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Materials Structure Toolkit

K-Dense-AI/claude-scientific-skills

Pymatgen is a Python toolkit for computational materials science that creates, manipulates, and analyzes crystal structures, converts among 100+ formats, computes phase diagrams, and accesses Materials Project data for high-throughput workflows.

Pymoo Multi Objective Optimizer

K-Dense-AI/claude-scientific-skills

Pymoo is a Python optimization toolkit focused on multi-objective engineering problems, providing algorithms like NSGA-II/III, MOEA/D, customizable operators, benchmarks, and visualization helpers for Pareto analysis and constrained search.

Pysam Genomic Toolkit

K-Dense-AI/claude-scientific-skills

Pysam provides Python bindings to htslib for reading and writing SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, letting developers query regions, compute coverage, and orchestrate NGS pipelines.

QuTiP Quantum Toolbox

K-Dense-AI/claude-scientific-skills

QuTiP is a Python library for simulating open and closed quantum systems, offering solvers, analysis, visualization, and advanced methods aimed at research, teaching, and modeling Lindblad dynamics or decoherence.

RDKit Cheminformatics Toolkit

K-Dense-AI/claude-scientific-skills

RDKit Cheminformatics Toolkit delivers Python APIs for reading/writing SMILES/SDF/InChI, sanitizing molecules, computing descriptors and fingerprints, running substructure searches/reactions, and visualizing structures for drug discovery and cheminformatics workflows.

Rowan Quantum Chemistry

K-Dense-AI/claude-scientific-skills

Rowan delivers cloud-based quantum chemistry via a Python API for pKa estimation, geometry optimization, conformer search, docking, and AI protein cofolding, giving scientists remote compute and automation for molecular workflows without local setup.

Microbiome Bioinformatics Toolkit

K-Dense-AI/claude-scientific-skills

scikit-bio is a Python biological data toolkit for sequence handling, alignments, phylogenetic trees, microbial diversity metrics, and ecological stats, ideal for microbiome research pipelines that need FASTA/Newick I/O and ordination methods.

SimPy Simulation Framework

K-Dense-AI/claude-scientific-skills

SimPy is a Python-based discrete-event simulation framework for modeling queues, resource contention, process-driven workflows, and system interactions across manufacturing, logistics, service operations, and network scenarios before deployment.

Python Symbolic Math

K-Dense-AI/claude-scientific-skills

Guides using SymPy for symbolic mathematics in Python, covering algebra, calculus, linear systems, physics, number theory, geometry, and code generation when exact formulas or symbolic output is required instead of numeric approximations.

USPTO Patent Database

K-Dense-AI/claude-scientific-skills

Provides access to USPTO PatentSearch, PEDS, TSDR, and related APIs for patent and trademark searches, examination history, assignments, citations, and litigation data, with helper scripts for Python-based IP research and portfolio insights.

Pyzotero Zotero Client

K-Dense-AI/claude-scientific-skills

Pyzotero wraps Zotero Web API v3 so Python scripts can read, write, search, and export references, collections, tags, and attachments. Use it to automate citation workflows, upload PDFs, or build Zotero-integrated research tools.

MCP Server Builder

mcp-server-builder

alirezarezvani/claude-skills

Automates scaffolding production-ready MCP servers from OpenAPI contracts, covering tool manifest generation, validation, versioning, and runtime selection for Python or TypeScript agents.

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