mlpack 4
mlpack 4: a fast, header-only C++ machine learning library - Published in JOSS (2023)
ReproZip
ReproZip: The Reproducibility Packer - Published in JOSS (2016)
volesti
volesti: A C++ library for sampling and volume computation on convex bodies - Published in JOSS (2025)
qnm
qnm: A Python package for calculating Kerr quasinormal modes, separation constants, and spherical-spheroidal mixing coefficients - Published in JOSS (2019)
AMReX
AMReX: a framework for block-structured adaptive mesh refinement - Published in JOSS (2019)
py-pde
py-pde: A Python package for solving partial differential equations - Published in JOSS (2020)
Sciris
Sciris: Simplifying scientific software in Python - Published in JOSS (2023)
Pyret
Pyret: A Python package for analysis of neurophysiology data - Published in JOSS (2017)
$hp\mathrm{3D}$
$hp\mathrm{3D}$: A Scalable MPI/OpenMP $hp$-Adaptive Finite Element Software Library for Complex Multiphysics Applications - Published in JOSS (2024)
diffsol: Rust crate for solving differential equations
diffsol: Rust crate for solving differential equations - Published in JOSS (2026)
WRF-CMake
WRF-CMake: integrating CMake support into the Advanced Research WRF (ARW) modelling system - Published in JOSS (2019)
OGRe
OGRe: An Object-Oriented General Relativity Package for Mathematica - Published in JOSS (2021)
OwlDE
OwlDE: making ODEs first-class Owl citizens - Published in JOSS (2019)
ambrosia
ambrosia: An R package for calculating and analyzing food demand that is responsive to changing incomes and prices - Published in JOSS (2021)
simpeg
Simulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications.
astrophot
A fast, flexible, automated, and differentiable astronomical image 2D forward modelling tool for precise parallel multi-wavelength photometry
itk
Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
avogadro
Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
best-of-atomistic-machine-learning
🏆 A ranked list of awesome atomistic machine learning projects ⚛️🧬💎.
collapse
Advanced and Fast Data Transformation in R
meshpy
2D/3D simplicial mesh generator interface for Python (Triangle, TetGen, gmsh)
qha
A Python package for calculating thermodynamic properties under quasi-harmonic approximation, using data from ab-initio calculations
casadi
CasADi is a symbolic framework for numeric optimization implementing automatic differentiation in forward and reverse modes on sparse matrix-valued computational graphs. It supports self-contained C-code generation and interfaces state-of-the-art codes such as SUNDIALS, IPOPT etc. It can be used from C++, Python or Matlab/Octave.
xyz2graph
Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.
fluidx3d
The fastest and most memory efficient lattice Boltzmann CFD software, running on all GPUs and CPUs via OpenCL. Free for non-commercial use.
https://github.com/pypr/pysph
A framework for Smoothed Particle Hydrodynamics in Python
NeuroDiffEq
NeuroDiffEq: A Python package for solving differential equations with neural networks - Published in JOSS (2020)
sundials
Official development repository for SUNDIALS - a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers. Pull requests are welcome for bug fixes and minor changes.
geoschem-gcpy
Python toolkit for GEOS-Chem. Contains basic plotting scripts, plus the suite of GEOS-Chem benchmarking utilities.
multiscale_spatial_image
Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.
myfempy
Myfempy is a python package based on finite element method to multiphysics analysis.
geos-chem
GEOS-Chem "Science Codebase" repository. Contains GEOS-Chem science routines, run directory generation scripts, and interface code. This repository is used as a submodule within the GCClassic and GCHP wrappers, as well as in other modeling contexts (external ESMs).
rockyml
⛰️ RockyML - A High-Performance Scientific Computing Framework for Non-smooth Machine Learning Problems
burn
Burn is a next generation Deep Learning Framework that doesn't compromise on flexibility, efficiency and portability.
pysiral
python package for scientific computing (satellite radar altimetry over ice-covered ocean)
polydeal
C++ implementation of Polygonal Discontinuous Galerkin method within the deal.II Finite Element library.
lintf2_ether_ana_postproc
Analysis postprocessing utilities for my molecular dynamics simulations of LiTFSI-Ether mixtures
itkwidgets
An elegant Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry.
hemco
The Harmonized Emissions Component (HEMCO), developed by the GEOS-Chem Support Team.
plip
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
gcclassic
This repository contains the "superproject" wrapper for the "Classic" configuration of the GEOS-Chem model of atmospheric chemistry and composition.
MeteoInfo
MeteoInfo: GIS, scientific computation and visualization environment.
p4pdes
C and Python examples from my book on using PETSc and Firedrake to solve PDEs
https://github.com/rubixml/tensor
A library and extension that provides objects for scientific computing in PHP.
https://github.com/usnistgov/fipy
FiPy is a Finite Volume PDE solver written in Python
dishtiny
DISHTINY: A Platform for Studying Open-Ended Evolutionary Transitions in Individuality
cytoflow
A Python toolbox for quantitative, reproducible flow cytometry analysis
handy
Some handy python functions for statistics, computation and plotting (which are missed in numpy and matplotlib).
https://github.com/cpmech/russell
Rust Scientific Libary. ODE and DAE (Runge-Kutta) solvers. Special functions (Bessel, Elliptic, Beta, Gamma, Erf). Linear algebra. Sparse solvers (MUMPS, UMFPACK). Probability distributions. Tensor calculus.
https://github.com/open-cogsci/datamatrix
An intuitive, Pythonic way to work with tabular data
https://github.com/mineralscloud/crystallographybase.jl
This package contains some basic functionalities of Crystallography.jl
https://github.com/conradsnicta/armadillo-code
Armadillo: fast C++ library for linear algebra & scientific computing - https://arma.sourceforge.net
3d-forest
Visualization, processing and analysis of Lidar point clouds, mainly focused on forest environment. New version of 3D Forest. Process files with terabytes of data. Edit new point attributes. Simple addition of new features by plugins.
gis4wrf
QGIS toolkit 🧰 for pre- and post-processing 🔨, visualizing 🔍, and running simulations 💻 in the Weather Research and Forecasting (WRF) model 🌀
https://github.com/mineralscloud/elastic-stability-conditions
A Python package that can verify the necessary and sufficient elastic stability conditions in various crystal systems
https://github.com/clandininlab/flystim
Visual stimulus generator for neuroscience experiments
https://github.com/althonos/rlinalg
Linear Algebra routines for Python as implemented in the R language.
https://github.com/agahkarakuzu/sunrise
NumPy, SciPy, MRI and Music | Presented at ISMRM 2021 Sunrise Educational Session
https://github.com/algebraicjulia/structured-epidemic-modeling
Results and software for our paper on structured epidemic modeling
https://github.com/angrymaciek/efcomp
Advanced methods for efficient scientific computing in Python/R/C++
