An open library for the analysis of molecular dynamics trajectories
- molecular-dynamics
- python
- mdtraj
- rmsd
Repository Index
47,133 repositories indexed
73–96 of 176 · Most stars
Clinical Histopathology Imaging Evaluation Foundation Model
Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry
A flexible framework for solving PDEs with modern spectral methods.
- spectral-methods
- fluid-dynamics
- pde-solver
Official release of the ProGen models
- language-model
- protein
- generative-model
Generation of protein sequences and evolutionary alignments via discrete diffusion models
- discrete-diffusion
- generative-model
- multiple-sequence-alignment
- protein-sequences
Firedrake is an automated system for the portable solution of partial differential equations using the finite element method (FEM)
Interactive network visualization in Python and Dash, powered by Cytoscape.js
- plotly-dash
- plotly
- dash
- cytoscape
⚗ A package useful for chemistry written in Python
- chemistry
- physical-chemistry
- chemical-kinetics
- chemical-formulas
Add built-in support for quaternions to numpy
A Free and Open Source Python Library for Multiobjective Optimization
- optimization
- multiobjective
- evolutionary
- algorithm
FiPy is a Finite Volume PDE solver written in Python
- scientific-computing
- scientific-computing-with-python
- phase-field
- materials-science
An elegant Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry.
- itk
- insight-toolkit
- jupyter
- jupyter-widget
Automated Attack Simulation in the Cloud, complete with detection use cases.
Module for statistical learning, with a particular emphasis on time-dependent modelling
- machine-learning
- python
- point-process
- optimization
🎯 A comprehensive gradient-free optimization framework written in Python
- metaheuristics
- optimization
- optimization-algorithms
- python
Universal SKILL.md catalog for research workflows: literature review, research design, project memory, manuscript writing, and cross-agent delegation for Claude Code, Codex, Gemini, Cursor, OpenClaw, and generic AI clients.
- academic-writing
- ai-skills
- notebooklm
- obsidian
The open source air traffic simulator
- python
- traffic
- aircraft
- simulation
Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)
Main yt repository
- data
- visualization
- analysis
- python
Molecular Processing Made Easy.
- python
- molecule
- rdkit
- drug-discovery
Generative biopolymer design with rich conditioning.
Benchmarks for generative chemistry
Engine for AI/ML/Data tracking, visualization, explainability, drift detection, and dashboards for Polyaxon.
- pandas
- pandas-summary
- dataframes
- data-science