For backend engineers

Safety guardrails for destructive commands. (gstack)

Restore working context saved earlier by /context-save. (gstack)

Save working context. (gstack)

Restrict file edits to a specific directory for the session. (gstack)

Upgrade gstack to the latest version.

Clear the freeze boundary set by /freeze, allowing edits to all directories again. (gstack)

Create and edit Obsidian Bases (.base files) with views, filters, formulas, and summaries. Use when working with .base files, creating database-like views of notes, or when the user mentions Bases, table views, card views, filters, or formulas in Obsidian.

Download an entire website as local files — markdown, screenshots, or multiple formats per page. Use this skill when the user wants to save a site locally, download documentation for offline use, bulk-save pages as files, or says "download the site", "save as local files", "offline copy", "download all the docs", or "save for reference". Combines site mapping and scraping into organized local directories.

Discover and list all URLs on a website, with optional search filtering. Use this skill when the user wants to find a specific page on a large site, list all URLs, see the site structure, find where something is on a domain, or says "map the site", "find the URL for", "what pages are on", or "list all pages". Essential when the user knows which site but not which exact page.

Web search with full page content extraction. Use this skill whenever the user asks to search the web, find articles, research a topic, look something up, find recent news, discover sources, or says "search for", "find me", "look up", "what are people saying about", or "find articles about". Returns real search results with optional full-page markdown — not just snippets. Provides capabilities beyond Claude's built-in WebSearch.

Use this skill whenever the user wants Claude to directly interact with their Obsidian vault — reading a note or daily note, writing or appending content, searching vault contents, counting or listing notes, managing tasks, moving or renaming files, finding orphaned notes or broken links. Without this skill, Claude has no way to access vault data or execute vault operations. Treat any request that implies "go into my vault and do X" as a trigger — the user is asking Claude to act, not to explain. Also trigger for vault automation, CLI scripting, or cron-based workflows involving Obsidian. Skip for pure conceptual questions: how Obsidian's GUI works, navigating settings menus, theme or plugin installation via the UI, or general Dataview query syntax — anything where the user needs an explanation rather than Claude performing a vault operation.

Use this skill whenever the user wants Claude to directly interact with their Obsidian vault — reading a note or daily note, writing or appending content, searching vault contents, counting or listing notes, managing tasks, moving or renaming files, finding orphaned notes or broken links. Without this skill, Claude has no way to access vault data or execute vault operations. Treat any request that implies "go into my vault and do X" as a trigger — the user is asking Claude to act, not to explain. Also trigger for vault automation, CLI scripting, or cron-based workflows involving Obsidian, managing sync history, querying Bases, restoring file versions via history, managing bookmarks, or running JavaScript against the Obsidian API. Skip for pure conceptual questions: how Obsidian's GUI works, navigating settings menus, theme or plugin installation via the UI, iCloud/third-party sync conflicts, general Dataview query syntax, keyboard shortcuts, or parsing vault files with external scripts — anything where the user needs an explanation rather than Claude performing a vault operation.

Reviews GitHub pull requests for the Medusa repository. Checks PR template compliance, contribution guidelines, code conventions, and community contribution limits. Posts a review comment and applies initial-approval or requires-more label. Use when a PR is opened or updated.

Writes and updates Medusa documentation MDX files for the book, resources, ui, user-guide, and cloud projects. Use when making documentation changes based on code diffs, adding new pages, updating existing content, or updating component examples. ALWAYS load this skill before modifying any MDX file in www/apps/.

Update CHANGELOG.md with merged PRs since the last changelog update, categorized by type

How to write and maintain `.claude/skills/*/SKILL.md` files: source-of-truth-first process, verification steps, and conventions.

Frontend standards for atopile extension webviews: architecture, contracts, design system, and testing workflow.

How the Faebryk parameter solver works (Sets/Literals, Parameters, Expressions), the core invariants enforced during mutation, and practical workflows for debugging and extending the solver. Use when implementing or modifying constraint solving, parameter bounds, or debugging expression simplification.

Generate short live progress summaries for the atopile agent from recent tool events, preambles, checklist changes, and build state. Use for ephemeral UI activity text only, never for transcript replies or autonomous reasoning.

How Faebryk's TypeGraph works (GraphView + Zig edges), how to traverse/resolve references, and how FabLL types/traits map onto edge types. Use when working with TypeGraph traversal, edge types, or building type-aware queries.

How the Zig↔Python binding layer works (pyzig), including build-on-import, wrapper generation patterns, ownership rules, and where to add new exported APIs. Use when adding Zig-Python bindings, modifying native extensions, or debugging C-API interactions.

How FabLL (faebryk.core.node) maps Python node/trait declarations into the TypeGraph + instance graph, including field/trait invariants and instantiation patterns. Use when defining new components or traits, working with the Node API, or understanding type registration.

How the Zig S-expression engine and typed KiCad models work, how they are exposed to Python (pyzig_sexp), and the invariants around parsing, formatting, and freeing. Use when working with KiCad file parsing, S-expression generation, or layout sync.

LLM-focused workflow for working in this repo: compile Zig, run the orchestrated test runner, consume test-report.json/html artifacts, and discover/debug ConfigFlags.

Have a focused discussion about a topic and reach a conclusion

Audit changed code for security sharp edges — dangerous defaults, type confusion, and silent failures

当用户执行系统级命令（sysctl、iptables、systemctl、Docker 配置、数据库 DDL）或进行服务器运维操作时触发。提供运维安全规范。

当代码涉及支付回调、webhook 通知、notify_url、微信支付/支付宝回调处理时触发。防止回调伪造、重放攻击、金额篡改等支付安全问题。

Python 开发规范，包含 PEP 8 风格、类型注解、异常处理、测试规范等

当代码涉及循环内查询、批量 ID 查询、IN 子句、BFS/递归遍历、嵌套 service 调用时触发。防止 N+1 查询、IN 子句过长、递归内存炸裂等性能陷阱。

当用户操作 .sh、Dockerfile、Makefile、.yml、.yaml 文件，或在 Markdown 中编写 bash 代码块时触发。提供 Bash 编写规范。

当 API/任务可能执行超过 10 秒（批量数据处理、远程 API 批量调用、全表扫描、跨租户聚合）时触发。防止同步接口被网关 30s 超时切断、用户重复点击触发并发、状态缓存内存泄漏等问题。提供异步任务状态机标准模板。

Java 开发规范，包含命名约定、异常处理、Spring Boot 最佳实践等

Rust 开发规范（聚焦 Axum + Tokio 后端栈），覆盖工具链、错误处理、异步陷阱、模块组织、依赖管理与测试规范

当设计或修改 REST API 响应结构、处理 API 返回值，或生成 Excel/CSV/PDF/对账文件等下游产物时触发。防止 API 设计缺陷导致的字段错位、类型歧义，以及生成产物时关键字段缺失但静默成功的问题。

当重构涉及字段映射（dataIndex、枚举映射、类型转换）时触发。防止字段名推测错误，确保字段映射的正确性。

Go 开发规范，包含命名约定、错误处理、并发编程、测试规范等

当使用 MinIO/OSS/S3 等对象存储、设计文件上传下载功能时触发。提供存储 URL 策略选择规范，防止 URL 过期、访问失败等问题。

当代码出现 LocalDate.now() / LocalDateTime.now() / Instant.now() / new Date() / Date.now() / time.Now() 等"当前时间"调用，或涉及周/月/日起点、跨时区比较、数据库时间字段时触发。防止生产环境时区漂移导致的统计错乱。

Use when an agent must inspect, draft, validate, edit, publish, unpublish, delete, or configure mx-space content through packages/cli or the mxs binary.

Use when verifying and porting an mx-core controller (Post/Note/Page/Comment/Category/etc.) after the MongoDB→PostgreSQL cutover, or when its data shape no longer matches what api-client and admin-vue3 expect. Triggers on "校验 controller"、"check controller"、"迁移 controller"、"修复迁移后的接口"、"data missing after PG migration"、"related/category 字段丢了" and similar.

Use when releasing mx-core server (apps/core), @mx-space/api-client, or @mx-space/cli (mxs) — version bump, changelog, git tag, Docker build, GitHub Release, and Dokploy redeploy. Triggers on "发版", "release a new version", "cut a release", "bump version", "publish api-client", "publish cli", "release mxs".

Create E2E test file for a specified module. Use when adding end-to-end tests for controllers or unit tests for services and repositories.

Author and review Drizzle SQL migrations safely for rolling deploys. Triggers when editing apps/core/src/database/schema/*.ts or apps/core/src/database/migrations/*.sql, when the user runs drizzle-kit generate, when "lint-migrations" reports a violation, or on prompts like "迁移", "改 schema", "alter table", "add a column", "drop column", "migration safety". Enforces the expand-contract pattern because mx-core ships rolling deploys (Dokploy, 2 replicas) where new and old pods coexist for tens of seconds during cutover.

Create a new NestJS module with repository, service, controller, schema, and Drizzle table definition. Use when adding new feature modules, API endpoints, or business domains.

Run tests. Supports running all tests, single file, or pattern-matched tests.

Review code for MX Space project conventions. Checks NestJS patterns, Drizzle ORM repositories, Zod schemas, API design, etc.

Crawl repository PRs, issues, and review comments to distill institutional knowledge into a shared knowledge base. Run periodically by "context agents" to maintain agent_artefacts/repo_context/REPO_CONTEXT.md. Trigger only on specific request.

Prepare a new release of inspect_evals by creating a release branch, collecting changelog fragments, and opening a PR. Use when user asks to cut/prepare/create a new release or version bump.

Fix code quality issues identified in a code quality review stored in agent_artefacts/code_quality/<topic>/. Systematically addresses issues found by the code-quality-review-all skill for ANY code quality topic, with validation and testing at each step. Use when user asks to fix issues from a code quality review, or asks to fix issues from agent_artefacts/code_quality/<topic>.

Deploy the BYOA wake-receiver Vercel Function from `deployment/vercel/`. Reads `.env.byoa`, pushes the operator's required env to the Vercel project, deploys via `npx vercel`, health-checks the URL, logs the operator in, and registers the resulting alias as the ship's `source_url` via `ship_byoa_configure`. Picks up from `/byoa-link` (which claims the ship and writes `.env.byoa`). Usage `/byoa-deploy-vercel [env]` (env defaults to `prod`; `live` is an accepted synonym for `prod`).

Onboard a Gradient Bang operator to run a Bring-Your-Own-Agent (BYOA) — logs in with email/password, claims a corp ship as BYOA, generates a per-ship wake secret, and writes `.env.byoa` for the `uv run byoa` CLI. Usage `/byoa-link [env]` (env defaults to `prod`; `live` is an accepted synonym for `prod`).

Generate Gradient News & Observer assets (banners, front pages, prompt experiments) by dispatching to the right newspaper script. Usage `/newspaper <asset-type> [args]` where asset-type is `banner`, `front-page`, or `prompt-experiment`.

Generate a Gradient News & Observer newspaper front page for a time window. Pulls game events into a structured digest, writes ten illustrated story ledes (7 straight news + 2 gossip + 1 market box) into a markdown file, then renders a 2160x3840 newspaper front-page PNG. Usage `/news-front-page [duration]` (default `24h`; e.g. `1h`, `6h`, `7d`).

Create a new game character with optional custom ship, credits, onboarding skip, and bulk contract completion. Usage `/character-create [env] <name> <email> <password> [credits <N>] [ship <type>] [skip-onboarding] [complete-contracts]`.

Toggle the server-side login killswitch on a Supabase environment. Usage `/maintenance <env> <on|off>` (e.g. `/maintenance prod on`). Sets or unsets the `MAINTENANCE_MODE` secret on the login edge function, which short-circuits new logins with HTTP 503 when enabled. Existing sessions keep working.

Calculate volumes of geometric shapes for engineering design and mathematical analysis.

Query EBI GWAS Catalog for GWAS statistical associations (p-value, effect size, risk allele) between a variant and traits/diseases.

Orphan Drug & Rare Disease Analysis - Analyze orphan drugs: Monarch disease phenotypes, OpenTargets targets, FDA drug data, and clinical studies. Use this skill for orphan drug development tasks involving get joint associated diseases by HPO ID list get associated targets by disease efoId get clinical studies info by drug name pubmed search. Combines 4 tools from 4 SCP server(s).

BioSample & Genome Cross-Reference - Cross-reference biosample and genome data: NCBI biosample, genome report, sequence reports, and taxonomy. Use this skill for genomics tasks involving get biosample report get genome dataset report by accession get genome sequence reports get taxonomy. Combines 4 tools from 1 SCP server(s).

Systems Pharmacology Analysis - Systems pharmacology: drug targets, protein interactions, pathway enrichment, and gene expression. Use this skill for systems pharmacology tasks involving get target by name get string network interaction get functional enrichment get gene expression across cancers. Combines 4 tools from 3 SCP server(s).

Geometry & Trigonometry Suite - Solve geometry problems: calculate area, height from sine, angle in degrees, and increase factor. Use this skill for mathematics tasks involving calculate area calculate height from length and sine calculate phi deg calculate increase factor. Combines 4 tools from 1 SCP server(s).

Generate new peptide molecules sampling from the input peptide sequence.

Protein Interaction Network Analysis - Build protein interaction network: map identifiers with STRING, get PPI network, compute enrichment, and link to KEGG pathways. Use this skill for systems biology tasks involving mapping identifiers get string network interaction get ppi enrichment kegg link. Combines 4 tools from 2 SCP server(s).

Compute the Tanimoto similarities between a target molecule and a list of candidate molecules using Morgan fingerprints.

Nuclear Physics Calculations - Nuclear physics: energy conversion MeV to J, calculate total power, photon rate, and error analysis. Use this skill for nuclear physics tasks involving convert energy MeV to J calculate total power calculate incident photon rate calculate absolute error. Combines 4 tools from 3 SCP server(s).

Given an rsID, query multiple databases (dbSNP, FAVOR, GWAS Catalog, ClinVar, gnomAD, PharmGKB, ClinGen) for comprehensive annotation. Use when user asks a general question about a variant without specifying which aspect.

Statistical Error Analysis - Analyze measurement errors: absolute error, scientific notation, max value, mean square, and formatting. Use this skill for statistics tasks involving calculate absolute error convert to scientific notation calculate max value calculate mean square format scientific notation. Combines 5 tools from 1 SCP server(s).

Generate new molecules de novo.

Search PubMed database for scientific articles and publications to retrieve biomedical literature.

Compute the drug-likeness metrics (QED score and Number of violations of Lipinski's Rule of Five) of the input candidate molecules (SMILES format).

Calculate disease reversal scores for the provided molecules relative to a specific disease.

Cross-Species Comparative Genomics - Compare genomes across species: Ensembl compara, alignment, gene trees, and NCBI taxonomy. Use this skill for comparative genomics tasks involving get info compara species sets get alignment region get genetree member symbol get taxonomy. Combines 4 tools from 2 SCP server(s).

Pandemic Preparedness Analysis - Pandemic analysis: virus genome, taxonomy, drug candidates, and literature intelligence. Use this skill for public health tasks involving get virus dataset report get virus by taxon genome get mechanism of action by drug name tavily search search literature. Combines 5 tools from 4 SCP server(s).

Calculate peptide sequence properties including molecular weight, isoelectric point, extinction coefficient, and chemical formula.

Search biomedical literature and web content using Tavily search engine for research and clinical information.

Given a gene symbol (e.g. TPMT), query 3 public databases (ClinGen CAR, PharmGKB, Monarch) to obtain gene registry info, FDA drug labels, clinical annotations, and gene-phenotype associations. Save all results into a JSON file.

Search for similar molecules using Tanimoto similarity with Morgan fingerprints to identify structurally related compounds.

Ring System Analysis - Analyze ring systems: count aliphatic carbocycles, analyze aromaticity, compute topology, and structure complexity. Use this skill for organic chemistry tasks involving GetAliphaticCarbocyclesNum AromaticityAnalyzer calculate mol topology calculate mol structure complexity. Combines 4 tools from 3 SCP server(s).

Structural Homology & Evolution Analysis - Analyze protein evolution: get gene tree from Ensembl, find homologs, compare sequences, and predict structure. Use this skill for evolutionary biology tasks involving get homology symbol get genetree member symbol calculate protein sequence properties pred protein structure esmfold. Combines 4 tools from 3 SCP server(s).

Predict protein-ligand binding affinity using Boltz-2 model to assess molecular interactions and binding probability for drug discovery.

Search the protein information from the input gene name and downloads the optimal PDB or AlphaFold structures.

Drug Metabolism Study - Study drug metabolism: FDA metabolism data, ChEMBL metabolism records, PubChem compound data, and clinical pharmacology. Use this skill for drug metabolism tasks involving get metabolism by id get pharmacokinetics by drug name get compound by name get clinical pharmacology by drug name. Combines 4 tools from 3 SCP server(s).

UCSC Genome Browser Exploration - Explore genome via UCSC: list genomes, list tracks, get sequence, get track data, and cytoband info. Use this skill for genomics tasks involving list genomes list tracks get sequence get track data get cytoband. Combines 5 tools from 1 SCP server(s).

Electromagnetic Field Analysis - Analyze EM fields: vacuum permittivity, total charge, radiation pressure, and photon calculations. Use this skill for electromagnetics tasks involving calculate vacuum permittivity calculate total charge calculate radiation pressure calculate total power. Combines 4 tools from 2 SCP server(s).

Alanine Scanning Mutagenesis Pipeline - Alanine scanning: design scan, compute properties for each mutant, predict interactions, and compare. Use this skill for protein biochemistry tasks involving AlanineScanningDesigner ComputeProtPara PredictDrugTargetInteraction calculate protein sequence properties. Combines 4 tools from 3 SCP server(s).

Calculate comprehensive protein sequence properties including isoelectric point, molecular weight, hydrophobicity, and physicochemical parameters.

Multi-Species Gene Analysis - Analyze gene across species: Ensembl homologs, NCBI orthologs, cross-species STRING similarity, and taxonomy. Use this skill for comparative genomics tasks involving get homology symbol get gene orthologs get best similarity hits between species get taxonomy. Combines 4 tools from 3 SCP server(s).

Combinatorial Chemistry Library Design - Design combinatorial library: validate core SMILES, generate variants, compute properties, and predict ADMET for library. Use this skill for combinatorial chemistry tasks involving is valid smiles calculate mol basic info calculate mol drug chemistry pred molecule admet. Combines 4 tools from 2 SCP server(s).

Comprehensive protein analysis combining InterProScan domain identification with BLAST similarity search to provide complete functional and evolutionary annotation.

Gene-Disease Association Analysis - Analyze gene-disease associations: NCBI gene metadata, OpenTargets disease associations, TCGA expression, and Monarch phenotypes. Use this skill for medical genetics tasks involving get gene metadata by gene name get associated targets by disease efoId get gene expression across cancers get joint associated diseases by HPO ID list. Combines 4 tools from 4 SCP server(s).

Protein Classification Analysis - Classify protein: ChEMBL protein classification, UniProt entry, InterPro domains, and Ensembl biotypes. Use this skill for protein science tasks involving search protein classification get uniprotkb entry by accession query interpro get info biotypes. Combines 4 tools from 4 SCP server(s).

Genetic Counseling Variant Report - Generate variant report for genetic counseling: VEP, ClinVar, gene phenotype, and literature evidence. Use this skill for clinical genetics tasks involving get vep hgvs clinvar search get phenotype gene pubmed search. Combines 4 tools from 2 SCP server(s).

Functional Group Profiling - Profile functional groups: radical assignment, H-bond analysis, aromaticity, and abbreviation condensation. Use this skill for organic chemistry tasks involving AssignRadicals GetHBANum AromaticityAnalyzer CondenseAbbreviationSubstanceGroups. Combines 4 tools from 2 SCP server(s).

Drug Target Identification Pipeline - Identify drug targets for a disease by querying OpenTargets for associated targets, then retrieve detailed target info from ChEMBL and protein data from UniProt. Use this skill for drug discovery tasks involving get associated targets by disease efoId get target by name get general info by protein or gene name. Combines 3 tools from 3 SCP server(s).

Comparative Drug Analysis - Compare drugs: structure analysis, PubChem data, FDA safety, and ChEMBL bioactivity. Use this skill for comparative pharmacology tasks involving ChemicalStructureAnalyzer get compound by name get adverse reactions by drug name search activity. Combines 4 tools from 4 SCP server(s).

Experimental Data Processing - Process experimental data: absolute error, mean square, max value, scientific notation formatting. Use this skill for experimental physics tasks involving calculate absolute error calculate mean square calculate max value format scientific notation convert to scientific notation. Combines 5 tools from 1 SCP server(s).

Retrieve gene information from NCBI Gene database by gene IDs to obtain genomic details, function, and expression data.

Chemical Structure Comparison - Compare chemical structures: get SMILES, analyze structures, compute similarity, and check PubChem records. Use this skill for cheminformatics tasks involving NameToSMILES ChemicalStructureAnalyzer calculate smiles similarity get compound by name. Combines 4 tools from 4 SCP server(s).

Gene Therapy Target Analysis - Analyze gene therapy target: gene info, variant pathogenicity, protein structure, and clinical evidence. Use this skill for gene therapy tasks involving get gene metadata by gene name get vep hgvs Protein structure prediction ESMFold clinvar search. Combines 4 tools from 4 SCP server(s).

Genome Annotation Pipeline - Annotate a genome: NCBI annotation report, Ensembl gene lookup, UCSC tracks, and KEGG pathway links. Use this skill for genomics tasks involving get genome annotation report get lookup symbol list tracks kegg link. Combines 4 tools from 4 SCP server(s).

Retrieve SMILES strings from PubChem using compound names.

Protein-Drug Interaction Profiling - Profile protein-drug interactions: protein properties, drug structure, binding affinity prediction, and interaction data. Use this skill for molecular pharmacology tasks involving calculate protein sequence properties ChemicalStructureAnalyzer boltz binding affinity PredictDrugTargetInteraction. Combines 4 tools from 4 SCP server(s).

Charge Carrier Mobility Analysis - Analyze carrier mobility: calculate new mobility, compute vacuum permittivity, and error analysis. Use this skill for semiconductor physics tasks involving calculate new mobility calculate vacuum permittivity calculate absolute error calculate mean square. Combines 4 tools from 2 SCP server(s).

Energy Unit Conversion Pipeline - Convert between energy units and analyze: MeV to Joules, scientific notation, and error calculation. Use this skill for physics tasks involving convert energy MeV to J convert to scientific notation format scientific notation calculate absolute error. Combines 4 tools from 2 SCP server(s).

Calculate sound speed in seawater from practical salinity, temperature, and pressure using the Gibbs Seawater Oceanographic Toolbox.

Assess drug risks and adverse effects using FDA drug database to retrieve safety information and risk profiles.

SNP Functional Impact Analysis - Analyze SNP function: VEP prediction, variation details, phenotype association, and literature evidence. Use this skill for functional genomics tasks involving get vep id get variation get phenotype accession pubmed search. Combines 4 tools from 2 SCP server(s).

Protein Engineering Workflow - Engineer a protein: predict structure, identify functional residues, predict beneficial mutations, and calculate properties. Use this skill for protein engineering tasks involving Protein structure prediction ESMFold predict functional residue zero shot sequence prediction calculate protein sequence properties. Combines 4 tools from 2 SCP server(s).

Perform meta-analysis on scientific studies to synthesize research findings and generate comprehensive reports with statistical summaries.

Enter explore mode - a thinking partner for exploring ideas, investigating problems, and clarifying requirements. Use when the user wants to think through something before or during a change.

Thermal & Heat Transfer Analysis - Analyze thermal system: calculate heat released, convert energy units, compute potential energy, and dynamic viscosity. Use this skill for thermal engineering tasks involving calculate heat released convert energy MeV to J calculate potential energy calculate dynamic viscosity. Combines 4 tools from 1 SCP server(s).

Search PubChem database using SMILES strings to retrieve compound information and chemical properties.

Retrieve phenotype information from Monarch Initiative using HPO (Human Phenotype Ontology) IDs to understand disease manifestations.

Bioassay Data Analysis - Analyze bioassay data: PubChem assay summary, ChEMBL activity search, compound properties, and target info. Use this skill for bioassay science tasks involving get assay summary by cid search activity calculate mol basic info get target by name. Combines 4 tools from 3 SCP server(s).

Generate new molecules sampling from the input scaffold.

Precision Oncology Workflow - Precision oncology: tumor expression profiling, variant analysis, targeted therapy lookup, and clinical trials. Use this skill for precision oncology tasks involving get gene expression across cancers get vep hgvs get associated drugs by target name get clinical studies info by drug name pubmed search. Combines 5 tools from 5 SCP server(s).

Scientific Literature Mining - Mine scientific literature: PubMed search, arXiv search, web search, and Tavily deep search. Use this skill for scientific informatics tasks involving pubmed search search literature search web tavily search. Combines 4 tools from 2 SCP server(s).

Convert SMILES strings to CAS registry numbers using material informatics tools to identify chemical substances.

Protein Complex Visualization & Analysis - Analyze protein complex: download structure, visualize complex, extract chains, and calculate quality metrics. Use this skill for structural biology tasks involving retrieve protein data by pdbcode visualize complex extract pdb chains calculate pdb basic info. Combines 4 tools from 1 SCP server(s).

Disease-Drug Landscape Analysis - Map the drug landscape for a disease: OpenTargets disease drugs, FDA indications, and clinical studies. Use this skill for drug discovery tasks involving get associated drugs by target name get drug names by indication get clinical studies info by drug name. Combines 3 tools from 2 SCP server(s).

Search scientific literature and research papers using FlowSearch to find relevant academic articles and publications.

AlphaFold Structure Analysis Pipeline - AlphaFold pipeline: download predicted structure, predict pockets, extract sequence, and compute properties. Use this skill for computational biology tasks involving download alphafold structure run fpocket extract pdb sequence calculate pdb basic info. Combines 4 tools from 3 SCP server(s).

Drug Repurposing Screening - Screen existing drugs for new indications by querying FDA indications, ChEMBL mechanisms, and OpenTargets drug-disease associations. Use this skill for drug discovery tasks involving get indications by drug name get mechanism of action by drug name get drug by name get associated drugs by target name. Combines 4 tools from 3 SCP server(s).

Pharmacogenomics Analysis - Pharmacogenomics analysis: FDA pharmacogenomics info, variant effects, ClinVar pathogenicity, and gene expression. Use this skill for pharmacogenomics tasks involving get pharmacogenomics info by drug name get vep hgvs clinvar search get gene expression across cancers. Combines 4 tools from 4 SCP server(s).

Calculate basic molecular properties from SMILES including molecular weight, formula, atom counts, and exact mass.

Pharmacokinetics Profile Builder - Build a PK profile: FDA pharmacokinetics, clinical pharmacology, dosage info, and molecular properties. Use this skill for pharmacology tasks involving get pharmacokinetics by drug name get clinical pharmacology by drug name get dosage and storage information by drug name get compound by name. Combines 4 tools from 2 SCP server(s).

Molecular Fingerprint Analysis - Fingerprint analysis: topology descriptors, structure complexity, similarity calculation, and AromaticityAnalysis. Use this skill for cheminformatics tasks involving calculate mol topology calculate mol structure complexity calculate smiles similarity AromaticityAnalyzer. Combines 4 tools from 2 SCP server(s).

Disease Protein Profiling - Profile a disease protein: UniProt data, AlphaFold structure, InterPro domains, phenotype associations from Ensembl. Use this skill for medical proteomics tasks involving query uniprot download alphafold structure query interpro get phenotype gene. Combines 4 tools from 2 SCP server(s).

Gene-Variant-Drug Nexus - Connect gene variants to drugs: variant effect, gene-disease link, drug associations, and clinical evidence. Use this skill for translational genomics tasks involving get vep hgvs get associated targets by disease efoId get associated drugs by target name clinvar search. Combines 4 tools from 3 SCP server(s).

SMILES Comprehensive Analysis - Comprehensive SMILES analysis: validate, convert name, compute all molecular descriptors, and predict ADMET. Use this skill for cheminformatics tasks involving is valid smiles ChemicalStructureAnalyzer calculate mol basic info pred molecule admet. Combines 4 tools from 3 SCP server(s).

One Health Pathogen Analysis - One Health analysis: pathogen genome, cross-species gene comparison, antimicrobial drugs, and environmental context. Use this skill for one health tasks involving get genome dataset report by taxon get homology symbol get mechanism of action by drug name tavily search get taxonomy. Combines 5 tools from 4 SCP server(s).

Check if the input protein sequence or molecule SMILES string is valid.

Enzyme Inhibitor Design - Design enzyme inhibitor: target structure, pocket prediction, compound screening, and ADMET assessment. Use this skill for enzyme pharmacology tasks involving retrieve protein data by pdbcode pred pocket prank quick molecule docking pred molecule admet calculate mol drug chemistry. Combines 5 tools from 2 SCP server(s).

Chemical Safety Assessment - Assess chemical safety: PubChem compound info, FDA drug data, ADMET prediction, and structural alerts from ChEMBL. Use this skill for chemical safety tasks involving get general info by compound name get warnings and cautions by drug name pred molecule admet get compound structural alert. Combines 4 tools from 4 SCP server(s).

Convert between molecular formats including SMILES, InChI, InChIKey, and SELFIES for cheminformatics applications.

Epigenetics & Drug Response - Link epigenetics to drug response: gene regulation, variant effects, drug interactions, and expression. Use this skill for epigenetic pharmacology tasks involving get overlap region get vep hgvs get drug interactions by drug name get gene expression across cancers. Combines 4 tools from 3 SCP server(s).

Multi-Omics Integration - Integrate multi-omics: gene expression, protein data, pathway enrichment, and metabolic pathways. Use this skill for multi-omics tasks involving get gene expression across cancers get uniprotkb entry by accession get functional enrichment kegg get. Combines 4 tools from 4 SCP server(s).

Drug Toxicity Assessment - Comprehensive toxicity assessment: FDA adverse reactions, nonclinical toxicology, carcinogenicity data, and ADMET prediction. Use this skill for toxicology tasks involving get adverse reactions by drug name get nonclinical toxicology info by drug name get carcinogenic mutagenic fertility impairment info by drug name pred molecule admet. Combines 4 tools from 2 SCP server(s).

Rare Disease Genetic Analysis - Analyze rare disease genetics: Monarch phenotype-disease mapping, ClinVar variants, NCBI gene data, and OpenTargets. Use this skill for rare disease genetics tasks involving get HPO ID by phenotype get joint associated diseases by HPO ID list clinvar search get associated targets by disease efoId. Combines 4 tools from 3 SCP server(s).

Infectious Disease Analysis - Analyze infectious disease: virus data, taxonomy, antimicrobial drugs, and resistance literature. Use this skill for infectious disease tasks involving get virus dataset report get taxonomy get mechanism of action by drug name pubmed search. Combines 4 tools from 3 SCP server(s).

Metabolomics Pathway Analysis - Analyze metabolomics: compound identification, KEGG pathway mapping, enzyme links, and PubChem data. Use this skill for metabolomics tasks involving search pubchem by name kegg find kegg link kegg get. Combines 4 tools from 2 SCP server(s).

Use when the user describes a research need in natural language and wants AI-assisted query expansion before searching for papers, including requests to find recent work on a topic, related papers in a direction, or similar Chinese requests for AI paper search.

Drug Warning Intelligence Report - Generate drug warning report: ChEMBL drug warnings, FDA boxed warnings, adverse reactions, and environmental warnings. Use this skill for pharmacovigilance tasks involving get drug warning by id get boxed warning info by drug name get adverse reactions by drug name get environmental warning by drug name. Combines 4 tools from 2 SCP server(s).

Gene Comprehensive Lookup - Comprehensive gene lookup: NCBI gene data, Ensembl gene info, UniProt protein data, and KEGG pathway links. Use this skill for bioinformatics tasks involving get gene metadata by gene name get lookup symbol get general info by protein or gene name kegg find. Combines 4 tools from 4 SCP server(s).

Calculate atmospheric parameters including Coriolis parameter, geostrophic wind, heat index, potential temperature, and dewpoint for meteorology and climate science.

CAS Number Compound Lookup - Look up compounds by CAS: convert CAS to price/availability, get PubChem data, get ChEMBL info, and structure analysis. Use this skill for chemical information tasks involving CASToPrice get compound by name get molecule by name ChemicalStructureAnalyzer. Combines 4 tools from 4 SCP server(s).

Convert physical quantities and units at nanoscale for materials science and nanotechnology applications.

Query dbSNP + NCBI Gene to get variant genomic position (chromosome, coordinates, ref/alt alleles, mutation type) and associated gene coordinates.

UniProt Deep Protein Analysis - Deep UniProt analysis: entry data, UniRef clusters, UniParc cross-references, and gene-centric view. Use this skill for protein science tasks involving get uniprotkb entry by accession get uniref cluster by id get uniparc entry by upi get gene centric by accession. Combines 4 tools from 1 SCP server(s).

Assess wind energy potential and perform site analysis using atmospheric science calculations.

Protein Structure Quality Assessment - Assess structure quality: basic info, geometry analysis, quality metrics, composition, and visualization. Use this skill for structural biology tasks involving calculate pdb basic info calculate pdb structural geometry calculate pdb quality metrics calculate pdb composition info visualize protein. Combines 5 tools from 1 SCP server(s).

Cross-Species Protein Comparison - Compare proteins across species: get orthologs from NCBI, compute properties for each, and compare similarity. Use this skill for comparative biology tasks involving get gene orthologs calculate protein sequence properties calculate smiles similarity get homology id. Combines 4 tools from 3 SCP server(s).

Use ESMFold model to predict 3D structure of the input protein sequence.

Analyze protein sequences using InterProScan to identify functional domains, protein families, and Gene Ontology (GO) annotations.

Antibody Drug Development - Develop antibody drug: target protein analysis, biotherapeutic lookup, protein properties, and interaction prediction. Use this skill for biologics tasks involving get uniprotkb entry by accession get biotherapeutic by name ComputeProtPara ComputeHydrophilicity. Combines 4 tools from 3 SCP server(s).

Calculate the freezing point temperature of seawater from absolute salinity and pressure using GSW thermodynamic equations.

Transcriptome Analysis Pipeline - Analyze transcriptome: Ensembl transcript lookup, sequence retrieval, haplotype analysis, and UCSC track data. Use this skill for transcriptomics tasks involving get lookup id get sequence id get transcript haplotypes get track data. Combines 4 tools from 2 SCP server(s).

Analyze DNA and RNA sequences including molecular weight calculation, reverse complement generation, and oligonucleotide properties.

NCBI Gene Deep Dive - Deep dive into NCBI gene: metadata, dataset report, product report, orthologs, and gene links. Use this skill for gene biology tasks involving get gene metadata by gene name get gene dataset report by id get gene product report by id get gene orthologs get gene links by id. Combines 5 tools from 1 SCP server(s).

Substance Toxicology Report - Toxicology report: PubChem substance data, FDA toxicology, carcinogenicity data, and environmental warnings. Use this skill for toxicology tasks involving get substance by name get nonclinical toxicology info by drug name get carcinogenic mutagenic fertility impairment info by drug name get environmental warning by drug name. Combines 4 tools from 2 SCP server(s).

Antibody-Target Analysis - Analyze an antibody target: UniProt protein info, InterPro domains, protein properties, and biotherapeutic data from ChEMBL. Use this skill for immunology tasks involving get uniprotkb entry by accession query interpro ComputeProtPara get biotherapeutic by name. Combines 4 tools from 4 SCP server(s).

Search ChEMBL database for molecule information by name to retrieve bioactivity data and chemical structures.

Comprehensive molecular property analysis covering basic info, hydrophobicity, H-bonding, structural complexity, topology, drug-likeness, charge distribution, and complexity metrics.

Chemical Property Profiling - Profile chemical properties: basic info, hydrophobicity, H-bonds, charges, and molecular complexity. Use this skill for physical chemistry tasks involving calculate mol basic info calculate mol hydrophobicity calculate mol hbond calculate mol charge calculate mol complexity. Combines 5 tools from 1 SCP server(s).

Proteome-Level Analysis - Analyze at proteome level: get proteome from UniProt, gene-centric view, functional annotation from STRING. Use this skill for proteomics tasks involving get proteome by id get gene centric by proteome get functional annotation. Combines 3 tools from 2 SCP server(s).

Tissue-Specific Expression Analysis - Analyze tissue-specific expression: ChEMBL tissue data, TCGA cancer expression, Ensembl gene info, and NCBI gene data. Use this skill for tissue biology tasks involving get tissue by id get gene expression across cancers get lookup symbol get gene metadata by gene name. Combines 4 tools from 4 SCP server(s).

Query IGVF Catalog for regulatory element–gene associations within a genomic region, including association scores, element types, and biosample context.

Epigenomic Landscape Mapping - Map epigenomic landscape: overlapping features, regulatory elements, binding matrices, and phenotype links. Use this skill for epigenomics tasks involving get overlap region get phenotype region get species binding matrix get track data. Combines 4 tools from 2 SCP server(s).

Structural Pharmacogenomics - Link structure to pharmacogenomics: variant effect, protein structure change, drug binding, and clinical data. Use this skill for pharmacogenomics tasks involving get vep hgvs pred protein structure esmfold boltz binding affinity get pharmacogenomics info by drug name. Combines 4 tools from 3 SCP server(s).

Predict a molecule's ability to reverse disease states using DLEPS (Disease-Ligand Embedding Projection Score) for drug repositioning and discovery.

Affinity Maturation Pipeline - Affinity maturation: compute binding affinity, predict mutations, compute hydrophilicity, and predict drug-target interaction. Use this skill for antibody engineering tasks involving ComputeAffinityCalculator zero shot sequence prediction ComputeHydrophilicity PredictDrugTargetInteraction. Combines 4 tools from 3 SCP server(s).

ADMET & Drug-Likeness Report - Generate comprehensive ADMET and drug-likeness report: molecular properties, H-bond analysis, hydrophobicity, topology, and ADMET prediction. Use this skill for medicinal chemistry tasks involving calculate mol basic info calculate mol hbond calculate mol hydrophobicity calculate mol topology pred molecule admet. Combines 5 tools from 2 SCP server(s).

Disease Knowledge Graph - Build disease knowledge graph: OpenTargets targets, drugs, publications, and phenotypes. Use this skill for disease informatics tasks involving get associated targets by disease efoId get associated drugs by target name get publications by drug name get associated phenotypes by disease efoId. Combines 4 tools from 1 SCP server(s).

Predict the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the input molecules.

Comprehensive drug screening pipeline from molecular filtering through QED/ADMET criteria to protein-ligand docking, identifying promising drug candidates.

Enzyme Active Site Engineering - Engineer enzyme: identify active site residues, predict pocket, analyze binding site, and predict mutations. Use this skill for enzymology tasks involving predict functional residue run fpocket get binding site by id pred mutant sequence. Combines 4 tools from 3 SCP server(s).

Gene Ontology Analysis - Analyze GO terms: ChEMBL GO slim, STRING functional enrichment, STRING annotation, and Ensembl ontology. Use this skill for functional genomics tasks involving get go slim by id get functional enrichment get functional annotation get ontology name. Combines 4 tools from 3 SCP server(s).

Analyze chemical structures from compound names to retrieve SMILES, molecular formulas, molecular weight, and LogP values.

Retrieve disease-associated targets from Open Targets using disease EFO IDs to identify therapeutic targets.

Personalized Medicine Report - Generate personalized medicine report: pharmacogenomics, variant effects, drug safety, and clinical pharmacology. Use this skill for precision medicine tasks involving get pharmacogenomics info by drug name get vep hgvs get adverse reactions by drug name get clinical pharmacology by drug name. Combines 4 tools from 2 SCP server(s).

Drug-Drug Interaction Checker - Check interactions between multiple drugs using FDA interaction data, PubChem compound info, and ChEMBL target overlap analysis. Use this skill for clinical pharmacology tasks involving get drug interactions by drug name get compound by name get target by name. Combines 3 tools from 3 SCP server(s).

Polymer & Material Property Analysis - Analyze polymer properties: composition, symmetry, density, and lattice parameters for material design. Use this skill for polymer science tasks involving MaterialCompositionAnalyzer CalculateSymmetry CalculateDensity MofLattice. Combines 4 tools from 2 SCP server(s).

Cross-Database Compound Lookup - Cross-reference compound across databases: PubChem, ChEMBL, KEGG, and CAS number lookup. Use this skill for chemical information tasks involving get compound by name get molecule by name kegg find CASToPrice. Combines 4 tools from 4 SCP server(s).

Virtual Screening Pipeline - Virtual screening: search PubChem by substructure, compute similarity, filter by drug-likeness, and predict binding affinity. Use this skill for drug discovery tasks involving search pubchem by smiles calculate smiles similarity calculate mol drug chemistry boltz binding affinity. Combines 4 tools from 3 SCP server(s).

Retrieve protein sequences and functional information from UniProt database by protein name, enabling protein analysis and bioinformatics workflows.

Molecular Visualization Suite - Visualize molecules: convert SMILES to formats, visualize molecule, visualize protein, visualize complex. Use this skill for chemical visualization tasks involving convert smiles to format visualize molecule visualize protein visualize complex. Combines 4 tools from 1 SCP server(s).

Clinical Pharmacology Report - Generate clinical pharmacology report: PK, PD, mechanism, drug interactions, and special populations. Use this skill for clinical pharmacology tasks involving get pharmacokinetics by drug name get pharmacodynamics by drug name get mechanism of action by drug name get drug interactions by drug name get geriatric use info by drug name. Combines 5 tools from 1 SCP server(s).

Calculate electrical capacitance from geometric parameters and dielectric properties for circuit design.

Multi-Unit Conversion Suite - Convert units across domains: length mm to m, radius m to cm, dimensions to meters, nm to um, volume to cm3. Use this skill for metrology tasks involving convert length mm to m convert radius m to cm convert dimensions to meters convert nm to um convert volume to cm3. Combines 5 tools from 1 SCP server(s).

Variant Pathogenicity Assessment - Assess variant pathogenicity: Ensembl VEP prediction, ClinVar lookup, variation details, and gene phenotype associations. Use this skill for clinical genetics tasks involving get vep hgvs clinvar search get variation get phenotype gene. Combines 4 tools from 2 SCP server(s).

Chemical Patent & Novelty Analysis - Analyze chemical novelty: PubChem substructure CAS search, ChEMBL similarity search, compound synonyms, and literature. Use this skill for patent chemistry tasks involving get substructure cas get similarity by smiles get compound synonyms by name search literature. Combines 4 tools from 3 SCP server(s).

Disease-Specific Compound Screening - Screen compounds for disease: get DLEPS score for disease relevance, predict ADMET, and check drug-likeness. Use this skill for drug discovery tasks involving calculate dleps score pred molecule admet calculate mol drug chemistry get compound by name. Combines 4 tools from 3 SCP server(s).

Query FAVOR API for variant functional prediction scores (CADD, SIFT, PolyPhen, REVEL, etc.) and gene annotation.

Regulatory Region Analysis - Analyze regulatory regions: get overlapping features, binding matrix, sequence, and phenotype associations. Use this skill for epigenomics tasks involving get overlap region get species binding matrix get sequence get phenotype region. Combines 4 tools from 2 SCP server(s).

Retrieve gene expression data from TCGA (The Cancer Genome Atlas) to analyze cancer-specific expression patterns.

Cell Line Assay Analysis - Analyze cell line assays: ChEMBL cell line info, assay search, activity data, and target info. Use this skill for cell biology tasks involving get cell line by id search assay search activity get target by name. Combines 4 tools from 1 SCP server(s).

Length & Dimension Measurement - Precision length measurement: convert mm to m, calculate length plus width, area, and error. Use this skill for metrology tasks involving convert length mm to m calculate length plus width calculate area calculate absolute error. Combines 4 tools from 3 SCP server(s).

Cancer Therapy Design - Design cancer therapy: identify targets, find drugs, check safety, and analyze differential expression. Use this skill for oncology tasks involving get associated targets by disease efoId get associated drugs by target name get adverse reactions by drug name tcga differential expression analysis. Combines 4 tools from 3 SCP server(s).

Retrieve SMILES strings from PubChem database using compound names to obtain molecular structures from common chemical names.

Organism Classification & Database - Classify organism: NCBI taxonomy, Ensembl taxonomy, ChEMBL organisms, and genome info. Use this skill for taxonomy tasks involving get taxonomy get taxonomy id get organism by id get genome dataset report by taxon. Combines 4 tools from 3 SCP server(s).

Protein Solubility Optimization - Optimize protein solubility: calculate properties, predict solubility, predict hydrophilicity, and suggest mutations. Use this skill for protein engineering tasks involving calculate protein sequence properties predict protein function ComputeHydrophilicity zero shot sequence prediction. Combines 4 tools from 3 SCP server(s).

Pediatric Drug Safety Review - Evaluate pediatric drug safety: pediatric use info, child safety, dosage forms, and overdosage info from FDA. Use this skill for pediatric pharmacology tasks involving get pediatric use info by drug name get child safety info by drug name get dosage forms and strengths by drug name get overdosage info by drug name. Combines 4 tools from 1 SCP server(s).

Full Protein Characterization - Complete protein characterization: validate sequence, compute all properties, predict structure, and analyze pockets. Use this skill for protein biochemistry tasks involving is valid protein sequence analyze protein ComputeProtPara pred protein structure esmfold run fpocket. Combines 5 tools from 4 SCP server(s).

Protein Similarity Search - Search for similar proteins: extract sequence from PDB, search structures with FoldSeek, find homologs with STRING, and check UniProt. Use this skill for bioinformatics tasks involving extract pdb sequence foldseek search get best similarity hits between species search uniprotkb entries. Combines 4 tools from 3 SCP server(s).

Compound-to-Drug Analysis Pipeline - Full compound-to-drug pipeline: name-to-SMILES conversion, structure analysis, drug-likeness, and FDA drug lookup. Use this skill for drug development tasks involving NameToSMILES ChemicalStructureAnalyzer calculate mol drug chemistry get drug by name. Combines 4 tools from 4 SCP server(s).

Retrieve genomic sequences from Ensembl database using transcript or gene IDs to obtain nucleotide and protein sequences.

Query ClinGen Allele Registry to map variant rsID to identifiers in other databases (ClinVar, gnomAD, COSMIC, UniProtKB, OMIM, etc.).

ATC Drug Classification Lookup - Look up drug in ATC classification: ChEMBL ATC class, FDA drug info, PubChem compound, and mechanism of action. Use this skill for pharmacology tasks involving get atc class by level5 get mechanism of action by drug name get compound by name get drug by name. Combines 4 tools from 3 SCP server(s).

Gene Family Evolution Analysis - Analyze gene family evolution: CAFE gene tree, homology, Ensembl gene tree, and taxonomy. Use this skill for molecular evolution tasks involving get cafe genetree member symbol get homology symbol get genetree member symbol get taxonomy classification. Combines 4 tools from 1 SCP server(s).

Protein Structure Comprehensive Analysis - Comprehensive structure analysis: download PDB, extract chains, calculate geometry, quality metrics, and composition. Use this skill for structural biology tasks involving retrieve protein data by pdbcode extract pdb chains calculate pdb structural geometry calculate pdb quality metrics calculate pdb composition info. Combines 5 tools from 1 SCP server(s).

Implement data transmission between the local computer and the MCP Server using Base64 encoding

Calculate advanced molecular descriptors including shape indices, connectivity indices, and structural features for QSAR and drug discovery.

Electrical Circuit Analysis - Analyze electrical circuit: compute capacitance, convert resistance units, calculate total charge, and duty cycle. Use this skill for electrical engineering tasks involving convert resistance kOhm to Ohm calculate geometric term calculate absolute error. Combines 3 tools from 3 SCP server(s).

Protein Function Annotation Pipeline - Annotate protein function: UniProt metadata, InterPro domains, functional prediction, and GO enrichment. Use this skill for proteomics tasks involving query uniprot query interpro predict protein function get functional enrichment. Combines 4 tools from 2 SCP server(s).

Process seismic waveform data including reading MinISEED/SAC files, extracting metadata, and visualizing earthquake signals.

InterProScan Analysis Pipeline - Run InterProScan for domain analysis, then enrich with UniProt data and STRING interactions. Use this skill for functional proteomics tasks involving interproscan analyze get uniprotkb entry by accession get functional enrichment query interpro. Combines 4 tools from 4 SCP server(s).

Calculate mass percentages and stoichiometric ratios for chemical reactions and compound compositions.

Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.

Query gnomAD for variant allele frequency across populations. Uses FAVOR to convert rsID→variant_id first, then queries gnomAD.

Clinical Trial Drug Profiling - Profile drug for clinical trials: FDA clinical studies, contraindications, pregnancy info, and geriatric use. Use this skill for clinical research tasks involving get clinical studies info by drug name get contraindications by drug name get pregnancy effects info by drug name get geriatric use info by drug name. Combines 4 tools from 1 SCP server(s).

Use before plan submission, major plan revision, and major stage transitions. Verify alignment, feasibility, rigor, completeness, and prevent unjustified regressions to earlier workflow phases.

Search for similar protein sequences in UniProt Swiss-Prot database using BLAST to identify homologous proteins and functional relationships.

Mouse Model Disease Analysis - Analyze mouse disease models: MouseMine search, NCBI mouse gene data, Ensembl cross-species comparison, and orthologs. Use this skill for model organisms tasks involving mousemine search get gene metadata by gene name get homology symbol get gene orthologs. Combines 4 tools from 3 SCP server(s).

Generate detailed laboratory protocols from natural language descriptions using AI, producing step-by-step experimental procedures ready for lab execution.

Drug-Target Structural Biology - Integrate drug and target structure: get drug from ChEMBL, target structure from PDB, dock them, and predict ADMET. Use this skill for structural pharmacology tasks involving get drug by name retrieve protein data by pdbcode quick molecule docking pred molecule admet. Combines 4 tools from 3 SCP server(s).

Lab Protocol from Literature - Extract and generate lab protocol: search PubMed, extract protocol from paper, and generate executable protocol. Use this skill for lab science tasks involving pubmed search extract protocol from pdf protocol generation generate executable json. Combines 4 tools from 2 SCP server(s).

Generate new molecules sampling from the input two warhead fragments.

PubChem Deep Dive Analysis - Deep dive into PubChem: compound info, bioassay summary, 3D conformers, synonyms, and general description. Use this skill for chemical databases tasks involving get pubchem compound by cid get assay summary by cid get conformers by cid get compound synonyms by name get general info by compound name. Combines 5 tools from 1 SCP server(s).

Microbiome Genomics Analysis - Analyze microbial genome: NCBI genome data, taxonomy, KEGG metabolic pathways, and annotation. Use this skill for metagenomics tasks involving get genome dataset report by taxon get taxonomy kegg find get genome annotation report. Combines 4 tools from 2 SCP server(s).

Convert laboratory protocols to executable JSON format using Thoth-OP for automated lab equipment control.

BLAST & Protein Analysis Pipeline - BLAST search followed by comprehensive protein analysis: BLAST, then structure prediction, properties, and function. Use this skill for sequence bioinformatics tasks involving blast search pred protein structure esmfold calculate protein sequence properties predict protein function. Combines 4 tools from 4 SCP server(s).

Query PharmGKB (clinPGx) for pharmacogenomic clinical annotations — how a variant affects drug response, dosing, and adverse reactions.

Drug-Indication Mapping - Map drug indications: ChEMBL drug indications, FDA indications, OpenTargets drug associations, and literature. Use this skill for clinical informatics tasks involving get drug indication by id get indications by drug name get associated drugs by target name pubmed search. Combines 4 tools from 4 SCP server(s).

Gene Expression Atlas - Build gene expression atlas: TCGA cancer expression, NCBI gene info, Ensembl gene details, and literature search. Use this skill for transcriptomics tasks involving get gene expression across cancers get gene metadata by gene name get lookup symbol search literature. Combines 4 tools from 4 SCP server(s).

Gene-to-Drug Discovery Pipeline - Full gene-to-drug pipeline: gene lookup, protein structure, binding pocket, virtual screening, and drug-likeness. Use this skill for translational medicine tasks involving get gene metadata by gene name pred protein structure esmfold run fpocket boltz binding affinity calculate mol drug chemistry. Combines 5 tools from 3 SCP server(s).

Optical System Analysis - Analyze optical system: calculate photon rate, frequency range, radiation pressure, and electron wavelength. Use this skill for optics tasks involving calculate incident photon rate calculate frequency range calculate radiation pressure electron wavelength. Combines 4 tools from 1 SCP server(s).

Biomarker Discovery Pipeline - Discover biomarkers: TCGA differential expression, NCBI gene data, OpenTargets associations, and clinical relevance. Use this skill for precision medicine tasks involving tcga differential expression analysis get gene metadata by gene name get associated targets by disease efoId clinvar search. Combines 4 tools from 4 SCP server(s).

Virus Genomics Analysis - Analyze virus genomics: NCBI virus dataset, annotation, taxonomy, and literature search. Use this skill for virology tasks involving get virus dataset report get virus annotation report get taxonomy search literature. Combines 4 tools from 2 SCP server(s).

Lead Compound Optimization - Optimize a lead compound: validate SMILES, compute drug-likeness, predict ADMET properties, and check ChEMBL bioactivity. Use this skill for medicinal chemistry tasks involving is valid smiles calculate mol drug chemistry pred molecule admet search activity. Combines 4 tools from 3 SCP server(s).

Generate new molecules sampling from the input molecule.

Calculate material density and volume from mass and geometric dimensions for materials mechanics analysis.

Analyze measurement errors, uncertainties, and statistical variations in experimental data for quality control.

Computational Analysis via Code Execution - Execute custom computational analysis code, analyze software, and search for reference implementations. Use this skill for computational science tasks involving exec code software analysis search dataset search literature. Combines 4 tools from 2 SCP server(s).

Calculate optical frequency and wavelength relationships for photonics and electromagnetic analysis.

Analyze protein-protein interaction enrichment using STRING database to identify functional networks and pathway associations.

Population Genetics Analysis - Analyze population genetics: Ensembl variation populations, linkage disequilibrium, and variant frequency data. Use this skill for population genetics tasks involving get info variation populations get ld get variation get variant recoder. Combines 4 tools from 1 SCP server(s).

Mutation Impact Analysis - Analyze mutation impact: predict structure, predict mutations from sequence and structure, and check variant effects with Ensembl VEP. Use this skill for molecular biology tasks involving pred protein structure esmfold zero shot sequence prediction predict zero shot structure get vep hgvs. Combines 4 tools from 3 SCP server(s).

Calculate seawater thermodynamic properties using TEOS-10 standard including density, salinity, sound speed, and freezing temperature for oceanography.

Chromosome Structure Analysis - Analyze chromosome: NCBI summary, UCSC cytoband, genome sequence, and Ensembl assembly info. Use this skill for cytogenetics tasks involving get chromosome summary get cytoband get chromosome sequence get info assembly. Combines 4 tools from 3 SCP server(s).

Signal Processing Analysis - Analyze signals: duty cycle, frequency range, electron wavelength, and measurement error analysis. Use this skill for signal processing tasks involving calculate duty cycle calculate frequency range electron wavelength calculate absolute error. Combines 4 tools from 3 SCP server(s).

Polypharmacology Analysis - Analyze a drug's multi-target pharmacology: get targets from ChEMBL, functional enrichment from STRING, and pathway links from KEGG. Use this skill for pharmacology tasks involving get target by name get functional enrichment kegg link get mechanism by id. Combines 4 tools from 3 SCP server(s).

Natural Product Analysis - Analyze natural products: name to SMILES, PubChem lookup, structural analysis, and KEGG natural product search. Use this skill for natural products chemistry tasks involving NameToSMILES search pubchem by name ChemicalStructureAnalyzer kegg find. Combines 4 tools from 4 SCP server(s).

Extract laboratory protocols from PDF documents using Thoth-Plan to convert experimental procedures into structured text.

Molecular Docking Pipeline - Complete docking workflow: retrieve protein structure, predict binding pockets, prepare receptor, and dock ligand. Use this skill for structural biology tasks involving retrieve protein data by pdbcode run fpocket convert pdb to pdbqt dock quick molecule docking. Combines 4 tools from 2 SCP server(s).

Calculate buoyancy forces and acceleration for fluid mechanics and hydrodynamics analysis.

Calculate different types of molecular properties based on SMILES strings, covering basic physicochemical properties, hydrophobicity, hydrogen bonding capability, molecular complexity, topological structures, charge distribution, and custom complexity metrics, respectively.

Binding Site Characterization - Characterize binding sites: predict pockets with fpocket and P2Rank, get binding site info from ChEMBL, and visualize. Use this skill for structural biology tasks involving run fpocket pred pocket prank get binding site by id visualize protein. Combines 4 tools from 3 SCP server(s).

Synthetic Biology Design - Design synthetic biology construct: gene lookup, codon optimization, protein property prediction, and structure prediction. Use this skill for synthetic biology tasks involving get sequence id DegenerateCodonCalculatorbyAminoAcid calculate protein sequence properties pred protein structure esmfold. Combines 4 tools from 4 SCP server(s).

Search KEGG database for gene information to retrieve pathway associations, functional annotations, and disease links.

Given a protein sequence and its structure, employ ProSST model to predict mutation effects and obtain the top-k mutated sequences.

Substructure-Activity Relationship - Analyze substructure-activity: ChEMBL substructure search, activity data, PubChem compounds, and similarity. Use this skill for medicinal chemistry tasks involving get substructure by smiles search activity search pubchem by smiles calculate smiles similarity. Combines 4 tools from 3 SCP server(s).

Protein Cross-Database Reference - Cross-reference protein: UniProt entry, NCBI gene, Ensembl xrefs, and PDB structure search. Use this skill for proteomics tasks involving get uniprotkb entry by accession get gene metadata by gene name get xrefs symbol retrieve protein data by pdbcode. Combines 4 tools from 4 SCP server(s).

Comprehensive Drug Safety Profile - Build a complete drug safety profile by combining FDA adverse reactions, boxed warnings, drug interactions, and contraindications. Use this skill for pharmacology tasks involving get adverse reactions by drug name get boxed warning info by drug name get drug interactions by drug name get contraindications by drug name. Combines 4 tools from 1 SCP server(s).

Enter explore mode - think through ideas, investigate problems, clarify requirements

Use the local InnoClaw CLI to run app workflows and Deep Research sessions from the terminal. Trigger when the user wants command-line control over this repository instead of only using the web UI.

Create a new PRIVATE GitHub repo that is a full-history copy of imbue-ai/forever-claude-template's current main branch, clone it to <parent-dir>/<repo-name> (default $HOME/project), and push. Use when the user asks to "spin up a new forever-claude clone", "fork the forever-claude template as a private repo", "make me a new private copy of forever-claude-template", or similar.

Create FIXME's in the codebase for each of the issues in the given input file.

End-to-end dev workflow for the minds app stack -- first-time bring-up, every-startup vendor/mngr sync, and the iteration loop against a running Docker agent. Use this when starting or restarting the dev Electron app, or after changing any minds component (mngr, the system interface, the FCT template).

Create 1-3 short asciinema demo recordings (5-20 seconds each) that demonstrate completed work. Use only when explicitly instructed to create demos.

List all conversation threads

Manage conversation threads (create, switch, update, delete, show)

为任何角色创建独立线程并开始工作

Usado para generar PRDs, especificaciones de requisitos, documentos de solicitud y revisiones. Se activa con solicitudes como 'crear un PRD', 'escribir especificaciones de requisitos', 'revisar esto', 'analizar actas de reunión', etc.

Se utiliza para generar planes de prueba, casos de prueba e informes de prueba. Se activa con solicitudes como 'Crear un plan de pruebas', 'Generar casos de prueba', 'Escribir pruebas E2E', etc.

Realiza búsquedas en tiempo real en X (Twitter) para recopilar y analizar tweets sobre un tema. Produce resultados de búsqueda como informes estructurados (Markdown + JSON + TXT). Se activa con 'Buscar en X', 'Investigar en Twitter', 'Analizar tweets', etc.

Habilidad para escribir SQL preciso y de alto rendimiento en los principales dialectos de almacenes de datos. Se activa con solicitudes como 'Escribir SQL', 'Optimizar consulta', 'Agregar en BigQuery', etc.

Usado para dashboards de marimo y visualización de progreso de proyectos. Se activa con solicitudes como 'crear un dashboard', 'visualizar progreso', 'mostrar resultados de pruebas', etc.

Habilidad para generar automáticamente storyboards para videos UGC con IA. Garantiza consistencia del personaje generando una sola hoja y luego recortando fotogramas individuales. Se activa con solicitudes como 'Crear un storyboard', 'Generar storyboard', 'Crear flujo de video UGC', etc.

Sub-agente que realiza conexiones a BigQuery/Snowflake, EDA, visualización y creación de notebooks Marimo. Integra cuatro reglas relacionadas (data_analysis, visualization, notebook, marimo_variable_naming). Se activa con solicitudes como 'analiza datos,' 'conectar a BigQuery,' 'ejecutar EDA,' 'analizar con Marimo,' etc.

Skill para generar imágenes a partir de texto y editar imágenes existentes usando la API de Generación de Imágenes de Gemini. Se activa con solicitudes como 'generar una imagen', 'crear una ilustración', 'editar una foto', etc.

Habilidad que agrega automáticamente anotaciones como recuadros rojos, flechas y globos de texto a capturas de pantalla. Se activa con solicitudes como 'Agregar anotaciones a la captura', 'Agregar flechas a la pantalla', 'Anotaciones para el manual'.

Habilidad que apoya el diseño de precios, empaquetado y estrategia de monetización. Se activa con solicitudes como 'Quiero definir precios', 'Diseñar planes de precios', 'Revisar la estrategia de precios'.

Kit de herramientas para el diseno de arquitectura de sistemas multiagente. Se activa con solicitudes como 'disenar un agente', 'configuracion multiagente', 'arquitectura de agentes', 'diseno de orquestacion', etc.

Habilidad que genera automáticamente Issues de auto-mejora al final de una sesión. Se activa con solicitudes como 'Crear Issue de retrospectiva', 'Retrospectiva', 'Crear Issues de mejora'.

Manage environment variables and credentials for ai-agent-camp. Use when setting up API keys, .env handling, or the credential manager safely.

Habilidad automatizada de revision de codigo compatible con TypeScript, JavaScript, Python, Go, Swift y Kotlin. Analisis de complejidad/riesgo de PR, deteccion de violaciones SOLID y code smells, y generacion de informes de revision. Se activa con solicitudes como 'revisar codigo', 'analizar PR', 'verificar calidad de codigo', 'informe de revision', etc.

Configure Codex tooling for ai-agent-camp. Use when enabling MCP servers, installing repo hooks, or explaining tool-specific setup.

Habilidad para analizar videos de TikTok/YouTube y convertirlos en plantillas. Descarga video, extrae fotogramas, ejecuta STT, analiza composición y genera JSON de plantilla. Se usa para análisis de competidores y aprendizaje de estructuras de videos populares. Se activa con 'Analizar video', 'Análisis de TikTok', 'Análisis de YouTube', etc.

Habilidad de carga de video usando YouTube Data API v3. Soporta detección automática de Shorts, inserción automática de enlaces UTM y publicación programada. Se activa con 'Publicar en YouTube', 'Subir video', 'Publicar Shorts', etc.

Habilidad para crear PRDs (Documentos de Requisitos de Producto), elaborar especificaciones de funcionalidades y definir criterios de aceptación. Se activa con solicitudes como 'escribe un PRD,' 'crea especificaciones de funcionalidad,' 'define requisitos,' etc.

Habilidad que extrae automáticamente afirmaciones factuales (números, fechas, nombres propios, estadísticas) de artículos y las verifica mediante búsqueda web. Se activa con solicitudes como 'verifica los hechos,' 'confirma la información,' 'comprueba las fuentes,' etc. Genera un reporte con puntuaciones de confianza.

Habilidad para apoyar el diseno e implementacion de pruebas A/B y experimentos. Se activa con solicitudes como 'disenar una prueba A/B', 'quiero hacer un split test', 'configurar una prueba de hipotesis', 'comparar variantes', etc. Para la implementacion del seguimiento, consulte analytics-tracking.

1行の説明文

Load and execute tool specs by category or name

Detect version, preview changes, apply workflow upgrades

Extract design patterns from code into specs and wiki

Register tool specs - extract, generate, or optimize

Manage editing boundary restrictions