Trending repositories

201.jarun / bcal

:1234: Bits, bytes and general-purpose calculator

• storage
• storage-unit-converter
• command-line
• standalone
• terminal
• calculator
• +6 more

202.softwareQinc / qpp

Modern C++ quantum computing library

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

203.pyamg / pyamg

Algebraic Multigrid Solvers in Python

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

204.usnistgov / fipy

FiPy is a Finite Volume PDE solver written in Python

• scientific-computing
• scientific-computing-with-python
• phase-field
• materials-science
• partial-differential-equations
• shared-memory-parallel
• +2 more

205.ginkgo-project / ginkgo

Numerical linear algebra software package

• linear-algebra
• hpc
• gpu-computing
• cuda
• krylov-methods
• preconditioning
• +6 more

206.CATIA-Systems / FMPy

Simulate Functional Mock-up Units (FMUs) in Python

• fmi
• python
• fmi-standard

207.chris-mcginnis-ucsf / DoubletFinder

R package for detecting doublets in single-cell RNA sequencing data

208.datamol-io / datamol

Molecular Processing Made Easy.

• python
• molecule
• rdkit
• drug-discovery
• drug-design
• molecules
• +2 more

209.mahmoodlab / CONCH

Vision-Language Pathology Foundation Model - Nature Medicine

• bioimage-analysis
• bioimage-informatics
• conch
• foundation-model
• health-informatics
• histopathology
• +9 more

210.arneschneuing / DiffSBDD

A Euclidean diffusion model for structure-based drug design.

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

211.mordred-descriptor / mordred

a molecular descriptor calculator

212.cclib / cclib

Parsers and algorithms for computational chemistry logfiles

• python
• computational-chemistry
• quantum-chemistry

213.esa / pykep

PyKEP is a scientific library providing basic tools for research in interplanetary trajectory design.

• interplanetary
• mission-analysis
• astrodynamics
• aerospace

214.Rolf-Hempel / PlanetarySystemStacker

Produce a sharp image of a planetary system object (moon, sun, planets) from many seeing-affected frames according to the "lucky imaging" technique.

215.DLR-SC / tigl

The TiGL Geometry Library to process aircraft geometries in pre-design.

• opencascade
• aircraft
• c-plus-plus
• geometry
• b-spline
• cpacs
• +1 more

216.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

217.dcjones / proseg

Probabilistic cell segmentation for in situ spatial transcriptomics

218.nasa / trick

Trick Simulation Environment. Trick provides a common set of simulation capabilities and utilities to build simulations automatically.

219.tensorflow / tfjs-coreArchived

WebGL-accelerated ML // linear algebra // automatic differentiation for JavaScript.

• deep-learning
• typescript
• webgl
• javascript
• machine-learning
• neural-network
• +2 more

220.spatie / laravel-analytics

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

• laravel
• php
• analytics
• google
• statistics

221.gradientspace / geometry3Sharp

C# library for 2D/3D geometric computation, mesh algorithms, and so on. Boost license.

222.NVIDIA / MatX

An efficient C++20 GPU numerical computing library with Python-like syntax

• cuda
• gpu
• gpgpu
• hpc
• gpu-computing

223.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

224.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

225.brandon-rhodes / pyephem

Scientific-grade astronomy routines for Python

226.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

227.yixuan / spectra

A header-only C++ library for large scale eigenvalue problems

• eigenvalues
• arpack
• linear-algebra
• spectra
• header-only

228.jwiegley / category-theory

An axiom-free formalization of category theory in Coq for personal study and practical work

• category-theory
• coq
• monad
• profunctor
• comonads
• monoid
• +7 more

229.salesforce / progen

Official release of the ProGen models

• language-model
• protein
• generative-model

230.firedrakeproject / firedrake

Firedrake is an automated system for the portable solution of partial differential equations using the finite element method (FEM)

231.PaddlePaddle / Quantum

The repository host gives no description.

232.BenevolentAI / guacamol

Benchmarks for generative chemistry

233.aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

234.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

235.rafat / wavelib

C Implementation of 1D and 2D Wavelet Transforms (DWT,SWT and MODWT) along with 1D Wavelet packet Transform and 1D Continuous Wavelet Transform.

• wavelets
• dwt
• continuous-wavelet-transform
• wavelet-packet-trees
• c
• cpp

236.theislab / scib

Benchmarking analysis of data integration tools

237.oemof / oemof-solph

A model generator for energy system modelling and optimisation (LP/MILP).

• energy
• energy-system
• modelling
• modelling-framework

238.NGSolve / netgen

The repository host gives no description.

• mesh-generator

239.songlab-cal / gpn

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

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

240.excessive / cpml

Cirno's Perfect Math Library: Just about everything you need for 2D/3D games. Hopefully.

• math

241.guanjq / targetdiff

The official implementation of 3D Equivariant Diffusion for Target-Aware Molecule Generation and Affinity Prediction (ICLR 2023)

• ai-for-science
• diffusion-models
• drug-design
• equivariant-networks
• iclr2023

242.mlange-42 / ark

Ark -- Archetype-based Entity Component System (ECS) for Go.

• ecs
• entity-component-system
• go
• golang
• agent-based-modeling
• gamedev
• +2 more

243.kexinhuang12345 / MolTrans

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)

244.theislab / nicheformer

Repository for Nicheformer: a foundation model for single-cell and spatial omics

245.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

246.vlang / vtl

The V Tensor Library

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

247.mreineck / pocketfft

Fork of https://gitlab.mpcdf.mpg.de/mtr/pocketfft to simplify external contributions

248.sustainable-processes / summit

Optimising chemical reactions using machine learning

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

249.weigertlab / spotiflow

Accurate and efficient spot detection for microscopy data

250.scikit-optimize / scikit-optimizeArchived

Sequential model-based optimization with a `scipy.optimize` interface

• bayesopt
• optimization
• scientific-computing
• machine-learning
• hyperparameter
• bayesian-optimization
• +9 more

251.golang / geo

S2 geometry library in Go

• go
• geometry
• geometry-library
• sphere

252.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

253.python-adaptive / adaptive

:chart_with_upwards_trend: Adaptive: parallel active learning of mathematical functions

• adaptive-learning
• machine-learning
• python
• live-plots
• parallel-computing
• adaptive-sampling
• +3 more

254.google / makaniArchived

Makani was a project to develop a commercial-scale airborne wind turbine, culminating in a flight test of the Makani M600 off the coast of Norway. All Makani software has now been open-sourced. This repository contains the working Makani flight simulator, controller (autopilot), visualizer, and command center flight monitoring tools. Additionally, almost all avionics firmware is also included, albeit potentially not in a buildable state, due to the removal of some third-party proprietary code. We hope that this code will be inspirational and useful to the kite-based windpower and wider communities.

• makani
• wind
• renewable-energy
• energy-kites
• wind-power

255.pydata / bottleneck

Fast NumPy array functions written in C

• c
• python
• numpy
• fast
• c-extension

256.broadinstitute / cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

• workflow-execution
• workflow
• cloud
• hpc
• bioinformatics
• executor
• +7 more

257.samtools / htslib

C library for high-throughput sequencing data formats

• htslib
• bioinformatics
• sam
• bam
• cram
• vcf
• +2 more

258.unknown-horizons / godot-port

Unknown Horizons Godot Engine Port

• simulation
• strategy
• game-development
• godot
• gdscript
• game

259.PetteriAimonen / libfixmath

Cross Platform Fixed Point Maths Library

260.LiangliangNan / PolyFit

Polygonal Surface Reconstruction from Point Clouds (C++ & Python)

• surface-reconstruction
• urban-modeling
• urban-reconstruction
• primitive-extraction
• piecewise-planar-object
• sharp-feature
• +2 more

261.attaswift / BigInt

Arbitrary-precision arithmetic in pure Swift

262.AstraZeneca / chemicalx

A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)

• deep-learning
• pytorch
• deep-chemistry
• graph-neural-network
• drug
• drug-pair
• +13 more

263.jerryji1993 / DNABERT

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

• kmer
• dnabert-model
• kmer-format
• gpu
• sequence
• genome
• +4 more

264.libMesh / libmesh

libMesh github repository

• fem
• finite-element-methods
• simulation
• parallel
• amr
• finite-element-analysis
• +2 more

265.JCash / voronoi

A C implementation for creating 2D Voronoi/Delauney diagrams

266.johnmcfarlane / cnl

A Compositional Numeric Library for C++

• cmake
• cpp
• fixed-point
• safe
• precision
• embedded
• +4 more

267.uwdb / Cosette

Cosette is an automated SQL solver.

• rosette
• coq
• sql
• database
• verification

268.microsoft / evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

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

269.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

270.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

271.prody / ProDy

A Python Package for Protein Dynamics Analysis

• python
• protein
• dynamics

272.MAGICS-LAB / DNABERT_2

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

• dataset
• dna
• dna-processing
• dna-training
• genome
• genome-analysis
• +10 more

273.theislab / scvelo

RNA Velocity generalized through dynamical modeling

274.stillwater-sc / universal

Large collection of number systems providing custom arithmetic for mixed-precision algorithm development and optimization for AI, Machine Learning, Computer Vision, Signal Processing, CAE, EDA, control, optimization, estimation, and approximation.

• arithmetic
• integer-arithmetic
• fixed-point-arithmetic
• rational-arithmetic
• floating-point-arithmetic
• posit-arithmetic
• +13 more

275.calico / basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

276.Dana-Farber-AIOS / pathml

Tools for computational pathology

• machine-learning
• digital-pathology
• computational-pathology
• biomedical-image-processing
• pathology
• histopathology
• +9 more

277.haddocking / pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

• python
• protein
• pdb
• bioinformatics
• structural-biology
• structural-bioinformatics
• +2 more

278.theislab / scarches

Reference mapping for single-cell genomics

• single-cell
• deep-learning
• rna-seq-analysis
• data-integration
• batch-correction
• multimodal-deep-learning
• +4 more

279.lemire / fastmod

A C/C++ header file for fast 32-bit division remainders (and divisibility tests) on 64-bit hardware.

• performance

280.hkmztrk / DeepDTA

Source code for "DeepDTA: deep drug-target binding affinity prediction"

• protein-ligand-interactions
• convolutional-neural-networks

281.biolink / biolink-model

Schema and generated objects for biolink data model and upper ontology

• biolink
• monarchinitiative
• gene-ontology
• datamodel
• standard
• specification
• +11 more

282.lilab-stanford / MUSK

The repository host gives no description.

283.brainglobe / brainglobe-atlasapi

A Python interface to access neuroanatomical atlases

• neuroscience
• python
• microscopy
• registration
• visualisation
• brain
• +1 more

284.J-SNACKKB / FLIP

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

• protein
• protein-sequences
• protein-design
• representation-learning
• protein-fitness-prediction
• protein-function-prediction

285.morphonets / SNT

The framework for quantification of neuronal anatomy

• neuroscience
• neuroanatomy-toolbox
• imagej
• imagej2
• scijava
• neurons
• +3 more

286.jokruger / dec128

Zero-dependency 128-bit fixed-point decimal for Go. Exact SQL NUMERIC / PostgreSQL semantics, no heap allocation, no panics — built for money, ledgers and banking arithmetic.

• decimal
• fixed-point
• go
• golang
• finance
• money
• +11 more

287.clean-css / clean-css

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

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

288.cpmech / gosl

Linear algebra, eigenvalues, FFT, Bessel, elliptic, orthogonal polys, geometry, NURBS, numerical quadrature, 3D transfinite interpolation, random numbers, Mersenne twister, probability distributions, optimisation, differential equations.

• scientific-computing
• linear-algebra
• differential-equations
• sparse-systems
• parallel-computations
• computational-geometry
• +6 more

289.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

290.hail-is / hail

Cloud-native genomic dataframes and batch computing

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

291.romeric / Fastor

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

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

292.qhull / qhull

Qhull development for www.qhull.org -- Qhull 2020.2 (8.1-alpha1) at https://github.com/qhull/qhull/wiki

• qhull
• computational-geometry
• convex-hull
• delaunay-triangulation
• voronoi-diagram
• halfspace-intersection
• +3 more

293.dib-lab / khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

• dna
• k-mer
• python
• bloom-filter
• count-min-sketch
• graph-traversal
• +1 more

294.Yixin-Hu / TetWild

Robust Tetrahedral Meshing in the Wild.

• geometry-processing
• tetrahedral-meshing
• surface-repair
• 3d-triangulation

295.hms-dbmi / CHIEF

Clinical Histopathology Imaging Evaluation Foundation Model

296.chebfun / chebfun

Chebfun: numerical computing with functions.

297.rpng / kalibr_allanArchived

IMU Allan standard deviation charts for use with Kalibr and inertial kalman filters.

• imu
• allan-variance
• kalibr
• calibration
• imu-noise
• noise-values
• +1 more

298.alphaville / optimization-engine

Nonconvex embedded optimization: code generation for fast real-time optimization + ROS support

• embedded-optimization
• nonconvex
• model-predictive-control
• rust-library
• rust
• rust-crate
• +14 more

299.HeliXonProtein / OmegaFold

OmegaFold Release Code

300.acado / acado

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.