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Add support for Qiskit from IBM: software stack for quantum computing and algorithms research. Build, optimize, and execute quantum workloads at scale.
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.claude-plugin/marketplace.json

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},
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"metadata": {
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"description": "Claude scientific skills from K-Dense Inc",
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"version": "2.5.1"
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"version": "2.6.0"
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},
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"plugins": [
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{
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"./scientific-skills/pysam",
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"./scientific-skills/pytdc",
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"./scientific-skills/pytorch-lightning",
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"./scientific-skills/qiskit",
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"./scientific-skills/qutip",
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"./scientific-skills/rdkit",
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"./scientific-skills/reportlab",

README.md

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# Claude Scientific Skills
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[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE.md)
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[![Skills](https://img.shields.io/badge/Skills-126-brightgreen.svg)](#whats-included)
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[![Skills](https://img.shields.io/badge/Skills-127-brightgreen.svg)](#whats-included)
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A comprehensive collection of **126+ ready-to-use scientific skills** for Claude, created by the K-Dense team. Transform Claude into your AI research assistant capable of executing complex multi-step scientific workflows across biology, chemistry, medicine, and beyond.
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A comprehensive collection of **127+ ready-to-use scientific skills** for Claude, created by the K-Dense team. Transform Claude into your AI research assistant capable of executing complex multi-step scientific workflows across biology, chemistry, medicine, and beyond.
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These skills enable Claude to seamlessly work with specialized scientific libraries, databases, and tools across multiple scientific domains:
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- 🧬 Bioinformatics & Genomics - Sequence analysis, single-cell RNA-seq, gene regulatory networks, variant annotation, phylogenetic analysis
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## 📦 What's Included
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This repository provides **126+ scientific skills** organized into the following categories:
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This repository provides **127+ scientific skills** organized into the following categories:
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- **26+ Scientific Databases** - Direct API access to OpenAlex, PubMed, ChEMBL, UniProt, COSMIC, ClinicalTrials.gov, and more
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- **53+ Python Packages** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioPython, PennyLane, and others
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- **54+ Python Packages** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioPython, PennyLane, Qiskit, and others
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- **15+ Scientific Integrations** - Benchling, DNAnexus, LatchBio, OMERO, Protocols.io, and more
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- **20+ Analysis & Communication Tools** - Literature review, scientific writing, peer review, document processing
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- **Multi-Step Workflows** - Execute complex pipelines with a single prompt
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### 🎯 **Comprehensive Coverage**
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- **126+ Skills** - Extensive coverage across all major scientific domains
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- **127+ Skills** - Extensive coverage across all major scientific domains
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- **26+ Databases** - Direct access to OpenAlex, PubMed, ChEMBL, UniProt, COSMIC, and more
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- **53+ Python Packages** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, PennyLane, and others
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- **54+ Python Packages** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, PennyLane, Qiskit, and others
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### 🔧 **Easy Integration**
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- **One-Click Setup** - Install via Claude Code or MCP server
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- Dimensionality reduction: UMAP-learn
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- Statistical modeling: statsmodels
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#### 🔮 **Materials Science, Chemistry & Physics** (4 skills)
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#### 🔮 **Materials Science, Chemistry & Physics** (7 skills)
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- Materials: Pymatgen
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- Metabolic modeling: COBRApy
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- Astronomy: Astropy
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- Quantum computing: Cirq
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- Quantum computing: Cirq, PennyLane, Qiskit, QuTiP
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#### ⚙️ **Engineering & Simulation** (3 skills)
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- Computational fluid dynamics: FluidSim

docs/scientific-skills.md

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- **PyMOO** - Python framework for multi-objective optimization using evolutionary algorithms. Provides implementations of state-of-the-art algorithms including NSGA-II, NSGA-III, MOEA/D, SPEA2, and reference-point based methods. Features include: support for constrained and unconstrained optimization, multiple problem types (continuous, discrete, mixed-variable), performance indicators (hypervolume, IGD, GD), visualization tools (Pareto front plots, convergence plots), and parallel evaluation support. Supports custom problem definitions, algorithm configuration, and result analysis. Designed for engineering design, parameter optimization, and any problem requiring optimization of multiple conflicting objectives simultaneously. Use cases: multi-objective optimization problems, Pareto-optimal solution finding, engineering design optimization, and research in evolutionary computation
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- **PyTorch Lightning** - Deep learning framework that organizes PyTorch code to eliminate boilerplate while maintaining full flexibility. Automates training workflows (40+ tasks including epoch/batch iteration, optimizer steps, gradient management, checkpointing), supports multi-GPU/TPU training with DDP/FSDP/DeepSpeed strategies, includes LightningModule for model organization, Trainer for automation, LightningDataModule for data pipelines, callbacks for extensibility, and integrations with TensorBoard, Wandb, MLflow for experiment tracking
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- **PennyLane** - Cross-platform Python library for quantum computing, quantum machine learning, and quantum chemistry. Enables building and training quantum circuits with automatic differentiation, seamless integration with PyTorch/JAX/NumPy, and device-independent execution across simulators and quantum hardware (IBM, Amazon Braket, Google, Rigetti, IonQ). Key features include: quantum circuit construction with QNodes (quantum functions with automatic differentiation), 100+ quantum gates and operations (Pauli, Hadamard, rotation, controlled gates), circuit templates and layers for common ansatze (StronglyEntanglingLayers, BasicEntanglerLayers, UCCSD for chemistry), gradient computation methods (parameter-shift rule for hardware, backpropagation for simulators, adjoint differentiation), quantum chemistry module (molecular Hamiltonian construction, VQE for ground state energy, differentiable Hartree-Fock solver), ML framework integration (TorchLayer for PyTorch models, JAX transformations, TensorFlow deprecated), built-in optimizers (Adam, GradientDescent, QNG, Rotosolve), measurement types (expectation values, probabilities, samples, state vectors), device ecosystem (default.qubit simulator, lightning.qubit for performance, hardware plugins for IBM/Braket/Cirq/Rigetti/IonQ), and Catalyst for just-in-time compilation with adaptive circuits. Supports variational quantum algorithms (VQE, QAOA), quantum neural networks, hybrid quantum-classical models, data encoding strategies (angle, amplitude, IQP embeddings), and pulse-level programming. Use cases: variational quantum eigensolver for molecular simulations, quantum circuit machine learning with gradient-based optimization, hybrid quantum-classical neural networks, quantum chemistry calculations with differentiable workflows, quantum algorithm prototyping with hardware-agnostic code, quantum machine learning research with automatic differentiation, and deploying quantum circuits across multiple quantum computing platforms
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- **Qiskit** - World's most popular open-source quantum computing framework for building, optimizing, and executing quantum circuits with 13M+ downloads and 74% developer preference. Provides comprehensive tools for quantum algorithm development including circuit construction with 100+ quantum gates (Pauli, Hadamard, CNOT, rotation gates, controlled gates), circuit transpilation with 83x faster optimization than competitors producing circuits with 29% fewer two-qubit gates, primitives for execution (Sampler for bitstring measurements and probability distributions, Estimator for expectation values and observables), visualization tools (circuit diagrams in matplotlib/LaTeX, result histograms, Bloch sphere, state visualizations), backend-agnostic execution (local simulators including StatevectorSampler and Aer, IBM Quantum hardware with 100+ qubit systems, IonQ trapped ion, Amazon Braket multi-provider), session and batch modes for iterative and parallel workloads, error mitigation with configurable resilience levels (readout error correction, ZNE, PEC reducing sampling overhead by 100x), four-step patterns workflow (Map classical problems to quantum circuits, Optimize through transpilation, Execute with primitives, Post-process results), algorithm libraries including Qiskit Nature for quantum chemistry (molecular Hamiltonians, VQE for ground states, UCCSD ansatz, multiple fermion-to-qubit mappings), Qiskit Optimization for combinatorial problems (QAOA, portfolio optimization, MaxCut), and Qiskit Machine Learning (quantum kernels, VQC, QNN), support for Python/C/Rust with modular architecture, parameterized circuits for variational algorithms, quantum Fourier transform, Grover search, Shor's algorithm, pulse-level control, IBM Quantum Runtime for cloud execution with job management and queuing, and comprehensive documentation with textbook and tutorials. Use cases: variational quantum eigensolver for molecular ground state energy, QAOA for combinatorial optimization problems, quantum chemistry simulations with multiple ansatze and mappings, quantum machine learning with kernel methods and neural networks, hybrid quantum-classical algorithms, quantum algorithm research and prototyping across multiple hardware platforms, quantum circuit optimization and benchmarking, quantum error mitigation and characterization, quantum information science experiments, and production quantum computing workflows on real quantum hardware
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- **QuTiP** - Quantum Toolbox in Python for simulating and analyzing quantum mechanical systems. Provides comprehensive tools for both closed (unitary) and open (dissipative) quantum systems including quantum states (kets, bras, density matrices, Fock states, coherent states), quantum operators (creation/annihilation operators, Pauli matrices, angular momentum operators, quantum gates), time evolution solvers (Schrödinger equation with sesolve, Lindblad master equation with mesolve, quantum trajectories with Monte Carlo mcsolve, Bloch-Redfield brmesolve, Floquet methods for periodic Hamiltonians), analysis tools (expectation values, entropy measures, fidelity, concurrence, correlation functions, steady state calculations), visualization (Bloch sphere with animations, Wigner functions, Q-functions, Fock distributions, matrix histograms), and advanced methods (Hierarchical Equations of Motion for non-Markovian dynamics, permutational invariance for identical particles, stochastic solvers, superoperators). Supports tensor products for composite systems, partial traces, time-dependent Hamiltonians, multiple dissipation channels, and parallel processing. Includes extensive documentation, tutorials, and examples. Use cases: quantum optics simulations (cavity QED, photon statistics), quantum computing (gate operations, circuit dynamics), open quantum systems (decoherence, dissipation), quantum information theory (entanglement dynamics, quantum channels), condensed matter physics (spin chains, many-body systems), and general quantum mechanics research and education
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- **scikit-learn** - Industry-standard Python library for classical machine learning providing comprehensive supervised learning (classification: Logistic Regression, SVM, Decision Trees, Random Forests with 17+ variants, Gradient Boosting with XGBoost-compatible HistGradientBoosting, Naive Bayes, KNN, Neural Networks/MLP; regression: Linear, Ridge, Lasso, ElasticNet, SVR, ensemble methods), unsupervised learning (clustering: K-Means, DBSCAN, HDBSCAN, OPTICS, Agglomerative/Hierarchical, Spectral, Gaussian Mixture Models, BIRCH, MeanShift; dimensionality reduction: PCA, Kernel PCA, t-SNE, Isomap, LLE, NMF, TruncatedSVD, FastICA, LDA; outlier detection: IsolationForest, LocalOutlierFactor, OneClassSVM), data preprocessing (scaling: StandardScaler, MinMaxScaler, RobustScaler; encoding: OneHotEncoder, OrdinalEncoder, LabelEncoder; imputation: SimpleImputer, KNNImputer, IterativeImputer; feature engineering: PolynomialFeatures, KBinsDiscretizer, text vectorization with CountVectorizer/TfidfVectorizer), model evaluation (cross-validation: KFold, StratifiedKFold, TimeSeriesSplit, GroupKFold; hyperparameter tuning: GridSearchCV, RandomizedSearchCV, HalvingGridSearchCV; metrics: 30+ evaluation metrics for classification/regression/clustering including accuracy, precision, recall, F1, ROC-AUC, MSE, R², silhouette score), and Pipeline/ColumnTransformer for production-ready workflows. Features consistent API (fit/predict/transform), extensive documentation, integration with NumPy/pandas/SciPy, joblib persistence, and scikit-learn-compatible ecosystem (XGBoost, LightGBM, CatBoost, imbalanced-learn). Optimized implementations using Cython/OpenMP for performance. Use cases: predictive modeling, customer segmentation, anomaly detection, feature engineering, model selection/validation, text classification, image classification (with feature extraction), time series forecasting (with preprocessing), medical diagnosis, fraud detection, recommendation systems, and any tabular data ML task requiring interpretable models or established algorithms
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- **scikit-survival** - Survival analysis and time-to-event modeling with censored data. Built on scikit-learn, provides Cox proportional hazards models (CoxPHSurvivalAnalysis, CoxnetSurvivalAnalysis with elastic net regularization), ensemble methods (Random Survival Forests, Gradient Boosting), Survival Support Vector Machines (linear and kernel), non-parametric estimators (Kaplan-Meier, Nelson-Aalen), competing risks analysis, and specialized evaluation metrics (concordance index, time-dependent AUC, Brier score). Handles right-censored data, integrates with scikit-learn pipelines, and supports feature selection and hyperparameter tuning via cross-validation

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