Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
- foundation-models
- genomics
- language-models
Repository Index
56,139 visible repositories in the index
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⚗ A package useful for chemistry written in Python
- chemistry
- physical-chemistry
- chemical-kinetics
- chemical-formulas
Add built-in support for quaternions to numpy
:spider_web: Mesh optimization, mesh smoothing.
- python
- pypi
- mathematics
- physics
Main yt repository
- data
- visualization
- analysis
- python
Exascale multiphase flow solver — 2025 Gordon Bell Prize Finalist | 200T grid points on 43K+ GPUs
- gpu
- exascale
- cfd
- fortran
Multibody dynamics tool kit.
- python
- dynamics
- physics
- simulation
Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star
- dna
- language-model
- variant-effect-prediction
- genomics
Bayesian Optimization using GPflow
- gpflow
- bayesian-optimization
- machine-learning
- hyperparameter-optimization
Open source math and physics engine that executes MATLAB-syntax code. Features a modern compiler, automatic GPU acceleration for large calculations, and support for math on geometry / FEA calculations.
- matlab
- rust
- jit-compiler
- linear-algebra
OPEM (Open Source PEM Fuel Cell Simulation Tool)
- chemistry
- pem
- fuel-cell
- opem
Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
- cancer-genomics
- cnv-detection
- single-cell
- phylogeny
A C# DICOM Library
- dicom
- medical-physics
- radiology
- radiation-oncology
:triangular_ruler: Orthogonal polynomials in all shapes and sizes.
- python
- mathematics
- engineering
- physics
PhyloNetworks: a julia package with utilities for phylogenetic networks
OFF, Open source Finite volume Fluid dynamics code
- fluid-dynamics
- fortran
- oop
- cfd
Astrophotography capture and processing
a physics library wrapper for love2d
The Mines Java Toolkit
- geophysics
- scientific-computing
- visualization
- mines-java-toolkit
Variations on Kirby & Paris' hydra battles and other entertaining math in Coq (collaborative, documented, includes exercises) [maintainer=@Casteran]
- coq
- hydra-battles
- ordinal-notations
- formal-proofs
An Elixir implementation of the CONREC algorithm for topographic or isochrone maps.
- gis
- conrec
- map
- elixir
The d-SEAMS C++ core engine
- molecular-dynamics-simulation
- molecular-dynamics
- trajectory-analysis
- lua
💬 Trace citation chains for any concept across research papers and render them as an interactive graph.
- academic-research
- bibliography
- citation-graph
- cli
Multi-stage Riemannian flow matching for physically valid molecular docking, with GNINA scoring, PoseBusters filtering, CLI inference, and benchmarks.
- alphafold3
- docking
- drug-design
- drug-discovery