169 件 ・ 関連度順
概要と使いどころ
Reactome is a free, open-source, curated and peer-reviewed pathway database. Their goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge.
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Graph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases.
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Guide to KEGG pathway enrichment for DEG results. Covers ORA vs GSEA, mandatory directionality splitting, KEGG organism codes, API failure handling with offline fallbacks, cross-condition comparisons, and answer-first reporting. Consult when running enrichment with clusterProfiler or gseapy.
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Query Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs. Content + Analysis services. Python wrapper: reactome2py. For KEGG use kegg-database; for PPIs use string-database-ppi.
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Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization. Use when taking DE results to pathway enrichment.
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Discover and invoke 1,676 deduplicated biomedical AI agent skills from the Awesome Bio Agent Skills repository (20 source repos, 15 categories). Use this skill as a router whenever a user needs a bioinformatics/biomedical task (genomics, transcriptomics, single-cell, proteomics, protein design, clinical, epigenomics, multi-omics, pathway, metagenomics, database queries, visualization, workflows): search the index, locate the best-matching skill, fetch its SKILL.md, and follow it.
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GitHub 解封 — 账号封禁/限制/恢复的领域操作系统。覆盖：(a) GitHub 官方政策体系 (TOS / 可接受使用政策 / Trust & Safety 执行模式 / 公开申诉路径 / 受制裁地区解读)；(b) 封号原因诊断学 (spam / abuse / 制裁误标 / 2FA 丢失 / ToS 违规 / 账号劫持误判 / ban evasion 等子类型 + 症状→原因映射 + 自我分诊压测)；(c) 申诉实操 craft (写一封能让 T&S 快速判误伤的英文申诉信 + 升级阶梯 + 法务介入边界 + Don'ts)；(d) 制裁与合规硬边界 (OFAC SDN 名单 / 哪些国家或地区真不可达 / VPN 误判路径 / 中国大陆不是美国制裁地区的反复重申)；(e) 中国大陆开发者特别处境 (sanctioned region 误标 + SMS 验证不支持 +86/+852 + Gitee/GitLab/Codeberg/JihuLab 备用迁移 + 私有自托管 Gitea/Forgejo)；(f) 真实案例库 (~30+ 公开案例分类拆解：误伤 / 真违规 / 制裁误标三类各自赔率与申诉成功路径)。伦理锚绝不软化：不教 ban evasion / 不教撒谎式申诉 / 真违规承认改进 / 丢 2FA 无恢复因子则诚实告知 / 中国制裁误标靠申诉不靠换 VPN / 申诉 6 个月窗口必算清 / 约 3% (业内估) 真违规恢复 vs 约 79% (业内估) 误伤申诉成功率分层标。 (GitHub Account Reinstatement — the domain operating system for GitHub (and analogous platform) account suspension, restriction, appeal, and recovery. Covers: (a) GitHub official policy architecture (TOS / Acceptable Use Policies / Trust & Safety enforcement patterns / public appeals pathways / sanctioned-region interpretation); (b) suspension-cause diagnostics (spam / abuse / sanctions mis-flag / 2FA loss / ToS violation / account hijack false-positive / ban evasion taxonomy + symptom→cause mapping + self-triage pressure test); (c) appeal craft (writing an English appeal letter that gets T&S to fast-track a false-positive ruling + escalation ladder + legal-engagement boundary + Don'ts); (d) sanctions and compliance hard boundaries (OFAC SDN list / which countries/regions are truly unreachable / VPN false-positive paths / China is NOT a US-sanctioned region — repeated emphasis); (e) mainland China developer special circumstances (sanctioned-region mis-flag + SMS verification does not support +86/+852 + Gitee/GitLab/Codeberg/JihuLab fallback migration + self-hosted Gitea/Forgejo); (f) real-case library (~30+ public cases with categorized analysis: false-positive / genuine violation / sanctions mis-flag, each with win-rate and appeal success path). Ethical anchors absolutely not softened: do NOT teach ban evasion (creating new accounts turns a temp ban into a permanent one — the single biggest mistake); do NOT teach social engineering or lying in appeals (misuse + actually confirms violation); genuine violations: admit + improve beats denial; lost 2FA + no recovery factor → do not pretend recovery is possible; China sanctioned-region mis-flag → fix via appeal, not repeated VPN switching; appeal form 6-month window must be counted carefully; historical 约 3% (业内估) genuine-violation recovery vs 约 79% (业内估) false-positive appeal success rate stratification must be honestly labeled. Anti-samples (explicitly describe harm, never endorse): developer permabanned for ban evasion / open-source team org-banned for personal attacks in public issues / cases where repeated VPN switching escalated risk-control severity.) Master OS — automated mastery of GitHub Account Reinstatement — the domain operating system for GitHub (and analogous platform) account suspension, restriction, appeal, and recovery. Covers: (a) GitHub official policy architecture (TOS / Acceptable Use Policies / Trust & Safety enforcement patterns / public appeals pathways / sanctioned-region interpretation); (b) suspension-cause diagnostics (spam / abuse / sanctions mis-flag / 2FA loss / ToS violation / account hijack false-positive / ban evasion taxonomy + symptom→cause mapping + self-triage pressure test); (c) appeal craft (writing an English appeal letter that gets T&S to fast-track a false-positive ruling + escalation ladder + legal-engagement boundary + Don'ts); (d) sanctions and compliance hard boundaries (OFAC SDN list / which countries/regions are truly unreachable / VPN false-positive paths / China is NOT a US-sanctioned region — repeated emphasis); (e) mainland China developer special circumstances (sanctioned-region mis-flag + SMS verification does not support +86/+852 + Gitee/GitLab/Codeberg/JihuLab fallback migration + self-hosted Gitea/Forgejo); (f) real-case library (~30+ public cases with categorized analysis: fa
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Present pathway options and orchestrate place-based curriculum design from a local place, curriculum requirement, or community issue. Use when place should become a primary text for learning.
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Present project-design pathway options and orchestrate regenerative projects using backwards design, PBL, SEEDS, compassionate systems action, or civic/service pathways.
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Expert-level biochemistry from a biology perspective covering metabolic pathways, enzyme kinetics, bioenergetics, signal transduction, and the biochemical basis of cellular processes.
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METAINFORMANT rules for directory src/metainformant/multiomics/pathways. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.
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METAINFORMANT rules for directory src/metainformant/ontology/pathway_enrichment. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.
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METAINFORMANT rules for directory src/metainformant/metabolomics/pathways. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.
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Strategic clinical trial design feasibility assessment. Analyzes 6 dimensions (endpoint, population, comparator, effect size, duration, regulatory pathway) using precedent trials and FDA guidance. Produces enrollment projections, endpoint recommendations, and approval-pathway analysis. Use for trial-protocol design, power/sample-size estimation, comparator selection, and FDA submission strategy. Driven by precedent-based reasoning rather than first-principles math.
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Orchestrates the untargeted LC-MS metabolomics pipeline end-to-end (xcms 4.x feature extraction, QC/drift/normalization, confidence-stratified annotation, permutation-validated statistics, background-aware pathway mapping), naming what each stage decides and where it silently fails. Use when running a full LC-MS metabolomics study from raw mzML to enriched pathways and needing the honest handoffs between stages. Each stage defers to its component skill for parameters and traps; for stable-isotope flux (a separate branch, not this untargeted flow) see metabolomics/isotope-tracing.
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Lipid analysis and lipid-disease associations using LIPID MAPS classification, HMDB metabolite data, KEGG/Reactome lipid pathways (sphingolipid, eicosanoid, steroid, fatty acid), and PubChem chemical info. Use for lipid identification, lipid metabolism pathway mapping, and lipid-associated disease analysis (cardiovascular, diabetes, NAFLD).
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Drug regulatory and approval research — FDA substance registry, ATC/EPC classification, EMA decisions, generic-drug status, FDA Orange Book exclusivity, NDA/BLA pathways. Use for jurisdiction-aware approval status (FDA vs EMA), generic vs brand availability, exclusivity expiry tracking, and regulatory pathway selection. Always specifies the market when reporting status.
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Designs and analyzes stable-isotope-resolved metabolomics (SIRM / isotope tracing / fluxomics) experiments that measure metabolic ACTIVITY via 13C/15N/2H tracers, distinct from steady-state pool profiling. Covers tracer choice, isotopologue vs isotopomer, mass-isotopomer distributions (MID), fractional enrichment, the mandatory natural-abundance + tracer-purity correction (IsoCor, AccuCor), and the metabolic/isotopic steady-state vs non-stationary (INST-MFA) distinction. Use when feeding a labeled tracer and interpreting labeling patterns, correcting raw isotopologue intensities, computing or plotting an MID, or deciding tracing vs abundance profiling. For absolute pool concentration and MRM mechanics see metabolomics/targeted-analysis; for constraint-based genome-scale flux (FBA, not empirical tracing) see systems-biology/flux-balance-analysis; for feature detection see metabolomics/xcms-preprocessing; for pathway enrichment that ignores the pool-vs-flux caveat see metabolomics/pathway-mapping.
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Decision-grade statistical analysis for metabolomics intensity tables. Covers transformation and scaling (Pareto vs unit-variance as a hidden hypothesis), unsupervised structure (PCA/HCA for QC), permutation-validated PLS-DA/OPLS-DA (R2 vs Q2, double CV, VIP as heuristic), univariate testing (Welch/Mann-Whitney/ANOVA/LMM with covariate adjustment), and dependence-aware multiple testing. Use when testing which metabolites differ, building or validating a discriminant model, choosing a scaling, or correcting many correlated tests. For sample-wise normalization/drift correction see metabolomics/normalization-qc; for ML classifiers and selection-inside-CV leakage see machine-learning/biomarker-discovery and machine-learning/model-validation; for pathway interpretation see metabolomics/pathway-mapping; for design/power/multiplicity regime see experimental-design/multiple-testing.
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Generates scientific diagram drafts using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.7 Flash for quality review. Refines when the review requests improvement, with at most two generations. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
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Provides a Python interface to bioinformatics services including UniProt, KEGG, ChEMBL, Reactome, QuickGO, and UniChem. Used for cross-database protein annotation, pathway retrieval, chemical identifier mapping, and integrated biological data workflows with BioServices.
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Generates or edits images with AI models through the OpenRouter Image API (Gemini, Seedream, Recraft, GPT-Image, Riverflow). Use for photos, illustrations, artwork, concept art, visual assets, logos, and image editing or compositing from reference images. For flowcharts, circuits, pathways, and other technical diagrams, use the scientific-schematics skill instead.
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Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart fitting, and flux-profile diagnostics. Use for 13C-MFA, carbon tracing, mass isotopomer distributions (MDVs/MIDs), positional isotopomers, parallel tracer experiments, and determining whether labeling data constrain a pathway flux. Distinguishes measured-label inference from COBRA flux balance analysis and flags experiments requiring nonstationary MFA.
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FDA regulatory consultant for medical device companies. Provides 510(k)/PMA/De Novo pathway guidance, QMSR (21 CFR 820, which incorporates ISO 13485:2016 by reference since 2026-02-02; formerly QSR) compliance, HIPAA assessments, and device cybersecurity. Use when user mentions FDA submission, 510(k), PMA, De Novo, QMSR, QSR, ISO 13485 for FDA, premarket, predicate device, substantial equivalence, HIPAA medical device, or FDA cybersecurity.
日本語の概要は準備中です。原文の説明を表示しています。