tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. Supports various graph types (Directed, Undirected, Multigraphs) and features a vast library of standard graph algorithms. Use for network analysis, graph theory, social network analysis, biological…
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
A Just-In-Time (JIT) compiler for Python that translates a subset of Python and NumPy code into fast machine code. Developed by Anaconda, Inc. Highly effective for accelerating loops, custom mathematical functions, and complex numerical algorithms. Use for @njit, @vectorize, prange, cuda.jit, numba.typed, JIT…
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Advanced sub-skill for NumPy focused on internal memory management, stride manipulation, structured arrays, and interfacing with C/Cython. Covers zero-copy operations and SIMD vectorization principles.
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Comprehensive guide for NumPy - the fundamental package for scientific computing in Python. Use for array operations, linear algebra, random number generation, Fourier transforms, mathematical functions, and high-performance numerical computing. Foundation for SciPy, pandas, scikit-learn, and all scientific Python.
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
A chemical toolbox designed to speak the many languages of chemical data. Supports over 110 formats and provides tools for conversion, 3D structure generation, molecular searching (SMARTS), and force field calculations. Use for chemical file format conversion (SDF, PDB, SMILES, CIF, Gaussian), 3D coordinate generation…
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Open Source Computer Vision Library (OpenCV) for real-time image processing, video analysis, object detection, face recognition, and camera calibration. Use when working with images, videos, cameras, edge detection, contours, feature detection, image transformations, object tracking, optical flow, or any computer…
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Google Optimization Tools. An open-source software suite for optimization, specialized in vehicle routing, flows, integer and linear programming, and constraint programming. Features the world-class CP-SAT solver. Use for vehicle routing problems (VRP), scheduling, bin packing, knapsack problems, linear programming…
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Advanced sub-skill for pandas focused on memory optimization, execution speed, and handling large-scale datasets (10M+ rows). Covers low-level dtypes, efficient indexing, and vectorization of complex logic.
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Cross-platform Python library for differentiable quantum computing. Integrated with machine learning libraries like PyTorch, TensorFlow, and JAX. Designed for quantum machine learning (QML), variational algorithms, and hardware-agnostic quantum programming. Use for Quantum Neural Networks (QNNs), Variational Quantum…
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
An Astropy coordinated package for detecting and performing photometry of astronomical sources. Provides tools for background estimation, source detection (DAOFIND, IRAF), aperture photometry, and PSF (Point Spread Function) fitting. Use when working with astronomical image analysis, star/galaxy detection, measuring…
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
A high-level interactive graphing library for Python. Ideal for web-based visualizations, 3D plots, and complex interactive dashboards. Built on plotly.js, it allows users to zoom, pan, and hover over data points in a browser-based environment. Use for interactive charts, web applications, Jupyter notebooks, 3D data…
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Blazingly fast DataFrame library written in Rust. Features a multi-threaded query engine, lazy evaluation, and efficient memory usage via Apache Arrow. Designed for high-performance data processing on a single machine. Use for large datasets (1GB-100GB+), fast data transformations, Parquet/CSV processing, complex…
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Protein Dynamics, Evolution, and Structure analysis. Specialized in Normal Mode Analysis (NMA) using Anisotropic (ANM) and Gaussian Network Models (GNM). Features tools for structural ensemble analysis, PCA, and co-evolutionary analysis (Evol). Use for protein flexibility prediction, collective motions, structural…
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Python package for working with DICOM files. It allows you to read, modify, and write DICOM data in a Pythonic way. Essential for medical imaging processing, clinical data extraction, and AI in radiology.
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Python Optimization Modeling Objects. A high-level framework for formulating, solving, and analyzing optimization models. Supports Linear Programming (LP), Mixed-Integer Linear Programming (MILP), and Non-Linear Programming (NLP). Part of the COIN-OR project. Use for mathematical optimization, linear programming…
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Python interface to PROJ (cartographic projections and coordinate transformations library). Handles transformations between different Coordinate Reference Systems (CRS) and performs geodetic calculations (distance, area on ellipsoids). Use for coordinate transformations, CRS conversions, geodetic calculations, UTM…
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Python module for reading, manipulating and writing genomic alignment formats (SAM/BAM/CRAM) and variant files (VCF/BCF). Wrapper for htslib.
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Comprehensive guide for PySCF - Python-based Simulations of Chemistry Framework. Use for ab initio quantum chemistry calculations including Hartree-Fock, DFT, MP2, CCSD, geometry optimization, excited states, and molecular properties. Industry-standard library for electronic structure calculations.
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Advanced sub-skill for PyTorch focused on model productionization and deployment. Covers TorchScript (JIT/Tracing), ONNX export, LibTorch (C++ API), and inference optimization (Quantization, Pruning).
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Advanced sub-skill for PyTorch focused on deep research and production engineering. Covers custom Autograd functions, module hooks, advanced initialization, Distributed Data Parallel (DDP), and performance profiling.
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Leading deep learning framework. Provides Tensors and Dynamic Computational Graphs with strong GPU acceleration. Widely used for research, neural networks, and differentiable programming.
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Advanced sub-skill for Qiskit focused on executing circuits on physical quantum processing units (QPUs). Covers IBM Quantum Runtime, error mitigation techniques (TREX, ZNE), hardware-aware transpilation, and low-level pulse control (OpenPulse).
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Comprehensive guide for Qiskit - IBM's quantum computing framework. Use for quantum circuit design, quantum algorithms (VQE, QAOA, Grover, Shor), quantum simulation, noise modeling, quantum machine learning, and quantum chemistry calculations. Essential for quantum computing research and applications.
tondevrel/scientific-agent-skills
Skill Claude CodeCodex
Quantum Toolbox in Python. Framework for simulating the dynamics of open quantum systems. Provides data structures for quantum objects (kets, bras, operators) and solvers for master equations, Monte Carlo trajectories, and time-dependent Hamiltonians. Use for quantum dynamics simulation, open quantum systems, master…