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Pymoo Multi Objective Optimizer

K-Dense-AI/claude-scientific-skills

Python framework for multi-objective optimization, offering NSGA-II/III, MOEA/D, benchmark suites, customizable operators, and visualization to help engineering teams explore Pareto fronts and make multi-criteria decisions.

PyOpenMS Mass Spectrometry

K-Dense-AI/claude-scientific-skills

PyOpenMS provides Python bindings for OpenMS to drive complete mass spectrometry workflows, covering data IO, spectral processing, feature/peptide-protein identification, quantitation, and metabolomics pipelines.

Pysam Genomic Toolkit

K-Dense-AI/claude-scientific-skills

Pysam offers Python bindings to htslib for reading and writing SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences, enabling coverage stats, pileup analysis, variant queries, and seamless integration into NGS pipelines.

Therapeutics Data Commons

K-Dense-AI/claude-scientific-skills

Provides AI-ready drug discovery datasets, splits, and benchmarks covering ADME, toxicity, DTI, DDI, and molecular generation so researchers can train, compare, and optimize therapeutic ML models with curated splits and oracles.

PyTorch Lightning Toolkit

pytorch-lightning

K-Dense-AI/claude-scientific-skills

PyTorch Lightning Toolkit streamlines PyTorch model training by organizing LightningModules, LightningDataModules, Trainer configs, callbacks, logging, and distributed strategies for scalable multi-GPU/TPU runs in research or production workflows.

Qiskit Quantum Computing Framework

K-Dense-AI/claude-scientific-skills

Qiskit is the world's leading open-source framework for building, optimizing, and executing quantum circuits. It provides comprehensive capabilities for quantum error mitigation, running algorithms on diverse hardware backends (including IBM Quantum and simulators), and supporting applications in chemistry and machine learning. Essential for researchers entering the quantum computing field.

QuTiP Quantum Toolbox

K-Dense-AI/claude-scientific-skills

QuTiP is a Python toolbox for simulating open and closed quantum systems, offering solvers for master equations, trajectory methods, visualization, and analysis tailored to quantum research, education, and exploratory physics studies.

Advanced Molecular Control

K-Dense-AI/claude-scientific-skills

RDKit delivers a Python-based cheminformatics toolkit for parsing SMILES/SDF, computing descriptors, generating 2D/3D coordinates, fingerprinting, searching substructures, managing reactions, and visualizing molecules, ideal for drug discovery and computational chemistry workflows.

Reactome Pathway Explorer

reactome-database

K-Dense-AI/claude-scientific-skills

Query the Reactome Content and Analysis Services (or the reactome2py client) to fetch pathway hierarchies, map genes, run overrepresentation/expression analyses, and explore disease interactions for systems biology research.

Agency Research Grant Writing

research-grants

K-Dense-AI/claude-scientific-skills

Craft competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC by aligning narratives with agency review criteria, detailing budgets, personnel plans, and broader impacts, and incorporating required AI-generated schematics via the scientific-schematics skill.

Research Information Lookup

research-lookup

K-Dense-AI/claude-scientific-skills

Real-time research lookup that auto-selects between Parallel Chat API and Perplexity sonar-pro-search to gather papers, facts, market data, and cited findings.

Cloud Molecular Modeling Workflows

K-Dense-AI/claude-scientific-skills

Cloud-native Rowan orchestrates medicinal chemistry and molecular modeling pipelines via a Python API, offering pKa prediction, docking, descriptors, dynamics, and AI-driven structure workflows for scalable batch screening without local HPC.

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