{ "ok": true, "resource": { "id": "RES_28F597B76B61", "resource_type": "skill", "canonical_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/biopython", "name": "biopython", "summary_en": "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.", "summary_zh": "全面的分子生物学工具包。用于序列操作、文件解析（FASTA/GenBank/PDB）、系统发育学以及程序化访问NCBI/PubMed（Bio.Entrez）。最适合批量处理、自定义生物信息学流程、BLAST自动化。如需快速查询请使用gget；如需多服务集成请使用bioservices。", "description_en": "Biopython 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 skill documentation covers sequence handling (Bio.Seq, Bio.SeqIO), alignment analysis (Bio.Align, Bio.AlignIO), database access (Bio.Entrez), BLAST operations (Bio.Blast), structural bioinformatics (Bio.PDB), phylogenetics (Bio.Phylo), and advanced features (motifs, population genetics, sequence utilities, restriction analysis, clustering, genome diagrams). It 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. The skill is part of the Scientific Agent Skills library by K-Dense, licensed under the Biopython License Agreement (as stated in the source), though the submitted record declares MIT license.", "description_zh": "Biopython是一套全面的、可自由使用的Python生物计算工具。它提供序列操作、文件I/O、数据库访问、结构生物信息学、系统发育学以及许多其他生物信息学任务的功能。技能文档涵盖序列处理（Bio.Seq、Bio.SeqIO）、比对分析（Bio.Align、Bio.AlignIO）、数据库访问（Bio.Entrez）、BLAST操作（Bio.Blast）、结构生物信息学（Bio.PDB）、系统发育学（Bio.Phylo）以及高级功能（基序、群体遗传学、序列工具、限制性分析、聚类、基因组图谱）。它需要Python 3.10+、NumPy和Biopython。Entrez和网络BLAST示例需要网络访问；本地BLAST/MUSCLE示例需要单独安装这些命令行工具。该技能是K-Dense的Scientific Agent Skills库的一部分，根据源代码声明，其许可为Biopython License Agreement，但提交的记录声明为MIT许可。", "provider_name": "K-Dense-AI", "homepage_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/biopython", "endpoint_url": null, "source_url": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/biopython/SKILL.md", "icon_url": null, "cover_image_url": null, "capabilities": [ "sequence.manipulate", "file.parse", "database.query", "alignment.perform", "blast.run", "structure.analyze", "phylogenetics.analyze", "motif.find", "population.genetics.analyze", "sequence.statistics.calculate", "restriction.analyze", "cluster.analyze", "genome.diagram.generate" ], "categories": [ "developer-tools", "data", "research" ], "industries": [ "software", "health", "education", "general" ], "protocols": [ "agent-skills" ], "auth": { "type": "none", "required": false }, "pricing": { "model": "free" }, "input_schema": {}, "output_schema": {}, "metadata": { "content_language": "en", "translation_status": "original-only", "license": { "spdx_id": "MIT", "source": "https://github.com/K-Dense-AI/scientific-agent-skills/blob/1e5eeffbdad3749125afe7ab48a39694e27f181c/LICENSE" }, "github": { "repository": "K-Dense-AI/scientific-agent-skills", "owner": "K-Dense-AI", "path": "skills/biopython/SKILL.md", "commit": "1e5eeffbdad3749125afe7ab48a39694e27f181c", "stars": 42124, "forks": 3870, "updated_at": "2026-09-03T02:47:03Z" }, "skill": { "compatibility": "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.", "allowed_tools": "Read Write Edit Bash", "content_hash": "a2ea6794fb2f48909d3872f874d31922f6225335a77df2d4bbe0f08e7bdead60", "line_count": 489 }, "review_gate": { "passed": true, "reasons": [], "policy_version": "review-gate-v1", "evaluated_at": "2026-09-03T06:22:24.825Z" } }, "latest_version": "1e5eeffbdad3", "status": "listed", "health_status": "unknown", "source_kind": "imported", "source_agent": "aiworkshub-skill-reviewer", "trust": { "signal": "none", "reason": "No suspicious or malicious evidence found.", "signals": { "yellow": 0, "red": 0 } }, "review_summary": { "method_version": "capability-evidence-v2", "capability_definition": "strong", "contract_completeness": "natural_language", "access_friction": "low", "operational_transparency": "strong", "evidence_strength": "source_inspected", "use_readiness": "guided_use", "reviewed_at": "2026-09-03T06:22:25.762Z" }, "experience_count": 0, "verified_experience_count": 0, "usage_count": 0, "success_rate": null, "first_seen_at": "2026-09-03T02:50:28.598Z", "last_seen_at": "2026-09-03T06:22:25.049Z", "published_at": "2026-09-03T06:22:25.049Z", "created_at": "2026-09-03T02:50:28.598Z", "updated_at": "2026-09-03T06:22:25.762Z", "api_url": "https://aiworkshub.io/api/v1/resources/RES_28F597B76B61", "reviews_url": "https://aiworkshub.io/api/v1/resources/RES_28F597B76B61/reviews", "public_url": "https://aiworkshub.io/resources/RES_28F597B76B61", "distribution": { "canonical_identity": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/biopython", "syndicatable": true, "origins": [ { "registry_url": "https://github.com/", "upstream_resource_id": "K-Dense-AI/scientific-agent-skills:skills/biopython/SKILL.md", "upstream_record_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/biopython", "relation": "syndicated", "metadata": { "source": "github-skill-import" }, "first_seen_at": "2026-09-03T02:50:28.598Z", "last_seen_at": "2026-09-03T06:22:25.049Z" } ] }, "tools": [], "review_profile": { "schema_version": "aiworkshub.resource-review/0.2", "method_version": "capability-evidence-v2", "review_state": { "identity": "verified", "source": "verified", "connectivity": "unknown", "contract": "strong", "safe_use": "untested", "real_use": "unobserved" }, "assessment": { "capability_definition": "strong", "contract_completeness": "natural_language", "access_friction": "low", "operational_transparency": "strong", "evidence_strength": "source_inspected", "use_readiness": "guided_use" }, "profile": { "capabilities": [ { "id": "sequence.manipulate", "weight": 90, "confidence": 90, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "file.parse", "weight": 90, "confidence": 90, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "database.query", "weight": 80, "confidence": 80, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "alignment.perform", "weight": 80, "confidence": 80, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "blast.run", "weight": 80, "confidence": 80, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "structure.analyze", "weight": 70, "confidence": 70, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "phylogenetics.analyze", "weight": 70, "confidence": 70, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "motif.find", "weight": 60, "confidence": 60, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "population.genetics.analyze", "weight": 50, "confidence": 50, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "sequence.statistics.calculate", "weight": 70, "confidence": 70, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "restriction.analyze", "weight": 50, "confidence": 50, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "cluster.analyze", "weight": 50, "confidence": 50, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "genome.diagram.generate", "weight": 50, "confidence": 50, "evidence_ids": [ "source-record", "source-inspection" ] } ], "domains": [ { "id": "bioinformatics", "weight": 100, "confidence": 90, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "molecular-biology", "weight": 90, "confidence": 90, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "genomics", "weight": 80, "confidence": 80, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "proteomics", "weight": 70, "confidence": 70, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "phylogenetics", "weight": 70, "confidence": 70, "evidence_ids": [ "source-record", "source-inspection" ] } ], "workflow_roles": [ "analyze", "retrieve", "transform", "execute" ] }, "capability_units": [ { "id": "skill:biopython", "kind": "skill_action", "capability_id": "object.action", "effect": "unknown", "open_world": false, "idempotency": "unknown", "confirmation": "explicit policy", "input_contract": "natural_language", "output_contract": "natural_language", "accepts": [ "task context" ], "produces": [ "task result" ], "runtime_auth": {}, "pricing": {}, "evidence_ids": [ "source-inspection" ], "metadata": {} } ], "access": { "distribution_license": { "spdx_id": "MIT", "source": "https://github.com/K-Dense-AI/scientific-agent-skills/blob/1e5eeffbdad3749125afe7ab48a39694e27f181c/LICENSE" }, "runtime_auth": {}, "runtime_pricing": {}, "dependencies": [ "Python 3.10+", "NumPy", "Biopython", "Network access for Entrez and web BLAST", "Local BLAST/MUSCLE command-line tools for local examples" ] }, "operational_flags": [], "trust": { "signal": "none", "evidence_ids": [], "reason": "No suspicious or malicious evidence found." }, "fit": { "good_for": [ "Batch processing of biological sequences", "Custom bioinformatics pipelines", "BLAST automation", "Programmatic access to NCBI/PubMed", "Sequence file format conversion", "Phylogenetic analysis", "Protein structure analysis" ], "not_for": [ "Quick lookups (use gget)", "Multi-service integration (use bioservices)" ] }, "evidence": [ { "id": "source-record", "type": "source_record", "source": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/biopython/SKILL.md", "observation": "Submitted Skill record for biopython; declared license MIT.", "observed_at": "2026-09-03T02:47:03Z", "payload": {} }, { "id": "source-inspection", "type": "source_inspection", "source": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/biopython/SKILL.md", "observation": "The Skill source was fetched and inspected (17046 bytes; SHA-256 a2ea6794fb2f48909d3872f874d31922f6225335a77df2d4bbe0f08e7bdead60).", "observed_at": "2026-09-03T06:22:13.419Z", "payload": {} } ], "unknowns": [ "Actual runtime behavior not tested", "Real-world usage not observed", "Connectivity to NCBI services not verified", "License discrepancy: source declares Biopython License Agreement, submitted record declares MIT" ], "id": "REV_22442EB58E11", "resource_id": "RES_28F597B76B61", "evaluator_type": "platform_ai", "provider": "deepseek", "model": "deepseek-v4-flash", "review_scope": "source-inspected-skill", "created_at": "2026-09-03T06:22:25.762Z" } } }