beacon-repeater
MLX↔JAX bidirectional beacon-repeater with spectral gap random walk,
beads-issue-tracker
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beeper-mcp
Unified messaging via Beeper Desktop MCP. Search chats, send messages, manage conversations across all networks (iMessage, WhatsApp, Signal, Telegram, Discord, Slack, etc.)
benchling-integration
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
bidirectional-navigator
Safe proof ↔ theorem navigation with non-backtracking constraint.
bifunctor-bridge
Bifunctors: two-argument functors for product categories.
bigquery-asi-interleave
Interleave layer bridging the BigQuery cluster to plurigrid/asi. Routes BigQuery queries through asi's DuckDB stack, wires patent search into asi knowledge graph, connects Looker Studio dashboards to CatColab, and feeds BigQuery ML into the lolita physics emulation pipeline.
biomni
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.
biopython
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.
biorxiv-database
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
bioservices
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).
bitbucket
Interact with Bitbucket repositories and pull requests using the BITBUCKET_TOKEN environment variable. Use when working with code hosted on Bitbucket or managing Bitbucket resources via API.
bivector-forum
Community knowledge from bivector.net - GA tutorials, discussions, and best practices
bmorphism-ies-env
Documentation and orchestration for the bmorphism/ies flox environment toolkit
bmorphism-video-interleave
bmorphism Video Archive Interleave
cc-trace
Interactive assistant for intercepting, debugging, analyzing and reviewing Claude Code API requests using mitmproxy. Guides setup, certificate configuration, and active traffic inspection via web or CLI interface. Supports learning Claude Code internals, debugging issues, and optimizing API usage.
botnet-disruption
Coordinated botnet takedown methodologies — sinkholing, infrastructure mapping, legal frameworks, BGP intervention, and post-disruption analysis. Studies Operation Endgame, Badbox 2.0, and emerging blockchain C2 countermeasures. Defensive disruption for authorized law enforcement, CERT, and academic research contexts.
botnet-studies
Botnet architecture taxonomy, detection techniques, and defensive analysis. Covers C2 topologies, DGA analysis, fast-flux detection, P2P overlay mapping, blockchain C2, and ML-based traffic fingerprinting. Defensive research for understanding and countering distributed malicious infrastructure.
braindance-validator
Validates GF(3) conservation across triadic braindance replays. Ensures MINUS+ERGODIC+PLUS=0.
brenda-database
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 metabolic pathway analysis.
c
World C Skill
cat-tripartite
'Category Theory Tripartite: SICP generic dispatch, CTP Racket categories,
catalyst-chemical
Chemical reaction network modeling with Catalyst.jl. Autopoietic systems,
categorical-composition
**Category:** Phase 3 Core - Compositional Architecture
catp
Category-theoretic pipes with GF(3) flow balance checking. Validates
cats-focus-monad
Cats Focus + Monad: Lawful composition for effect management
cellxgene-census
Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.
cgx-acquisition-re
Reverse engineer CGX Cognionics Quick-20 EEG acquisition protocol using MCP RE tooling (Binary Ninja, Ghidra, radare2)
chembl-database
Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
chemical-abstract-machine
Berry & Boudol''s CHAM: computation as chemical reactions on multisets.
chemical-organization-theory
**Category:** Phase 3 Core - Autopoietic Systems
cirq
Quantum computing framework for building, simulating, optimizing, and executing quantum circuits. Use this skill when working with quantum algorithms, quantum circuit design, quantum simulation (noiseless or noisy), running on quantum hardware (Google, IonQ, AQT, Pasqal), circuit optimization and compilation, noise modeling and characterization, or quantum experiments and benchmarking (VQE, QAOA, QPE, randomized benchmarking).
citation-management
Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.
claude-in-chrome-troubleshooting
Diagnose and fix Claude in Chrome MCP extension connectivity issues. Use when mcp__claude-in-chrome__* tools fail, return "Browser extension is not connected", or behave erratically.
claude-opus-4-5-migration
Migrate prompts and code from Claude Sonnet 4.0, Sonnet 4.5, or Opus 4.1 to Opus 4.5. Use when the user wants to update their codebase, prompts, or API calls to use Opus 4.5. Handles model string updates and prompt adjustments for known Opus 4.5 behavioral differences. Does NOT migrate Haiku 4.5.
claude-questions-leaderboard
Track Claude''s best and worst questions in DuckDB. Use when Claude asks a notably good or bad question, or to review question quality. Triggers: leaderboard, bad question, good question, question quality.
clifford-acset-bridge
Bridge between Clifford Algebras (ganja.js/Grassmann.jl) and ACSets with grade-preserving morphisms
clinical-decision-support
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis.
clinical-reports
Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.
clinicaltrials-database
Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.
clinpgx-database
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
clinvar-database
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
cloudflare-deploy
Deploy applications and infrastructure to Cloudflare using Workers, Pages, and related platform services. Use when the user asks to deploy, host, publish, or set up a project on Cloudflare.
cloudflare
Comprehensive Cloudflare platform skill covering Workers, Pages, storage (KV, D1, R2), AI (Workers AI, Vectorize, Agents SDK), networking (Tunnel, Spectrum), security (WAF, DDoS), and infrastructure-as-code (Terraform, Pulumi). Use for any Cloudflare development task.
codereview-roasted
Brutally honest code review in the style of Linus Torvalds, focusing on data structures, simplicity, and pragmatism. Use when you want critical, no-nonsense feedback that prioritizes engineering fundamentals over style preferences.
colored-vertex-model
Colored stochastic six-vertex model with rainbow initial data, projection properties, and height functions tracking particle counts by color.
comfy-skills
Manage and deploy ComfyUI workflow skills using the comfy-skills CLI.
Command Development
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.
commit-security-scan
Analyze code changes for security vulnerabilities using LLM reasoning and threat model patterns. Use for PR reviews, pre-commit checks, or branch comparisons.
comonad-context
Comonads: dual to Monad. Extract + Extend.
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