Antibody and nanobody binder design using BoltzGen (BoltzGen diffusion + Protenix refolding). Covers entity YAML specification, CLI invocation, protocol selection (nanobody-anything / antibody-anything), MSA modes, and output parsing. Use this skill whenever the user needs to design an antibody or nanobody binder against a protein target.
AI-driven patient-to-trial matching for precision medicine and oncology. Given a patient profile (disease, molecular alterations, stage, prior treatments), discovers and ranks clinical trials from ClinicalTrials.gov using multi-dimensional matching across molecular eligibility, clinical criteria, drug-biomarker alignment, evidence strength, and geographic feasibility. Produces a quantitative Trial Match Score (0-100) per trial with tiered recommendations and a comprehensive markdown report. Use when oncologists, molecular tumor boards, or patients ask about clinical trial options for specific cancer types, biomarker profiles, or post-progression scenarios.
Generates comprehensive drug research reports with compound disambiguation, evidence grading, and mandatory completeness sections. Covers identity, chemistry, pharmacology, targets, clinical trials, safety, pharmacogenomics, and ADMET properties. Use when users ask about drugs, medications, therapeutics, or need drug profiling, safety assessment, or clinical development research.
Comprehensive computational validation of drug targets for early-stage drug discovery. Evaluates targets across 10 dimensions (disambiguation, disease association, druggability, chemical matter, clinical precedent, safety, pathway context, validation evidence, structural insights, validation roadmap) using 60+ ToolUniverse tools. Produces a quantitative Target Validation Score (0-100) with GO/NO-GO recommendation. Use when users ask about target validation, druggability assessment, target prioritization, or "is X a good drug target for Y?"
Predict patient response to immune checkpoint inhibitors (ICIs) using multi-biomarker integration. Given a cancer type, somatic mutations, and optional biomarkers (TMB, PD-L1, MSI status), performs systematic analysis across 11 phases covering TMB classification, neoantigen burden estimation, MSI/MMR assessment, PD-L1 evaluation, immune microenvironment profiling, mutation-based resistance/sensitivity prediction, clinical evidence retrieval, and multi-biomarker score integration. Generates a quantitative ICI Response Score (0-100), response likelihood tier, specific ICI drug recommendations with evidence, resistance risk factors, and a monitoring plan. Use when oncologists ask about immunotherapy eligibility, checkpoint inhibitor selection, or biomarker-guided ICI treatment decisions.
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance mechanisms, matches clinical trials. Use when oncologist asks about treatment options for specific mutations (EGFR, KRAS, BRAF, etc.), therapy resistance, or clinical trial eligibility.
Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data. Matches symptoms to HPO terms, identifies candidate diseases from Orphanet/OMIM, prioritizes genes for testing, interprets variants of uncertain significance. Use when clinician asks about rare disease diagnosis, unexplained phenotypes, or genetic testing interpretation.
Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use for standard RL experiments, quick prototyping, and well-documented algorithm implementations. Best for single-agent RL with Gymnasium environments. For high-performance parallel training, multi-agent systems, or custom vectorized environments, use pufferlib instead.
Detect and analyze adverse drug event signals using FDA FAERS data, drug labels, disproportionality analysis (PRR, ROR, IC), and biomedical evidence. Generates quantitative safety signal scores (0-100) with evidence grading. Use for post-market surveillance, pharmacovigilance, drug safety assessment, adverse event investigation, and regulatory decision support.
Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches. Creates actionable reports with candidate compounds, ADMET profiles, and synthesis feasibility. Use when users ask to find small molecules for a target, identify novel binders, perform virtual screening, or need hit-to-lead compound identification.
Comprehensive chemical safety and toxicology assessment integrating ADMET-AI predictions, CTD toxicogenomics, FDA label safety data, DrugBank safety profiles, and STITCH chemical-protein interactions. Performs predictive toxicology (AMES, DILI, LD50, carcinogenicity), organ/system toxicity profiling, chemical-gene-disease relationship mapping, regulatory safety extraction, and environmental hazard assessment. Use when asked about chemical toxicity, drug safety profiling, ADMET properties, environmental health risks, chemical hazard assessment, or toxicogenomic analysis.
Comprehensive CRISPR screen analysis for functional genomics. Analyze pooled or arrayed CRISPR screens (knockout, activation, interference) to identify essential genes, synthetic lethal interactions, and drug targets. Perform sgRNA count processing, gene-level scoring (MAGeCK, BAGEL), quality control, pathway enrichment, and drug target prioritization. Use for CRISPR screen analysis, gene essentiality studies, synthetic lethality detection, functional genomics, drug target validation, or identifying genetic vulnerabilities.
Archive a completed change in the experimental workflow. Use when the user wants to finalize and archive a change after implementation is complete.
Verify implementation matches change artifacts. Use when the user wants to validate that implementation is complete, correct, and coherent before archiving.
Use when the user asks about Synthetic Monitoring check health, status, or trends. Trigger on phrases like "are my checks healthy", "check status", "synth check", "probe status", or when users mention specific check names or IDs. For investigating failing checks use synth-investigate-check. For creating or managing checks use synth-manage-checks.
(Experimental) End-to-end observability setup for Grafana Cloud. Covers instrumentation, SLOs, alerting, synthetic monitoring, k6 load testing, IRM on-call, dashboards, cost optimization, and GitOps export.
將已完成的人工檢查項目從 tasks artifact 遷移到 docs/manual-review-archive.md，保留追溯資訊。
Autonomous experiment loop for optimization research. Use when the user wants to: - Optimize a metric through systematic experimentation (ML training loss, test speed, bundle size, build time, etc.) - Run an automated research loop: try an idea, measure it, keep improvements, revert regressions, repeat - Set up autoresearch for any codebase with a measurable optimization target Implements the autoresearch pattern with MAD-based confidence scoring, git branch isolation, and structured experiment logging.
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
Comprehensive patient stratification for precision medicine by integrating genomic, clinical, and therapeutic data. Given a disease/condition, genomic data (germline variants, somatic mutations, expression), and optional clinical parameters, performs multi-phase analysis across 9 phases covering disease disambiguation, genetic risk assessment, disease-specific molecular stratification, pharmacogenomic profiling, comorbidity/DDI risk, pathway analysis, clinical evidence and guideline mapping, clinical trial matching, and integrated outcome prediction. Generates a quantitative Precision Medicine Risk Score (0-100) with risk tier assignment (Low/Intermediate/High/Very High), treatment algorithm (1st/2nd/3rd line), pharmacogenomic guidance, clinical trial matches, and monitoring plan. Use when clinicians ask about patient risk stratification, treatment selection, prognosis prediction, or personalized therapeutic strategy across cancer, metabolic, cardiovascular, neurological, or rare diseases.
Pre-built research workflow templates that execute complete multi-step analyses from a single user prompt. Triggers on gene analysis, target validation, literature review, differential expression, clinical queries, researcher profiling, drug repurposing, or molecular dynamics simulation. Use when the user's query matches a Recipe pattern defined in SCIENCE.md.
Conducts a focused review from ONE specific specialist's perspective (e.g., Security Specialist, Performance Expert). Use when the user requests "Ask [specialist role] to review [target]", "Get [specialist]'s opinion on [topic]", "Have [role] review [code/component]", or when they want deep expertise in ONE specific domain. Do NOT use for comprehensive multi-perspective reviews (use architecture-review instead) or for listing available specialists (use list-members instead).
Spec doğrulama, implementation karşılaştırma ve completeness kontrolü rehberi.
