Master systematic debugging techniques, profiling tools, and root cause analysis to efficiently track down bugs across any codebase or technology stack. Use when investigating bugs, performance...
Search and navigate The Fold's skill lattice using meta-tooling. Use for finding functions, exploring dependencies, type-aware queries, and cross-reference analysis. Invoke when searching for...
Technical research methodology with YAGNI/KISS/DRY principles. Phases: scope definition, information gathering, analysis, synthesis, recommendation. Capabilities: technology evaluation,...
Assess a codebase's readiness for autonomous agent development and provide tailored recommendations. Use when asked to evaluate how well a project supports unattended agent execution, assess...
Analyzes codebases to generate comprehensive documentation including structure, languages, frameworks, dependencies, design patterns, and technical debt. Use when user says "analyze repository",...
Use when auditing a codebase for semantic duplication - functions that do the same thing but have different names or implementations. Especially useful for LLM-generated codebases where new...
Use this skill when the user wants to analyze or explore a codebase (remote repository or local repository) using Repomix. Triggers on: 'analyze this repo', 'explore codebase', 'what's the...
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
Access USPTO APIs for patent/trademark searches, examination history (PEDS), assignments, citations, office actions, TSDR, for IP analysis and prior art searches.
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
Analyze a codebase to extract its conventions, patterns, and style. Spawns specialized analyzer agents that each focus on one aspect (structure, naming, patterns, testing, frontend). Generates a...
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and...
Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration...
Evaluate how well a codebase supports autonomous AI development. Analyzes repositories across eight technical pillars (Style & Validation, Build System, Testing, Documentation, Dev Environment,...
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and...
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases,...