Skill Claude CodeCodex
MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differential equations, optimization, statistics, or creating scientific visualizations. Also use when…
Skill Claude CodeCodex
Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publication. For quick statistical plots use seaborn; for interactive plots use plotly; for…
Skill Claude CodeCodex
Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
Skill Claude CodeCodex
Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.
Skill Claude CodeCodex
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
Skill Claude CodeCodex
Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks…
Skill Claude CodeCodex
Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for heart rate…
Skill Claude CodeCodex
Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular…
Skill Claude CodeCodex
Self-hosted, open-source alternative to Google NotebookLM for AI-powered research and document analysis. Use when organizing research materials into notebooks, ingesting diverse content sources (PDFs, videos, audio, web pages, Office documents), generating AI-powered notes and summaries, creating multi-speaker…
Skill Claude CodeCodex
Search 10 academic paper databases via REST APIs for research papers, preprints, and scholarly articles. Covers PubMed, PMC (full text), bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall. Use when searching for papers, citations, DOI/PMID lookups, abstracts, full text, open access…
Skill Claude CodeCodex
Chat with your agent about projects, recommendations, and canonical papers in Paperzilla. Use when users ask for recent project recommendations, canonical paper details, markdown-based summaries, recommendation feedback, feed export, or Atom feed URLs.
Skill Claude CodeCodex
Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be…
Skill Claude CodeCodex
Structured manuscript/grant review with checklist-based evaluation. Use when writing formal peer reviews with specific criteria methodology assessment, statistical validity, reporting standards compliance (CONSORT/STROBE), and constructive feedback. Best for actual review writing, manuscript revision. For evaluating…
Skill Claude CodeCodex
Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability across IBM/Google/Rigetti/IonQ. Best for variational algorithms (VQE, QAOA), quantum neural networks, and integration with…
MCP server Claude CodeCodexCursor +2
MCP server "skill-shelf" as configured in halflifezyf2680/Skill-Shelf. Runs locally from the skill-shelf npm package.
MCP server Claude CodeCodexCursor +2
MCP server "forge-think" as configured in halflifezyf2680/forge-think. Runs /absolute/path/to/forge-think/server.py with python.