Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
Repository Index
47,133 repositories indexed
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Scientific-grade astronomy routines for Python
C++ library for solving large sparse linear systems with algebraic multigrid method
- amg
- c-plus-plus
- sparse-linear-systems
- opencl
Polygonal Surface Reconstruction from Point Clouds (C++ & Python)
- surface-reconstruction
- urban-modeling
- urban-reconstruction
- primitive-extraction
An axiom-free formalization of category theory in Coq for personal study and practical work
- category-theory
- coq
- monad
- profunctor
3D medical imaging reconstruction software
- dicom
- dicom-viewer
- magnetic-resonance-imaging
- medical-image-processing
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
An open library for the analysis of molecular dynamics trajectories
- molecular-dynamics
- python
- mdtraj
- rmsd
VexCL is a C++ vector expression template library for OpenCL/CUDA/OpenMP
- opencl
- cuda
- c-plus-plus
- gpgpu
Clinical Histopathology Imaging Evaluation Foundation Model
RBDL is a C++ library that contains some essential and efficient rigid body dynamics algorithms such as the Articulated Body Algorithm (ABA) for forward dynamics, Recursive Newton-Euler Algorithm (RNEA) for inverse dynamics, the Composite Rigid Body Algorithm (CRBA) for the efficient computation of the joint space inertia matrix and is also able to compute forward dynamics with external contact constraints and collision impulses. Furthermore it has some basic support for forward and inverse kinematics.
- articulated-body-algorithm
- inverse-dynamics
- forward-dynamics
- multi-body-dynamics
Interactive network visualization in Python and Dash, powered by Cytoscape.js
- plotly-dash
- plotly
- dash
- cytoscape
FiPy is a Finite Volume PDE solver written in Python
- scientific-computing
- scientific-computing-with-python
- phase-field
- materials-science
ACADO Toolkit is a software environment and algorithm collection for automatic control and dynamic optimization. It provides a general framework for using a great variety of algorithms for direct optimal control, including model predictive control, state and parameter estimation and robust optimization.
2D/3D simplicial mesh generator interface for Python (Triangle, TetGen, gmsh)
- python
- mesh-generation
- scientific-computing
- triangle
🎯 A comprehensive gradient-free optimization framework written in Python
- metaheuristics
- optimization
- optimization-algorithms
- python
A pure JavaScript medical research image viewer.
Main yt repository
- data
- visualization
- analysis
- python
Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.
- histopathology-images
- microscopy
- sliding-windows
- medical-image-analysis
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
skimpy is a light weight tool that provides summary statistics about variables in data frames within the console.
- eda
- pandas
- data-science
- exploratory-data-analysis
A Python native dynamical system simulation framework in the block diagram paradigm.
- blockdiagram
- control-systems
- hierarchical-modeling
- nonlinear-dynamics
bert-loves-chemistry: a repository of HuggingFace models applied on chemical SMILES data for drug design, chemical modelling, etc.
- huggingface
- bert
- chemical-modelling
- chemical-smiles-data
Graph-linked unified embedding for single-cell multi-omics data integration
- bioinformatics
- deep-learning
- single-cell
- single-cell-multiomics