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reference-mmcif
Reference documentation for PDBx/mmCIF dictionary queries and category lookup
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tools scientific computing AI Skills
Discover tools scientific computing skills, compare source repositories and read the instructions for each workflow.
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phoenix-capital-exit-investigator
Capital allocation and exit recycling investigator. Use when working on low-confidence modules like capital allocation and exit recycling.
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cross-system-analyst
Analyzes relationships and connections between body systems, identifying root causes and hidden patterns in medical data.
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html-builder
Transforms medical analysis reports into stunning, personalized, data-driven Health Realms using intelligent visualization.
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data-structurer
Extracts structured, chart-ready JSON data from medical analysis for visualization, including diagnoses, timeline, prognosis, and supplement schedules.
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medical-analysis
Agentic medical analyst that explores extracted documents iteratively like a real physician - forming hypotheses, seeking evidence, cross-referencing, and building comprehensive analysis through multiple explor...
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research-voids
Research voids (cognitive gaps, unchartable territories). Daily. Outputs research notes for voids articles.
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rfd3-reference
RFdiffusion3 protein design reference. Use when working with RFD3, contigs, symmetry, hotspots, fixed atoms, RASA conditioning, H-bond conditioning, or Foundry API. Covers all input parameters, design types, an...
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GitHub
bindcraft-reference
BindCraft protein binder design reference. Use when working with AF2 backpropagation, binder design, interface optimization, PyRosetta metrics, design filtering, or comparing with RFdiffusion approaches.
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GitHub
ligandmpnn-reference
LigandMPNN sequence design reference. Use when working with LigandMPNN, ProteinMPNN, sequence design, amino acid biasing, fixed residues, temperature, side chain packing, or membrane protein design.
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deep-research
Perform comprehensive research using the diffusion research loop - parallel worker agents, iterative gap detection, and structured synthesis. Use when you need thorough, multi-perspective research with citation...
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foundry-research
AI-powered research skill with five workflows - chat (single-model conversation), consensus (multi-model synthesis), thinkdeep (systematic investigation), ideate (creative brainstorming), and deep (multi-phase...
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calc-bode
python-controlを使用して、メカニカルシステムの状態空間モデルから伝達関数（Bode Plot）を計算・表示する
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convergence-diagnostics
MCMC convergence diagnostics using CmdStanPy and ArviZ
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research-planner
Create detailed research plans by decomposing structured prompts into subtopics, search strategies, and agent deployment configurations. Extracted from Phase 2 of research-executor for standalone planning capab...
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goap-orchestrator
Central Goal-Oriented Action Planning orchestrator that plans and executes clinical analysis pipelines
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use-research
Find relevant research and guide implementation based on it. Use when implementing features, fixing bugs, or exploring techniques where existing research in docs/research/ may provide guidance. Trigger phrases...
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academic-writing
Create polished research manuscripts with professional formatting and scholarly precision. Guides the full writing process from outline to submission-ready document.
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hypothesis-dev
Develop testable scientific hypotheses through systematic observation analysis, literature grounding, and rigorous experimental design. Guides the journey from observation to testable prediction.
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research
Deep research using web, docs, and code search. Triggers on: "research", "look into", "what's the best", "how should I", evaluating libraries, unfamiliar patterns, state of the art.
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scifi-figure-generator
Generate high-quality scientific figures for SCI papers based on project code analysis
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data-analysis
Statistical analysis and data exploration workflows for effective data-driven insights. Use when analyzing datasets, performing exploratory data analysis (EDA), statistical hypothesis testing, data visualizatio...
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data-analysis
Analyze and interpret data to generate meaningful insights using statistical methods and visualization. Use when working with datasets, metrics, statistics, or when insights from data are needed.
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quota-manager
Manage Gemini Deep Research API quotas with rate limiting, exponential backoff, and client-side tracking. Use when handling API quota errors, implementing rate limiting, batch job submission, or when asked abou...
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