Trending repositories

1.ml-explore / mlx

MLX: An array framework for Apple silicon

• mlx

2.PavelDoGreat / WebGL-Fluid-Simulation

Play with fluids in your browser (works even on mobile)

• fluid
• webgl
• simulation
• gpu
• navier-stokes

3.boyter / scc

Sloc, Cloc and Code: scc is a very fast accurate code counter with complexity calculations and COCOMO estimates written in pure Go

• sloccount
• cloc
• complexity
• tokei
• windows
• linux
• +7 more

4.deepchem / deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

• drug-discovery
• quantum-chemistry
• deep-learning
• biology
• materials-science
• hacktoberfest

5.cupy / cupy

NumPy & SciPy for GPU

• cuda
• cudnn
• cublas
• cusolver
• nccl
• python
• +12 more

6.jwohlwend / boltz

Official repository for the Boltz biomolecular interaction models

• binding-prediction
• drug-discovery
• protein-structure

7.OHIF / Viewers

OHIF zero-footprint DICOM viewer and oncology specific Lesion Tracker, plus shared extension packages

• nci-itcr
• nci-qin
• quantitative-imaging
• imaging-informatics
• cancer-imaging-research
• dicom
• +10 more

8.pyvista / pyvista

3D visualization and mesh analysis for science and engineering

• vtk
• python
• visualization
• 3d
• meshviewer
• scientific-visualization
• +6 more

9.Turfjs / turf

A modular geospatial engine written in JavaScript and TypeScript

• javascript
• algorithm
• computational-geometry
• geojson
• turf
• gis
• +3 more

10.pathsim / pathsim

A Python native dynamical system simulation framework in the block diagram paradigm.

• blockdiagram
• control-systems
• hierarchical-modeling
• nonlinear-dynamics
• simulation
• system-simulation
• +14 more

11.dauparas / ProteinMPNN

Code for the ProteinMPNN paper

12.guofei9987 / scikit-opt

Genetic Algorithm, Particle Swarm Optimization, Simulated Annealing, Ant Colony Optimization Algorithm,Immune Algorithm, Artificial Fish Swarm Algorithm, Differential Evolution and TSP(Traveling salesman)

• genetic-algorithm
• pso
• particle-swarm-optimization
• tsp
• travelling-salesman-problem
• simulated-annealing
• +7 more

13.mikedh / trimesh

Python library for loading and using triangular meshes.

• mesh
• triangular-meshes
• geometry
• python

14.meta-pytorch / botorch

Bayesian optimization in PyTorch

15.meta / Ax

Adaptive Experimentation Platform

16.bowang-lab / scGPT

The repository host gives no description.

• foundation-model
• gpt
• single-cell

17.alexdobin / STAR

RNA-seq aligner

18.bayesian-optimization / BayesianOptimization

A Python implementation of global optimization with gaussian processes.

• optimization
• gaussian-processes
• bayesian-optimization
• python
• simple

19.zarr-developers / zarr-python

An implementation of chunked, compressed, N-dimensional arrays for Python.

• zarr
• ndimensional-arrays
• compressed
• python

20.MFlowCode / MFC

Exascale multiphase flow solver — 2025 Gordon Bell Prize Finalist | 200T grid points on 43K+ GPUs

• gpu
• exascale
• cfd
• fortran
• hpc
• mpi
• +14 more

21.gcorso / DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

• diffusion-models
• docking
• binding
• computational-biology
• equivariance
• machine-learning
• +2 more

22.HIPS / autograd

Efficiently computes derivatives of NumPy code.

• autograd
• automatic-differentiation
• numpy
• python
• deep-learning
• derivative
• +8 more

23.aidenybai / million

Optimizing compiler for React

• hacktoberfest
• million
• millionjs
• virtual-dom
• react
• blockdom
• +11 more

24.deepmodeling / Uni-Mol

Official Repository for the Uni-Mol Series Methods

• molecular-modeling
• pre-trained-model
• pretraining
• deep-learning

25.mims-harvard / PrimeKG

Precision Medicine Knowledge Graph (PrimeKG)

• knowledge-graph
• precision-medicine
• therapeutics
• bioinformatics
• dataset
• graph-machine-learning
• +2 more

26.songlab-cal / gpn

Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star

• dna
• language-model
• variant-effect-prediction
• genomics

27.microsoft / DirectXMath

DirectXMath is an all inline SIMD C++ linear algebra library for use in games and graphics apps

• microsoft
• directx
• simd
• neon
• cpp-library
• sse
• +10 more

28.RosettaCommons / RoseTTAFold

This package contains deep learning models and related scripts for RoseTTAFold

29.PythonOT / POT

POT : Python Optimal Transport

• optimal-transport
• numerical-optimization
• machine-learning
• emd
• ot-mapping-estimation
• wasserstein-barycenter
• +10 more

30.snap-stanford / GEARS

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

31.brick / math

Arbitrary-precision arithmetic library for PHP

• php
• arbitrary-precision
• biginteger
• bigdecimal
• bigrational
• gmp
• +1 more

32.TUDelft-CNS-ATM / bluesky

The open source air traffic simulator

• python
• traffic
• aircraft
• simulation
• air-traffic-control
• air-transport
• +11 more

33.zoharbabin / web-researcher-mcp

Search the web and primary sources, read full pages, and check every citation. MCP server for Claude, Cursor, Codex and more. Runs on your machine.

• ai
• claude
• content-extraction
• go
• llm
• mcp
• +14 more

34.snap-stanford / UCE

UCE is a zero-shot foundation model for single-cell gene expression data

35.OATML-Markslab / ProteinGym

Official repository for the ProteinGym benchmarks

• benchmark
• computational-biology
• protein
• protein-design
• protein-fitness

36.mathnet / mathnet-numerics

Math.NET Numerics

• math
• numerics
• linear-algebra
• fsharp
• matrix
• random
• +8 more

37.DavidArayan / ezy-slice

An open source mesh slicer framework for Unity3D Game Engine. Written in C#.

38.Aceinna / gnss-ins-sim

Open-source GNSS + inertial navigation, sensor fusion simulator. Motion trajectory generator, sensor models, and navigation

• inertial-navigation-systems
• gnss
• gps
• imu
• integrated-navigation

39.suyashkumar / dicom

⚡High Performance DICOM Medical Image Parser in Go.

• dicom
• dicom-images
• golang
• golang-library
• golang-package
• parser
• +10 more

40.vqdang / hover_net

Simultaneous Nuclear Instance Segmentation and Classification in H&E Histology Images.

41.pydata / numexpr

Fast numerical array expression evaluator for Python, NumPy, Pandas, PyTables and more

42.DTolm / VkFFT

Vulkan/CUDA/HIP/OpenCL/Level Zero/Metal Fast Fourier Transform library

• vulkan
• fft
• convolution
• r2c
• c2r
• hpc
• +7 more

43.PyWavelets / pywt

PyWavelets - Wavelet Transforms in Python

• wavelets
• wavelet-transform
• signal-processing
• image-processing
• continuous-wavelet

44.dpilger26 / NumCpp

C++ implementation of the Python Numpy library

• python
• numpy
• c-plus-plus
• numerical-analysis
• scientific-computing
• algorithms
• +3 more

45.arneschneuing / DiffSBDD

A Euclidean diffusion model for structure-based drug design.

• ddpm
• drug-design
• equivariance
• generative-model
• graph-neural-networks
• machine-learning

46.hms-dbmi / viv

Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.

• hubmap
• imaging
• openmicroscopy
• ome-tiff
• zarr
• viv
• +1 more

47.marcomusy / vedo

A python module for scientific analysis of 3D data based on VTK and Numpy

• 3d-graphics
• vtk
• 3d
• mesh
• simulations
• scientific-visualization
• +5 more

48.dan2097 / opsin

Open Parser for Systematic IUPAC Nomenclature. Chemical name to structure conversion

49.autodiff / autodiff

automatic differentiation made easier for C++

• automatic-differentiation
• auto-differentiation
• autodiff
• autodifferentiation
• differentiation
• derivatives
• +1 more

50.Teichlab / celltypist

A tool for semi-automatic cell type classification

• python
• single-cell
• machine-learning
• scrna-seq
• cell-type-classification
• label-transfer

51.facebookresearch / esmArchived

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

52.pmp-library / pmp-library

The Polygon Mesh Processing Library

• mesh-processing
• geometry-processing
• polygon-mesh
• triangle-mesh
• c-plus-plus
• surface-mesh
• +9 more

53.owlbarn / owl

Owl - OCaml Scientific Computing @ https://ocaml.xyz

• matrix
• linear-algebra
• ndarray
• statistical-functions
• topic-modeling
• regression
• +14 more

54.ElliotXie / autozyme

Autonomous multi-agent framework to optimize scientific software

• acceleration
• agentic-ai
• ai-agents
• bioinformatics
• code-optimization
• genomics
• +11 more

55.hail-is / hail

Cloud-native genomic dataframes and batch computing

• genetics
• vcf
• genomics
• gwas
• bioinformatics
• python
• +2 more

56.softwareQinc / qpp

Modern C++ quantum computing library

• quantum-computing
• c-plus-plus
• cpp
• cpp11
• quantum
• simulator
• +2 more

57.KangBoming / BulkFormer

BulkFormer: A large-scale foundation model for human bulk transcriptomes

58.ddemidov / amgcl

C++ library for solving large sparse linear systems with algebraic multigrid method

• amg
• c-plus-plus
• sparse-linear-systems
• opencl
• cuda
• gpgpu
• +6 more

59.JCash / voronoi

A C implementation for creating 2D Voronoi/Delauney diagrams

60.chainer / chainer-chemistry

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

• deep-learning
• chemistry
• neural-network
• biology
• chainer
• python
• +1 more

61.microsoft / evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

• discrete-diffusion
• generative-model
• multiple-sequence-alignment
• protein-sequences

62.gao-lab / GLUE

Graph-linked unified embedding for single-cell multi-omics data integration

• bioinformatics
• deep-learning
• single-cell
• single-cell-multiomics

63.brandon-rhodes / python-sgp4

Python version of the SGP4 satellite position library

64.MikeMcl / bignumber.js

A JavaScript library for arbitrary-precision decimal and non-decimal arithmetic

• bignumber
• javascript
• arbitrary-precision
• decimal-places
• bigdecimal

65.spatie / laravel-analytics

A Laravel package to retrieve pageviews and other data from Google Analytics

• laravel
• php
• analytics
• google
• statistics

66.Habrador / Computational-geometry

Computational Geometry Unity library with implementations of intersection algorithms, triangulations like delaunay, voronoi diagrams, polygon clipping, bezier curves, ear clipping, convex hulls, mesh simplification, etc

• unity3d
• computational-geometry
• voronoi
• intersections
• convex-hull
• polygon-clipping
• +14 more

67.molecularsets / moses

Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models

• machine-learning
• generative-models
• drug-discovery
• benchmark

68.BenevolentAI / guacamol

Benchmarks for generative chemistry

69.SoloByte / godot-polygon2d-fracture

A simple script for fracturing polygons. Also adds nice helper functions for polygons like calculateArea, triangulate, getRandomPointsInPolygon, getBoundingRect)

• gdscript
• polygon2d-fracture
• godot-engine
• godot
• polygon-triangulation
• gamedev-library
• +7 more

70.marcpinet / citracer

💬 Trace citation chains for any concept across research papers and render them as an interactive graph.

• academic-research
• bibliography
• citation-graph
• cli
• grobid
• literature-review
• +5 more

71.ljvmiranda921 / pyswarms

A research toolkit for particle swarm optimization in Python

• particle-swarm-optimization
• optimization-tools
• pso
• global-optimization
• swarm-intelligence
• machine-learning
• +5 more

72.msteinbeck / tinyspline

ANSI C library for NURBS, B-Splines, and Bézier curves with interfaces for C++, C#, D, Go, Java, Javascript, Lua, Octave, PHP, Python, R, and Ruby.

• nurbs
• b-splines
• bezier-curves
• splines

73.ASC-Community / AngouriMath

Open-source cross-platform symbolic algebra library for C# and F#. Can be used for both production and research purposes.

• csharp
• algebra
• integration
• latex
• parsing
• solver
• +13 more

74.Mariewelt / OpenChem

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

• computational-chemistry
• computational-biology
• deep-learning
• deep-neural-networks
• graph-convolutional-networks
• drug-discovery
• +5 more

75.pyamg / pyamg

Algebraic Multigrid Solvers in Python

• amg
• solver
• python
• multigrid
• sparse-matrix
• pyamg
• +2 more

76.Martinsos / edlib

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

• sequence-alignment
• edit-distance
• levehnstein-distance
• library
• c-plus-plus
• alignment-path
• +2 more

77.theislab / scib

Benchmarking analysis of data integration tools

78.architecture-building-systems / CityEnergyAnalyst

City Energy Analyst (CEA) is an open-source urban building energy modeling (UBEM) platform and computation tool for the design of low-carbon and highly efficient cities.

• python
• urban-design
• urban-analytics
• ubem
• open-source
• decarbonization
• +5 more

79.zcang / COMMOT

The repository host gives no description.

80.markrogoyski / math-php

Powerful modern math library for PHP: Features descriptive statistics and regressions; Continuous and discrete probability distributions; Linear algebra with matrices and vectors, Numerical analysis; special mathematical functions; Algebra

• math
• mathematics
• linear-algebra
• statistics
• matrix
• probability
• +11 more

81.agemagician / ProtTrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

82.MolSSI / cookiecutter-cms

Python-centric Cookiecutter for Molecular Computational Chemistry Packages

• cookiecutter
• python-packages
• molecular-sciences
• conda-environment
• pytest
• conda-forge
• +2 more

83.tequilahub / tequila

A High-Level Abstraction Framework for Quantum Algorithms

84.peterstace / simplefeatures

Simple Features is a pure Go Implementation of the OpenGIS Simple Feature Access Specification

• postgis
• spatial-analysis
• gis
• go
• golang
• geometry
• +4 more

85.ElliotXie / CASSIA

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

• ai4science
• llm
• multiagent-systems
• prompt-engineering
• retrieved-augmented-generation
• singlecell
• +7 more

86.clean-css / clean-css

Fast and efficient CSS optimizer for node.js and the Web

• css
• minification
• optimization
• css-optimizations
• css-optimizer
• clean-css

87.giacomelli / GeneticSharp

GeneticSharp is a fast, extensible, multi-platform and multithreading C# Genetic Algorithm library that simplifies the development of applications using Genetic Algorithms (GAs).

• genetic-algorithms
• artificial-intelligence
• c-sharp
• dotnet
• dotnet-core
• dotnet-standard
• +3 more

88.vcflib / vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

• variant-calling
• genomics
• vcf-manipulation
• genotyping
• haplotypecaller

89.shenwei356 / taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

• bioinformatics
• taxonomy
• cross-platform
• lineage
• lca
• taxid
• +2 more

90.vlang / vtl

The V Tensor Library

• v
• hacktoberfest
• autograd
• deep-learning
• linear-algebra
• machine-learning
• +5 more

91.kreshuklab / panseg

A tool for cell instance aware segmentation in densely packed 3D volumetric images

• segmentation
• deep-learning
• bioinformatics
• neural-network
• bioimage-analysis
• image-segmentation
• +1 more

92.rawify / Fraction.js

The RAW rational numbers library written in JavaScript

• fraction
• javascript
• math
• rational-numbers
• numbers

93.snap-stanford / SATURN

The repository host gives no description.

94.theislab / chemCPA

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

• disentanglement
• drug-discovery
• genomics
• perturbation
• single-cell
• transfer-learning

95.kzampog / cilantro

A lean C++ library for working with point cloud data

• point-cloud
• icp
• ransac
• convex-hull
• 3d-visualization
• k-means
• +14 more

96.attaswift / BigInt

Arbitrary-precision arithmetic in pure Swift

97.vlang / vsl

V library to develop Artificial Intelligence and High-Performance Scientific Computations

• v
• hacktoberfest
• linear-algebra
• optimization
• sparse-systems
• computational-geometry
• +7 more

98.chembl / ChEMBL_Structure_Pipeline

ChEMBL database structure pipelines

99.sustainable-processes / summit

Optimising chemical reactions using machine learning

• chemistry
• machine-learning
• optimization
• bayesian-optimization
• neural-networks
• drug-discovery
• +4 more

100.peizhenbai / DrugBAN

Interpretable bilinear attention network with domain adaptation improves drug-target prediction.