-ai-biopython","audit":"https://www.openagentskill.com/skills/k-dense-ai-biopython/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=k-dense-ai-biopython&task=Use%20biopython%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20biopython%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20biopython%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/k-dense-ai-biopython/install","manifest":"https://www.openagentskill.com/api/registry/manifest/k-dense-ai-biopython"}},"supply_profile":{"track":{"slug":"design","label":"Design and creative production","shortLabel":"Design","description":"Design assets, images, video, audio, multimodal media, presentation, and creative production skills."},"scenario":{"label":"Multimodal media","description":"I need my agent to process images, video, or audio and extract useful information.","useCases":[{"slug":"workflow-automation","title":"Workflow automation"},{"slug":"document-processing","title":"Document processing"},{"slug":"local-desktop","title":"Local desktop"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":38487,"starsLabel":"38K","forks":3607,"license":"Biopython License Agreement","qualityScore":92,"trustScore":69,"auditScore":82},"maintenance":{"status":"fresh","label":"6d since push","daysSincePush":6,"lastPushedAt":"2026-08-30T13:19:27+00:00"},"risk":{"level":"needs_review","label":"Needs review","requiresReview":true,"notes":["Dependency or permission surface needs review","Permission surface may require sandboxing","SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","The NCBI_EMAIL environment variable is listed as optional in metadata, while the documentation correctly states that NCBI policy requires an email for Entrez. The example hardcodes a placeholder instead of reading from the environment, which may cause failed Entrez calls.","The skill does not include an explicit license/attribution notice beyond the repository license declaration. If the content is derived from Biopython documentation, upstream copyright and license notices should be preserved."]},"coverageTags":["Design","Multimodal media","design-creative","agent-skill"]},"audit":{"audit_score":82,"risk_level":"needs_review","risk_label":"Needs review","quality_score":92,"trust_score":69,"maintenance_score":100,"security_score":69,"install_score":92,"warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","SKILL.md references `references/sequence_io.md` for sequence handling, but the submitted skill directory only includes `advanced.md`, `alignment.md`, `blast.md`, `databases.md`, and `phylogenetics.md`. The referenced file appears to be missing.","The NCBI_EMAIL environment variable is listed as optional in metadata, while the documentation correctly states that NCBI policy requires an email for Entrez. The example hardcodes a placeholder instead of reading from the environment, which may cause failed Entrez calls.","The skill does not include an explicit license/attribution notice beyond the repository license declaration. If the content is derived from Biopython documentation, upstream copyright and license notices should be preserved.","Permission surface needs review: secrets or environment access, shell or command execution","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"quality_signals":{"model":"v2","star_score":32.1,"usage_score":0,"review_score":4.95,"metadata_score":3,"freshness_score":15},"platforms":["Claude Code"],"use_cases":[{"slug":"workflow-automation","title":"Workflow automation","url":"https://www.openagentskill.com/use-cases/workflow-automation"},{"slug":"document-processing","title":"Document processing","url":"https://www.openagentskill.com/use-cases/document-processing"},{"slug":"local-desktop","title":"Local desktop","url":"https://www.openagentskill.com/use-cases/local-desktop"},{"slug":"browser-automation","title":"Browser automation","url":"https://www.openagentskill.com/use-cases/browser-automation"}],"stacks":[{"slug":"content-growth-agent","title":"Content growth agent","url":"https://www.openagentskill.com/collections/content-growth-agent"},{"slug":"browser-qa-agent","title":"Browser QA agent","url":"https://www.openagentskill.com/collections/browser-qa-agent"},{"slug":"frontend-product-ui","title":"Frontend and UI","url":"https://www.openagentskill.com/collections/frontend-product-ui"}],"install":"npx skills add K-Dense-AI/scientific-agent-skills --skill biopython","install_targets":[{"id":"openagentskill-cli","label":"CLI","title":"OpenAgentSkill CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add k-dense-ai-biopython","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 \"biopython\" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython. 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: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices. 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-biopython\",\"task\":\"Install biopython\",\"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 \"biopython\" as a Claude Code skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython. 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: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices. 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-biopython\",\"task\":\"Install biopython\",\"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 \"biopython\" from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython 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: Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices. 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-biopython\",\"task\":\"Install biopython\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this when installing as Cursor project rules or reusable agent instructions.","copyLabel":"Copy prompt"}],"repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython","github_repo":"K-Dense-AI/scientific-agent-skills","version":"1.0.0","license":"Biopython License Agreement","urls":{"web":"https://www.openagentskill.com/skills/k-dense-ai-biopython","repository":"https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython","api":"/api/agent/skills/k-dense-ai-biopython","install_api":"/api/skills/k-dense-ai-biopython/install"},"meta":{"created_at":"2026-08-30T13:23:11.06432+00:00","updated_at":"2026-09-01T11:59:28.941454+00:00","agent_friendly":true}}