Trending repositories

1.ml-explore / mlx

MLX: An array framework for Apple silicon

• mlx

2.WenyuChiou / ai-research-skills

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
• zotero
• claude-code
• +14 more

3.PavelDoGreat / WebGL-Fluid-Simulation

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

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

4.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

5.deepchem / deepchem

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

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

6.cupy / cupy

NumPy & SciPy for GPU

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

7.mtahiraslan / data-analyst-roadmap

Based on my own experience, I believe this roadmap provides clear answers to all the key questions about becoming a data analyst from scratch, including which technologies and programming languages to learn, what soft skills are essential, and how to start a professional career in this field.

• blogs
• businessintelligence
• courses
• data
• dataanalysis
• dataanalyst
• +14 more

8.jwohlwend / boltz

Official repository for the Boltz biomolecular interaction models

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

9.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

10.pyvista / pyvista

3D visualization and mesh analysis for science and engineering

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

11.microsoft / MarS

MarS: a Financial Market Simulation Engine Powered by Generative Foundation Model

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.Turfjs / turf

A modular geospatial engine written in JavaScript and TypeScript

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

14.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

15.mikedh / trimesh

Python library for loading and using triangular meshes.

• mesh
• triangular-meshes
• geometry
• python

16.appsinacup / godot-rapier-physics

Godot Rapier Physics – 2D and 3D physics engine for the Godot game engine. with better stability, performance, liquids, determinism, state serialization and no ghost collisions.

• godot
• godot-engine
• godot4
• godotengine
• rapier
• 2d
• +3 more

17.meta-pytorch / botorch

Bayesian optimization in PyTorch

18.godot-jolt / godot-jolt

Godot Jolt is a Godot extension that integrates the Jolt physics engine

• game-development
• gdextension
• godot
• godot-engine
• godotengine
• physics
• +2 more

19.meta / Ax

Adaptive Experimentation Platform

20.bayesian-optimization / BayesianOptimization

A Python implementation of global optimization with gaussian processes.

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

21.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

22.gcorso / DiffDock

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

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

23.HIPS / autograd

Efficiently computes derivatives of NumPy code.

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

24.aidenybai / million

Optimizing compiler for React

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

25.songlab-cal / gpn

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

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

26.mims-harvard / PrimeKG

Precision Medicine Knowledge Graph (PrimeKG)

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

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.PythonOT / POT

POT : Python Optimal Transport

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

29.paulmillr / noble-post-quantum

Auditable & minimal JS implementation of public-key post-quantum cryptography

• dilithium
• kyber
• ml-kem
• post-quantum-cryptography
• sphincs
• sphincs-plus
• +14 more

30.nschloe / meshio

:spider_web: input/output for many mesh formats

• vtk
• pypi
• python
• mesh
• mathematics
• engineering
• +1 more

31.TUDelft-CNS-ATM / bluesky

The open source air traffic simulator

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

32.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

33.OATML-Markslab / ProteinGym

Official repository for the ProteinGym benchmarks

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

34.ikpil / Box2D.NET

Box2D.NET - a C# port of Box2D, is a 2D physics engine for games, .NET, Unity3D, servers

• 2d
• 2d-game
• box2d
• csharp
• game
• game-development
• +8 more

35.datoviz / datoviz

⚡ Datoviz: high-performance GPU rendering for scientific data visualization

• visualization
• graphics
• data-visualization
• scientific-visualization
• gpu
• vulkan
• +6 more

36.vincentlaucsb / csv-parser

A modern C++ CSV parser and serializer that doesn't make you choose between ease of use or performance.

• csv
• parser
• json
• tab-separated
• csv-parser
• statistics
• +5 more

37.mathnet / mathnet-numerics

Math.NET Numerics

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

38.TileDB-Inc / TileDB

The Universal Storage Engine

• tiledb
• arrays
• storage-engine
• scientific-computing
• data-analysis
• hdfs
• +7 more

39.DTolm / VkFFT

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

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

40.pydata / numexpr

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

41.dpilger26 / NumCpp

C++ implementation of the Python Numpy library

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

42.slembcke / Chipmunk2D

A fast and lightweight 2D game physics library.

• c
• 2d
• 2d-physics
• rigid-body

43.facebookresearch / esmArchived

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

44.plotly / plotly.rs

Plotly for Rust

• plot
• rust
• chart
• financial
• financial-analysis
• data-visualization
• +8 more

45.owlbarn / owl

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

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

46.ElliotXie / autozyme

Autonomous multi-agent framework to optimize scientific software

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

47.bencheeorg / benchee

Easy and extensible benchmarking in Elixir providing you with lots of statistics!

• benchmarking
• elixir
• microbenchmarks
• extensible
• graphs
• statistics

48.hail-is / hail

Cloud-native genomic dataframes and batch computing

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

49.softwareQinc / qpp

Modern C++ quantum computing library

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

50.chainer / chainer-chemistry

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

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

51.MikeMcl / bignumber.js

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

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

52.molecularsets / moses

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

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

53.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

54.spatie / laravel-analytics

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

• laravel
• php
• analytics
• google
• statistics

55.gao-lab / GLUE

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

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

56.MLT-OSS / FirstData

The World's Most Comprehensive, Authoritative, and Structured Open Source Data Source Knowledge Base

• mcp
• data-sources
• ai
• awesome-list
• datasets
• fact-checking
• +14 more

57.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

58.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

59.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

60.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

61.BenevolentAI / guacamol

Benchmarks for generative chemistry

62.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

63.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

64.tequilahub / tequila

A High-Level Abstraction Framework for Quantum Algorithms

65.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

66.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

67.clean-css / clean-css

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

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

68.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

69.ReversecLabs / leonidas

Automated Attack Simulation in the Cloud, complete with detection use cases.

70.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

71.MolSSI / cookiecutter-cms

Python-centric Cookiecutter for Molecular Computational Chemistry Packages

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

72.fbcosentino / godot-simplified-flightsim

Simplified Flight Simulation library (addon) for Godot Engine

73.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

74.kjkrol / goke

High-performance, zero-allocation ECS for Go. Cache-friendly data orchestrator with type-safe iterators.

• ecs
• entity-component-system
• gamedev
• go
• goalng
• geme-engine
• +2 more

75.Genbox / VelcroPhysics

High performance 2D collision detection system with realistic physics responses.

• physics-engine
• physics-2d

76.rawify / Fraction.js

The RAW rational numbers library written in JavaScript

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

77.particle-clicker / particle-clicker

An addictive incremental game that teaches players the history of high energy particle physics

78.vlang / vtl

The V Tensor Library

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

79.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

80.uber-common / metta

An information security preparedness tool to do adversarial simulation.

• uber
• vagrant
• yaml
• celery
• python
• redis
• +7 more

81.StanfordVL / GibsonEnv

Gibson Environments: Real-World Perception for Embodied Agents

• computer-vision
• robotics
• simulator
• sim2real
• deep-learning
• deep-reinforcement-learning
• +4 more

82.erayzesen / QuarkPhysics

A 2D Soft Body and Rigid Body Physics Engine.

• 2d-physics-engine
• game-development
• physics-engine
• rigid-bodies
• soft-bodies
• physics-simulation

83.juan-leon / lowcharts

Tool to draw low-resolution graphs in terminal

• plot
• shell
• troubleshooting
• log
• analysis
• command-line
• +2 more

84.mojaie / MolecularGraph.jl

Graph-based molecule modeling toolkit for cheminformatics

• cheminformatics
• molecular-modeling
• chemistry
• toolkit
• julia
• julia-language
• +3 more

85.sustainable-processes / summit

Optimising chemical reactions using machine learning

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

86.MartinThoma / LaTeX-examples

Examples for the usage of LaTeX

• latex
• tex
• tikz
• mathematics
• science
• research

87.djezzzl / database_consistency

The tool to avoid various issues due to inconsistencies and inefficiencies between a database schema and application models.

• ruby-on-rails
• activerecord
• tool
• database
• consistency
• optimization
• +3 more

88.bebop / poly

A Go package for engineering organisms.

• synthetic-biology
• synbio
• genetic-engineering
• molecular-biology
• bioengineering
• computational-biology
• +14 more

89.seyonechithrananda / bert-loves-chemistry

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

90.vlang / vsl

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

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

91.maximtrp / scikit-posthocs

Multiple Pairwise Comparisons (Post Hoc) Tests in Python

• posthoc-comparisons
• posthoc-tests
• python
• scikit
• statistical-analysis
• statistics
• +1 more

92.MaxHalford / eaopt

:four_leaf_clover: Evolutionary optimization library for Go (genetic algorithm, partical swarm optimization, differential evolution)

• go
• optimization
• parallel
• machine-learning
• genetic-algorithm
• speciation
• +5 more

93.romeric / Fastor

A lightweight high performance tensor algebra framework for modern C++

• tensors
• tensor-contraction
• multidimensional-arrays
• simd
• hpc
• small-blas
• +1 more

94.ForNeVeR / xaml-math

A collection of .NET libraries for rendering mathematical formulae using the LaTeX typesetting style, for the WPF and Avalonia XAML-based frameworks

• wpf
• latex
• formula
• dotnet
• math
• tex
• +3 more

95.aeturrell / skimpy

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
• summary-statistics
• statistics

96.brndnmtthws / dryoc

Don't Roll Your Own Crypto: fast, type-safe, pure-Rust cryptography with post-quantum support

• libsodium
• crypto
• rust
• cryptography
• cryptography-library
• nacl
• +3 more

97.DmitriBogdanov / UTL

Collection of self-contained header-only libraries for C++17

• async
• json
• logger
• math
• parallel
• prng
• +12 more

98.ECSIM / opem

OPEM (Open Source PEM Fuel Cell Simulation Tool)

• chemistry
• pem
• fuel-cell
• opem
• script
• python
• +8 more

99.PytorchConnectomics / pytorch_connectomics

PyTorch Connectomics: segmentation toolbox for EM connectomics

• computer-vision
• neuroscience
• connectomics
• pytorch
• segmentation
• biomedical-image-processing
• +2 more

100.jimmyorourke / plotlypp

Plotly for C++. A C++ interface to the Plotly.js figure spec, for creating interactive data visualizations.

• charts
• cpp
• graphs
• plotly
• plotting
• visualization
• +4 more