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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.
flybrainlabs native and WebAssembly simulation engines and browser mining.
:christmas_tree:Visualization and annotation of phylogenetic trees
- r
- visualization
- phylogenetic-trees
- annotations
QuadriFlow: A Scalable and Robust Method for Quadrangulation
- quadriflow
- quad
- remeshing
- quadrangulation
LibTomMath is a free open source portable number theoretic multiple-precision integer library written entirely in C.
- mpi
- libtommath
- c
- math
Python package for graph neural networks in chemistry and biology
- deep-learning
- graph-neural-networks
- dgl
- cheminformatics
Pathology Foundation Model - Nature Medicine
- foundation
- foundation-model
- histopathology
- mahmoodlab
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
- dna
- k-mer
- python
- bloom-filter
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
- kmer
- dnabert-model
- kmer-format
- gpu
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
- deep-learning
- protein-sequences
- protein-structure
- semi-supervised-learning
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
Cosette is an automated SQL solver.
Firedrake is an automated system for the portable solution of partial differential equations using the finite element method (FEM)
Chebfun: numerical computing with functions.
Nonconvex embedded optimization: code generation for fast real-time optimization + ROS support
- embedded-optimization
- nonconvex
- model-predictive-control
- rust-library
DiffSharp: Differentiable Functional Programming
- machine-learning
- tensor
- dotnet
- autodiff
🎯 A comprehensive gradient-free optimization framework written in Python
- metaheuristics
- optimization
- optimization-algorithms
- python
Vision-Language Pathology Foundation Model - Nature Medicine
- bioimage-analysis
- bioimage-informatics
- conch
- foundation-model
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
A tool for semi-automatic cell type classification
- python
- single-cell
- machine-learning
- scrna-seq
RNA Velocity generalized through dynamical modeling
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
a numpy-like fast vector module for micropython, circuitpython, and their derivatives
- micropython-ulab
- numpy
- micropython
- module