For ml engineers
302 skills // curated for ml-engineers
Use when starting feature work that needs isolation from current workspace or before executing implementation plans - creates isolated git worktrees with smart directory selection and safety verification
Use when implementing any feature or bugfix, before writing implementation code
Use when starting any conversation - establishes how to find and use skills, requiring Skill tool invocation before ANY response including clarifying questions
Use when facing 2+ independent tasks that can be worked on without shared state or sequential dependencies
Use when you have a written implementation plan to execute in a separate session with review checkpoints
Use when implementation is complete, all tests pass, and you need to decide how to integrate the work - guides completion of development work by presenting structured options for merge, PR, or cleanup
Use when creating new skills, editing existing skills, or verifying skills work before deployment
Use when about to claim work is complete, fixed, or passing, before committing or creating PRs - requires running verification commands and confirming output before making any success claims; evidence before assertions always
Use when executing implementation plans with independent tasks in the current session
Toolkit for styling artifacts with a theme. These artifacts can be slides, docs, reportings, HTML landing pages, etc. There are 10 pre-set themes with colors/fonts that you can apply to any artifact that has been creating, or can generate a new theme on-the-fly.
Build, debug, and optimize Claude API / Anthropic SDK apps. Apps built with this skill should include prompt caching. Also handles migrating existing Claude API code between Claude model versions (4.5 → 4.6, 4.6 → 4.7, retired-model replacements). TRIGGER when: code imports `anthropic`/`@anthropic-ai/sdk`; user asks for the Claude API, Anthropic SDK, or Managed Agents; user adds/modifies/tunes a Claude feature (caching, thinking, compaction, tool use, batch, files, citations, memory) or model (Opus/Sonnet/Haiku) in a file; questions about prompt caching / cache hit rate in an Anthropic SDK project. SKIP: file imports `openai`/other-provider SDK, filename like `*-openai.py`/`*-generic.py`, provider-neutral code, general programming/ML.
Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when users request creating art using code, generative art, algorithmic art, flow fields, or particle systems. Create original algorithmic art rather than copying existing artists' work to avoid copyright violations.
Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.
Use this skill any time a .pptx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from any .pptx file (even if the extracted content will be used elsewhere, like in an email or summary); editing, modifying, or updating existing presentations; combining or splitting slide files; working with templates, layouts, speaker notes, or comments. Trigger whenever the user mentions "deck," "slides," "presentation," or references a .pptx filename, regardless of what they plan to do with the content afterward. If a .pptx file needs to be opened, created, or touched, use this skill.
Knowledge and utilities for creating animated GIFs optimized for Slack. Provides constraints, validation tools, and animation concepts. Use when users request animated GIFs for Slack like "make me a GIF of X doing Y for Slack."
Toolkit for interacting with and testing local web applications using Playwright. Supports verifying frontend functionality, debugging UI behavior, capturing browser screenshots, and viewing browser logs.
Create distinctive, production-grade frontend interfaces with high design quality. Use this skill when the user asks to build web components, pages, artifacts, posters, or applications (examples include websites, landing pages, dashboards, React components, HTML/CSS layouts, or when styling/beautifying any web UI). Generates creative, polished code and UI design that avoids generic AI aesthetics.
Guide for creating high-quality MCP (Model Context Protocol) servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).
Applies Anthropic's official brand colors and typography to any sort of artifact that may benefit from having Anthropic's look-and-feel. Use it when brand colors or style guidelines, visual formatting, or company design standards apply.
Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterheads. Also use when extracting or reorganizing content from .docx files, inserting or replacing images in documents, performing find-and-replace in Word files, working with tracked changes or comments, or converting content into a polished Word document. If the user asks for a 'report', 'memo', 'letter', 'template', or similar deliverable as a Word or .docx file, use this skill. Do NOT use for PDFs, spreadsheets, Google Docs, or general coding tasks unrelated to document generation.
Suite of tools for creating elaborate, multi-component claude.ai HTML artifacts using modern frontend web technologies (React, Tailwind CSS, shadcn/ui). Use for complex artifacts requiring state management, routing, or shadcn/ui components - not for simple single-file HTML/JSX artifacts.
Cross-model benchmark for gstack skills. Runs the same prompt through Claude, GPT (via Codex CLI), and Gemini side-by-side — compares latency, tokens, cost, and optionally quality via LLM judge. Answers "which model is actually best for this skill?" with data instead of vibes. Separate from /benchmark, which measures web page performance. Use when: "benchmark models", "compare models", "which model is best for X", "cross-model comparison", "model shootout". (gstack) Voice triggers (speech-to-text aliases): "compare models", "model shootout", "which model is best".
Chief Security Officer mode. Infrastructure-first security audit: secrets archaeology, dependency supply chain, CI/CD pipeline security, LLM/AI security, skill supply chain scanning, plus OWASP Top 10, STRIDE threat modeling, and active verification. Two modes: daily (zero-noise, 8/10 confidence gate) and comprehensive (monthly deep scan, 2/10 bar). Trend tracking across audit runs. Use when: "security audit", "threat model", "pentest review", "OWASP", "CSO review". (gstack) Voice triggers (speech-to-text aliases): "see-so", "see so", "security review", "security check", "vulnerability scan", "run security".
Design shotgun: generate multiple AI design variants, open a comparison board, collect structured feedback, and iterate. Standalone design exploration you can run anytime. Use when: "explore designs", "show me options", "design variants", "visual brainstorm", or "I don't like how this looks". Proactively suggest when the user describes a UI feature but hasn't seen what it could look like. (gstack)
Pre-landing PR review. Analyzes diff against the base branch for SQL safety, LLM trust boundary violations, conditional side effects, and other structural issues. Use when asked to "review this PR", "code review", "pre-landing review", or "check my diff". Proactively suggest when the user is about to merge or land code changes. (gstack)
This skill should be used when the user asks to "demonstrate skills", "show skill format", "create a skill template", or discusses skill development patterns. Provides a reference template for creating Claude Code plugin skills.
An example user-invoked skill that demonstrates frontmatter options and the skills/<name>/SKILL.md layout
Create distinctive, production-grade frontend interfaces with high design quality. Use this skill when the user asks to build web components, pages, or applications. Generates creative, polished code that avoids generic AI aesthetics.
This skill should be used when the user asks to "create a hookify rule", "write a hook rule", "configure hookify", "add a hookify rule", or needs guidance on hookify rule syntax and patterns.
Solve competition math problems (IMO, Putnam, USAMO, AIME) with adversarial verification that catches the errors self-verification misses. Activates when asked to 'solve this IMO problem', 'prove this olympiad inequality', 'verify this competition proof', 'find a counterexample', 'is this proof correct', or for any problem with 'IMO', 'Putnam', 'USAMO', 'olympiad', or 'competition math' in it. Uses pure reasoning (no tools) — then a fresh-context adversarial verifier attacks the proof using specific failure patterns, not generic 'check logic'. Outputs calibrated confidence — will say 'no confident solution' rather than bluff. If LaTeX is available, produces a clean PDF after verification passes.
This skill should be used when the user asks to "build an MCP server", "create an MCP", "make an MCP integration", "wrap an API for Claude", "expose tools to Claude", "make an MCP app", or discusses building something with the Model Context Protocol. It is the entry point for MCP server development — it interrogates the user about their use case, determines the right deployment model (remote HTTP, MCPB, local stdio), picks a tool-design pattern, and hands off to specialized skills.
This skill should be used when the user wants to build an "MCP app", add "interactive UI" or "widgets" to an MCP server, "render components in chat", build "MCP UI resources", make a tool that shows a "form", "picker", "dashboard" or "confirmation dialog" inline in the conversation, or mentions "apps SDK" in the context of MCP. Use AFTER the build-mcp-server skill has settled the deployment model, or when the user already knows they want UI widgets.
This skill should be used when the user wants to "package an MCP server", "bundle an MCP", "make an MCPB", "ship a local MCP server", "distribute a local MCP", discusses ".mcpb files", mentions bundling a Node or Python runtime with their MCP server, or needs an MCP server that interacts with the local filesystem, desktop apps, or OS and must be installable without the user having Node/Python set up.
This skill should be used when the user asks to "create a slash command", "add a command", "write a custom command", "define command arguments", "use command frontmatter", "organize commands", "create command with file references", "interactive command", "use AskUserQuestion in command", or needs guidance on slash command structure, YAML frontmatter fields, dynamic arguments, bash execution in commands, user interaction patterns, or command development best practices for Claude Code.
This skill should be used when the user wants to "create a skill", "add a skill to plugin", "write a new skill", "improve skill description", "organize skill content", or needs guidance on skill structure, progressive disclosure, or skill development best practices for Claude Code plugins.
Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Claude's capabilities with specialized knowledge, workflows, or tool integrations.
This skill should be used when the user asks about "plugin settings", "store plugin configuration", "user-configurable plugin", ".local.md files", "plugin state files", "read YAML frontmatter", "per-project plugin settings", or wants to make plugin behavior configurable. Documents the .claude/plugin-name.local.md pattern for storing plugin-specific configuration with YAML frontmatter and markdown content.
This skill should be used when the user asks to "create a hook", "add a PreToolUse/PostToolUse/Stop hook", "validate tool use", "implement prompt-based hooks", "use ${CLAUDE_PLUGIN_ROOT}", "set up event-driven automation", "block dangerous commands", or mentions hook events (PreToolUse, PostToolUse, Stop, SubagentStop, SessionStart, SessionEnd, UserPromptSubmit, PreCompact, Notification). Provides comprehensive guidance for creating and implementing Claude Code plugin hooks with focus on advanced prompt-based hooks API.
This skill should be used when the user asks to "add MCP server", "integrate MCP", "configure MCP in plugin", "use .mcp.json", "set up Model Context Protocol", "connect external service", mentions "${CLAUDE_PLUGIN_ROOT} with MCP", or discusses MCP server types (SSE, stdio, HTTP, WebSocket). Provides comprehensive guidance for integrating Model Context Protocol servers into Claude Code plugins for external tool and service integration.
This skill should be used when the user asks to "create an agent", "add an agent", "write a subagent", "agent frontmatter", "when to use description", "agent examples", "agent tools", "agent colors", "autonomous agent", or needs guidance on agent structure, system prompts, triggering conditions, or agent development best practices for Claude Code plugins.
Generate an explorable HTML report of Claude Code session usage (tokens, cache, subagents, skills, expensive prompts) from ~/.claude/projects transcripts.
Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, update or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.
This skill should be used when generating comprehensive test cases from PRD documents or user requirements. Triggers when users request test case generation, QA planning, test scenario creation, or need structured test documentation. Produces detailed test cases covering functional, edge case, error handling, and state transition scenarios.
This skill should be used for structured feature development with codebase understanding. Triggers on /do command. Provides a 5-phase workflow (Understand, Clarify, Design, Implement, Complete) using codeagent-wrapper to orchestrate code-explorer, code-architect, code-reviewer, and develop agents in parallel.
Reviews code for bugs, logic errors, security vulnerabilities, code quality issues, and adherence to project conventions, using confidence-based filtering to report only high-priority issues that truly matter
Designs feature architectures by analyzing existing codebase patterns and conventions, then providing comprehensive implementation blueprints with specific files to create/modify, component designs, data flows, and build sequences
Interactive Product Owner skill for requirements gathering, analysis, and PRD generation. Triggers when users request product requirements, feature specification, PRD creation, or need help understanding and documenting project requirements. Uses quality scoring and iterative dialogue to ensure comprehensive requirements before generating professional PRD documents.
This skill should be used for multi-session autonomous agent work requiring progress checkpointing, failure recovery, and task dependency management. Triggers on '/harness' command, or when a task involves many subtasks needing progress persistence, sleep/resume cycles across context windows, recovery from mid-task failures with partial state, or distributed work across multiple agent sessions. Synthesized from Anthropic and OpenAI engineering practices for long-running agents.
Execute codeagent-wrapper for multi-backend AI code tasks. Supports Codex, Claude, Gemini, and OpenCode backends with agent presets, skill injection, file references (@syntax), worktree isolation, parallel execution, and structured output.
Minimal SPARV workflow (Specify→Plan→Act→Review→Vault) with 10-point spec gate, unified journal, 2-action saves, 3-failure protocol, and EHRB risk detection.
Craft Stable Diffusion prompts — SDXL, LoRA triggers, ControlNet hints, and ComfyUI workflow design.
Transform and reshape data — pivot, melt, aggregate, join, and apply complex business rules to datasets.
Design and create ML features — encoding, scaling, interaction terms, embeddings, and feature selection.
Perform SQL-based data analysis — exploratory queries, aggregations, funnels, cohorts, and insight narratives.
Build end-to-end ML pipelines — data prep, feature engineering, model training, evaluation, and MLflow tracking.
PR Automation Orchestrator: poll open PRs, check CI, run review, fix, and merge eligible PRs. Use when: (1) Invoked by daemon via scripts/pr-automation.sh, (2) User says "/pr-automation".
PR Verification & Merge: verify bot:ready-to-merge PRs with impact analysis, test supplementation, and one-click merge. Use when: (1) User says "/pr-verify", (2) User wants to verify and merge ready PRs.
PR Review Fix: automatically fix all issues identified in a pr-review report. Use when: (1) User says "fix all review issues", (2) User says "/pr-fix", (3) After pr-review skill has produced a report, (4) User wants to address PR review feedback.
Auto-fix high-frequency Sentry issues: fetch issues > N occurrences, analyze stack traces, fix code, create GitHub issues, and submit PRs. Supports user feedback issues (event.type "default") with attachment analysis (logs, screenshots) when include_feedback=true. Use when: (1) User says "/fix-sentry", (2) User asks to fix Sentry issues.
Internationalization (i18n) workflow and standards for managing translations. Use when: (1) Adding new user-facing text, (2) Creating new components with user-facing text, (3) Reviewing code for i18n compliance, (4) Adding a new translation module.
PR Code Review (Local): perform a thorough local code review with full project context. Use when: (1) User asks to review a PR, (2) User says "/pr-review", (3) User wants to review code changes before merging.
Canonical commit workflow for Gas Town crew members: pre-flight checks, branch creation, gt commit with agent identity, push, and PR creation. Use when ready to commit and submit work for review.
PR Sheriff workflow: triage PRs into easy-wins and crew assignments. Prints recommendations inline - does NOT post to GitHub.
Run a grouped, bisectable Go dependency security sweep on the Fission repo. Use when the user asks to upgrade outdated/vulnerable Go dependencies, run a dep security pass, or process CVE findings from govulncheck. Produces one commit per logical dependency group on a dedicated branch so failures are attributable and revertable.
Perform comprehensive code reviews for TypeScript projects, analyzing type safety, best practices, performance, security, and code quality with actionable feedback
Commit staged/unstaged changes and push to the remote branch in one step
SpringBlade 通用 Git 提交工具。基于 Gitmoji 规范生成提交信息。当用户要求提交代码、commit 变更、生成 commit message、或使用 /blade-commit 时触发。默认强制简单模式（gitmoji + 一句话描述），仅当显式传入 --d 或 --detail 参数时才启用详细模式（gitmoji + conventional commit + 变更列表）。只执行 commit，绝不 push 或执行其他远程操作。确保每次提交都带有 gitmoji 图标。
Avue 组件代码生成与配置指南。当用户需要创建、配置或生成基于 Avue (avue-crud, avue-form, avue-tree 等) 的 Vue 页面代码时使用此 skill。覆盖 CRUD 表格、表单、树组件、数据展示等全部 Avue 组件。支持 Composition API 和 Options API 两种代码风格。当用户提到 avue、crud表格、动态表单、JSON配置表单、低代码表单、avue-crud、avue-form 等关键词时，务必使用此 skill。
Create distinctive, production-grade frontend interfaces with high design quality. Use this skill when the user asks to build web components, pages, artifacts, posters, or applications (examples include websites, landing pages, dashboards, React components, HTML/CSS layouts, or when styling/beautifying any web UI). Generates creative, polished code and UI design that avoids generic AI aesthetics.
Analyze and optimize Python code performance in critical paths
Set up a dev environment in an existing worktree (make dev + copy secrets)
Switch the current session to work in an existing git worktree
Analyze a GitHub pull request including diff, comments, related issues, and local code context
Create or reuse a git worktree for a pull request or branch so reviews and work happen in isolation
Create a git worktree with a new branch for implementing a fix or feature for a GitHub issue
Update Claude Code releases tracking (guide + landing + version bump)
Check guide/landing synchronization status
How to write and maintain `.claude/skills/*/SKILL.md` files: source-of-truth-first process, verification steps, and conventions.
Reference for the `.ato` declarative DSL: type system, connection semantics, constraint model, and standard library. Use when authoring or reviewing `.ato` code.
LLM-focused code review process for this repo: what to check, how to ground feedback in invariants/tests, and how to verify changes efficiently (including test-report.json).
How the Zig-backed instance graph works (GraphView/NodeReference/EdgeReference), the real Python API surface, and the invariants around allocation, attributes, and cleanup. Use when working with low-level graph APIs, memory management, or building systems that traverse the instance graph.
Instructions for electronics-specific logic and build processes: netlists, PCBs, build steps, and exporters. Use when implementing or modifying build steps, exporters, PCB generation, or BOM/netlist output.
Spec-driven planning for complex design tasks: when to plan, how to write specs as .ato files, and how to verify against requirements.
How the Faebryk component library is structured, how `_F.py` is generated, and the conventions/invariants for adding new library modules. Use when adding or modifying library components, traits, or module definitions.
How the atopile Language Server works (pygls), how it builds per-document graphs for completion/hover/defs, and the invariants for keeping it fast and crash-proof.
Core runtime behavior for the atopile sidebar agent: identity, persistence model, execution rules, and tool recipes.
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.
How the atopile compiler builds and links TypeGraphs from `.ato` (ANTLR front-end → AST → TypeGraph → Linker → DeferredExecutor), plus the key invariants and test entrypoints. Use when modifying the compiler pipeline, grammar, AST visitors, or type resolution.
GROWI testing patterns with Vitest, React Testing Library, and vitest-mock-extended.
Quick spec generation with interactive or automatic mode
Implement approved tasks using TDD with native subagent dispatch. Runs all pending tasks autonomously or selected tasks manually.
Initialize a new specification with detailed project description
Verify completion and success claims with fresh evidence. Use before claiming a task is complete, a fix works, tests pass, or a feature is ready for GO.
GROWI technology stack, build tools, and global commands. Auto-invoked for all GROWI development work.
Investigate implementation failures using root-cause-first debugging. Use when an implementer is blocked, verification fails, or repeated remediation does not converge.
Review a task implementation against approved specs, task boundaries, and verification evidence. Use after an implementer finishes a task, after remediation, or before accepting a task as complete.
Validate feature-level integration after all tasks are implemented. Checks cross-task consistency, full test suite, and overall spec coverage.
Create complete specs (requirements, design, tasks) for all features in roadmap.md using parallel subagent dispatch by dependency wave.
/learn - Pattern Extraction for GROWI
Embedding images in Remotion using the <Img> component
Embedding videos in Remotion - trimming, volume, speed, looping, pitch
Embedding Lottie animations in Remotion.
Systematically debug a problem using a four-phase workflow
Query openspec documents and answer questions based on spec content
Update an existing OpenSpec change from external context
Implement or resume tasks from an OpenSpec change
分析职业健康数据、识别工作相关健康风险、评估职业健康状况、提供个性化职业健康建议。支持与睡眠、运动、心理健康等其他健康数据的关联分析。
分析旅行健康数据、评估目的地健康风险、提供疫苗接种建议、生成多语言紧急医疗信息卡片。支持WHO/CDC数据集成的专业级旅行健康风险评估。
分析一段时间内健康数据的趋势和模式。关联药物、症状、生命体征、化验结果和其他健康指标的变化。识别令人担忧的趋势、改善情况，并提供数据驱动的洞察。当用户询问健康趋势、模式、随时间的变化或"我的健康状况有什么变化？"时使用。支持多维度分析（体重/BMI、症状、药物依从性、化验结果、情绪睡眠），相关性分析，变化检测，以及交互式HTML可视化报告（ECharts图表）。
分析健康目标数据、识别目标模式、评估目标进度,并提供个性化目标管理建议。支持与营养、运动、睡眠等健康数据的关联分析。
分析康复训练数据、识别康复模式、评估康复进展，并提供个性化康复建议
分析营养数据、识别营养模式、评估营养状况，并提供个性化营养建议。支持与运动、睡眠、慢性病数据的关联分析。
分析家族病史、评估遗传风险、识别家庭健康模式、提供个性化预防建议
AI驱动的综合健康分析系统，整合多维度健康数据、识别异常模式、预测健康风险、提供个性化建议。支持智能问答和AI健康报告生成。
生成紧急情况下快速访问的医疗信息摘要卡片。当用户需要旅行、就诊准备、紧急情况或询问"紧急信息"、"医疗卡片"、"急救信息"时使用此技能。提取关键信息（过敏、用药、急症、植入物），支持多格式输出（JSON、文本、二维码），用于急救或快速就医。
Use when deploying changes to staging across relay, relay-dashboard, and relay-cloud repos - coordinates multi-repo branch syncing using git worktrees, automatically triggers staging deployments via GitHub Actions
Use when building multi-agent workflows with the relay broker-sdk - covers the WorkflowBuilder API, DAG step dependencies, agent definitions, step output chaining via {{steps.X.output}}, verification gates, evidence-based completion, owner decisions, dedicated channels, dynamic channel management (subscribe/unsubscribe/mute/unmute), swarm patterns, error handling, event listeners, step sizing rules, authoring best practices, and the lead+workers team pattern for complex steps
Use when coordinating multiple AI agents in real-time - provides inter-agent messaging via MCP tools
Use when creating new Claude Code skills or improving existing ones - ensures skills are discoverable, scannable, and effective through proper structure, CSO optimization, and real examples
Create distinctive, production-grade frontend interfaces with high design quality. Use this skill when the user asks to build web components, pages, or applications. Generates creative, polished code that avoids generic AI aesthetics.
Run headless multi-agent orchestration sessions via Agent Relay. Use when spawning teams of agents, creating channels for coordination, managing agent lifecycle, and running parallel workloads across Claude/Codex/Gemini/Pi/Droid agents.
Use when adding new multi-agent coordination patterns to agent-relay - provides checklist for types, schema, templates, and docs updates
Creates properly formatted Git commits following conventional commit standards for the MCPSpy project. Use when asked to commit changes, stage files, or manage git workflows. Has access to git status, diff, checkout, add, and commit commands.
Handles all Golang testing tasks including running tests, writing new tests, and fixing test failures. Follows MCPSpy testing conventions with require for critical assertions and assert for non-critical ones.
Use this agent when working with prompt injection detection integration tests, including running tests, debugging failures, or adding new test samples.
Use when consolidating open Dependabot PRs into a single branch. Fetches all open Dependabot PRs from the repo, applies dependency updates locally, tests for breakage, and creates a single PR that closes all Dependabot PRs.
Use when MCP server code is modified and needs full E2E verification against a real dbt project. Triggers after changes to recce/mcp_server.py, MCP tool handlers, single-env logic, or error classification. Also use before merging MCP PRs.
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).
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.
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.
Generate new molecules de novo.
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.
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).
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.
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).
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).
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).
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).
Search PubChem database using SMILES strings to retrieve compound information and chemical properties.
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).
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).
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).
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).
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).
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).
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).
Use when the user wants keyword-based academic paper discovery in Paper Study, including requests to search papers by topic, date range, or source such as arXiv, Semantic Scholar, bioRxiv, PubMed, Hugging Face daily papers, or similar Chinese requests about paper search.
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).
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).
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.
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).
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).
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).
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).
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).
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.
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).
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).
Search for similar protein sequences in UniProt Swiss-Prot database using BLAST to identify homologous proteins and functional relationships.
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).
Generate new molecules sampling from the input two warhead fragments.
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).
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-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).
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.
Analyze protein-protein interaction enrichment using STRING database to identify functional networks and pathway associations.
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).
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).
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).
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 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).
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).
Convert a file containing identified issues into GitHub issues. Use after running identify-* commands to create corresponding GitHub issues.
Set up and iterate on the minds app stack (desktop client, workspace server, mngr, forever-claude-template) with a running Docker agent
Interactively triage the user's local engineering backlog file into GitHub issues. Use when the user wants to process their raw thought notes / ticket backlog into proper GitHub issues.
Write high quality, user-facing documentation. Use any time you need to write, improve, or update a significant amount of user-facing documentation (e.g., files in a "docs/" folder or README file).
Identify divergences from the style guide in the $1 library
Send a message to another mngr agent. Use when you need to communicate with a peer agent.
Match tutorial script blocks to e2e pytest functions and add missing tests
Identify places in the $1 library where the docs and code disagree
Come up with good ideas about what to fix. Use when you have to fix something, but you're not sure what.
Convert triaged autoclaude GitHub issues into FIXMEs in the codebase. Use when you want to process issues that have been triaged by authorized users.
Convert a file containing identified issues into a tracked file in current_tasks/. Use after running identify-* commands to create a local record of current issues.
Create FIXME's in the codebase for each of the issues in the given input file.
Write high quality specifications or design docs for a program. Use any time you are asked to write, improve, or update specs / design docs (e.g., files in a `specs/` folder).
Resolve an agent name or description to an exact mngr agent name. Used by other skills that target agents.
Identify inconsistencies in the $1 library
Fix a GitHub issue given its number or URL. Replicates the bug, finds root cause, implements a fix, and opens a PR.
SpringBlade 通用 Git 提交工具。基于 Gitmoji 规范生成提交信息。当用户要求提交代码、commit 变更、生成 commit message、或使用 /blade-commit 时触发。默认强制简单模式（gitmoji + 一句话描述），仅当显式传入 --d 或 --detail 参数时才启用详细模式（gitmoji + conventional commit + 变更列表）。只执行 commit，绝不 push 或执行其他远程操作。确保每次提交都带有 gitmoji 图标。
Avue 组件代码生成与配置指南。当用户需要创建、配置或生成基于 Avue (avue-crud, avue-form, avue-tree 等) 的 Vue 页面代码时使用此 skill。覆盖 CRUD 表格、表单、树组件、数据展示等全部 Avue 组件。支持 Composition API 和 Options API 两种代码风格。当用户提到 avue、crud表格、动态表单、JSON配置表单、低代码表单、avue-crud、avue-form 等关键词时，务必使用此 skill。