Tools

Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.

Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.

Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system dynamics, and educational simulations. NOT for circuit-based quantum computing—use qiskit, cirq, or pennylane for quantum algorithms and hardware execution.

Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pipelines, faster pandas replacement. For larger-than-RAM data use dask or vaex.

Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.

Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

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.

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.

Use when you have a plan file ready and need to create an isolated git worktree for implementation - creates worktree in parent directory following project conventions and moves the plan file

Analyzes Claude Code usage patterns and provides comprehensive recommendations. Runs usage analysis, discovers GitHub community resources, suggests CLAUDE.md improvements, and fetches latest docs on-demand. Use when user wants to optimize their Claude Code workflow, create configurations (agents/skills/commands), or set up project documentation.

This skill should be used when the user asks to "follow red team methodology", "perform bug bounty hunting", "automate reconnaissance", "hunt for XSS vulnerabilities", "enumerate subdomains", or needs security researcher techniques and tool configurations from top bug bounty hunters.

This skill should be used when the user asks to "search for exposed devices on the internet," "perform Shodan reconnaissance," "find vulnerable services using Shodan," "scan IP ranges with Shodan," or "discover IoT devices and open ports." It provides comprehensive guidance for using Shodan's search engine, CLI, and API for penetration testing reconnaissance.

This skill should be used when the user asks to "escalate privileges on Linux", "find privesc vectors on Linux systems", "exploit sudo misconfigurations", "abuse SUID binaries", "exploit cron jobs for root access", "enumerate Linux systems for privilege escalation", or "gain root access from low-privilege shell". It provides comprehensive techniques for identifying and exploiting privilege escalation paths on Linux systems.

This skill should be used when the user asks to "create bash scripts", "automate Linux tasks", "monitor system resources", "backup files", "manage users", or "write production shell scripts". It provides ready-to-use shell script templates for system administration.

This skill should be used when the user asks to "identify web application vulnerabilities", "explain common security flaws", "understand vulnerability categories", "learn about injection attacks", "review access control weaknesses", "analyze API security issues", "assess security misconfigurations", "understand client-side vulnerabilities", "examine mobile and IoT security flaws", or "reference the OWASP-aligned vulnerability taxonomy". Use this skill to provide comprehensive vulnerability definitions, root causes, impacts, and mitigation strategies across all major web security categories.

This skill should be used when the user asks to "test for XSS vulnerabilities", "perform cross-site scripting attacks", "identify HTML injection flaws", "exploit client-side injection vulnerabilities", "steal cookies via XSS", or "bypass content security policies". It provides comprehensive techniques for detecting, exploiting, and understanding XSS and HTML injection attack vectors in web applications.