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Found 35 Skills
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
Use when designing chaos experiments, implementing failure injection frameworks, or conducting game day exercises. Invoke for chaos experiments, resilience testing, blast radius control, game days, antifragile systems.
Review only changes since last commit using impact analysis. Token-efficient delta review with automatic blast-radius detection.
Review a PR or branch diff using the knowledge graph for full structural context. Outputs a structured review with blast-radius analysis.
Performs security-focused differential review of code changes (PRs, commits, diffs). Adapts analysis depth to codebase size, uses git history for context, calculates blast radius, checks test coverage, and generates comprehensive markdown reports. Automatically detects and prevents security regressions.
Python toolkit for computational biology. Use when asked to "parse FASTA", "read GenBank", "query NCBI", "run BLAST", "analyze protein structure", "build phylogenetic tree", or work with biological sequences. Handles sequence I/O, database access, alignments, structure analysis, and phylogenetics.
NCBI BLAST sequence similarity search using BioPython. Use when a user wants to run BLAST programmatically with blastn/blastp and retrieve results in JSON format.
Plan safe refactors using blast radius and dependency mapping
Searches for homologous protein sequences using MMseqs2 (fast, default) or BLAST (comprehensive, fallback). Trigger this whenever the user provides a protein sequence or FASTA file and asks to find homologues, sequence matches, or wants to infer protein function based on sequence similarity, but not when the user wants to infer protein function based on structural similarity.
Use when planning, running, or learning from chaos engineering experiments. Triggers on "chaos experiment", "fault injection", "gameday", "resilience test", "blast radius", "steady state", "abort criteria", "Chaos Toolkit", "Chaos Mesh", "Litmus", "Gremlin", "AWS FIS", or any deliberate failure-injection question. Ships experiment designer, blast-radius calculator, and postmortem generator (all stdlib Python), 4 references on chaos principles + experiment design + attack taxonomy + tooling landscape, and a /chaos-experiment slash command. Composes with feature-flags-architect (kill switches as abort triggers) and kubernetes-operator (common chaos targets).
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.