Mesa 3
Mesa 3: Agent-based modeling with Python in 2025 - Published in JOSS (2025)
DART
DART: Dynamic Animation and Robotics Toolkit - Published in JOSS (2018)
cellular_raza
cellular_raza: Cellular Agent-based Modeling from a Clean Slate - Published in JOSS (2025)
FURY
FURY: advanced scientific visualization - Published in JOSS (2021)
simstudy
simstudy: Illuminating research methods through data generation - Published in JOSS (2020)
UXsim
UXsim: lightweight mesoscopic traffic flow simulator in pure Python - Published in JOSS (2025)
New developments in PySDM and PySDM-examples v2
New developments in PySDM and PySDM-examples v2: collisional breakup, immersion freezing, dry aerosol initialization, and adaptive time-stepping - Published in JOSS (2023)
pyro
pyro: a framework for hydrodynamics explorations and prototyping - Published in JOSS (2019)
TESPy
TESPy: Thermal Engineering Systems in Python - Published in JOSS (2020)
VILLASnode
VILLASnode: An Open-Source Real-time Multi-protocol Gateway - Published in JOSS (2025)
Monte Carlo / Dynamic Code (MC/DC)
Monte Carlo / Dynamic Code (MC/DC): An accelerated Python package for fully transient neutron transport and rapid methods development - Published in JOSS (2024)
EPyT
EPyT: An EPANET-Python Toolkit for Smart Water Network Simulations - Published in JOSS (2023)
PyRolL - An Extensible OpenSource Framework for Rolling Simulation
PyRolL - An Extensible OpenSource Framework for Rolling Simulation - Published in JOSS (2024)
t8code - modular adaptive mesh refinement in the exascale era
t8code - modular adaptive mesh refinement in the exascale era - Published in JOSS (2025)
EPyT-Flow
EPyT-Flow: A Toolkit for Generating Water Distribution Network Data - Published in JOSS (2024)
swiftsimio
swiftsimio: A Python library for reading SWIFT data - Published in JOSS (2020)
epiworldR
epiworldR: Fast Agent-Based Epi Models - Published in JOSS (2023)
OMG
OMG: A Scalable and Flexible Simulation and Testing Environment Toolbox for Intelligent Microgrid Control - Published in JOSS (2020)
A Python Library for Pre- and Post-Processing of DAMASK Simulations
A Python Library for Pre- and Post-Processing of DAMASK Simulations - Published in JOSS (2025)
pyGCodeDecode
pyGCodeDecode: A Python package for time-accurate GCode simulation in material extrusion processes - Published in JOSS (2024)
Pooltool
Pooltool: A Python package for realistic billiards simulation - Published in JOSS (2024)
spINAR
spINAR: An R Package for Semiparametric and Parametric Estimation and Bootstrapping of Integer-Valued Autoregressive (INAR) Models - Published in JOSS (2024)
UnfoldSim.jl
UnfoldSim.jl: Simulating continuous event-based time series data for EEG and beyond - Published in JOSS (2025)
SimuPy
SimuPy: A Python framework for modeling and simulating dynamical systems - Published in JOSS (2017)
WATTS
WATTS: Workflow and template toolkit for simulation - Published in JOSS (2022)
ProgPy
ProgPy: Python Packages for Prognostics and Health Management of Engineering Systems - Published in JOSS (2023)
SHARPy
SHARPy: A dynamic aeroelastic simulation toolbox for very flexible aircraft and wind turbines - Published in JOSS (2019)
TrixiParticles.jl
TrixiParticles.jl: Particle-based multiphysics simulation in Julia - Published in JOSS (2025)
DisCoTec
DisCoTec: Distributed higher-dimensional HPC simulations with the sparse grid combination technique - Published in JOSS (2025)
Adamantine 1.0
Adamantine 1.0: A Thermomechanical Simulator for Additive Manufacturing - Published in JOSS (2024)
rsimsum
rsimsum: Summarise results from Monte Carlo simulation studies - Published in JOSS (2018)
OPEM
OPEM : Open Source PEM Cell Simulation Tool - Published in JOSS (2018)
Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape
Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape - Published in JOSS (2023)
BlueCelluLab
BlueCelluLab: Biologically Detailed Neural Network Experimentation API - Published in JOSS (2024)
PlantSimEngine
PlantSimEngine: A Simulation Engine For The Soil-Plant-Atmosphere System - Published in JOSS (2023)
deeplenstronomy
deeplenstronomy: A dataset simulation package for strong gravitational lensing - Published in JOSS (2021)
RFBzero
RFBzero: A Python package for zero-dimensional simulation of redox flow battery cycling - Published in JOSS (2024)
villager
villager: A framework for designing and executing agent-based models in R - Published in JOSS (2022)
OpenCMP
OpenCMP: An Open-Source Computational Multiphysics Package - Published in JOSS (2022)
RidePy
RidePy: A fast and modular framework for simulating ridepooling systems - Published in JOSS (2024)
NLSE
NLSE: A Python package to solve the nonlinear Schrödinger equation - Published in JOSS (2024)
RustBCA
RustBCA: A High-Performance Binary-Collision-Approximation Code for Ion-Material Interactions - Published in JOSS (2021)
popsynth
popsynth: A generic astrophysical population synthesis framework - Published in JOSS (2021)
SCONE
SCONE: Open Source Software for Predictive Simulation of Biological Motion - Published in JOSS (2019)
GridFormat
GridFormat: header-only C++-library for grid file I/O - Published in JOSS (2023)
ViMMS 2.0
ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics - Published in JOSS (2022)
FlowerMD
FlowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics - Published in JOSS (2023)
DeepBench
DeepBench: A simulation package for physical benchmarking data - Published in JOSS (2025)
Simframe
Simframe: A Python Framework for Scientific Simulations - Published in JOSS (2022)
Simulating instrumental systematics of Cosmic Microwave Background experiments with s4cmb
Simulating instrumental systematics of Cosmic Microwave Background experiments with s4cmb - Published in JOSS (2021)
Copper
Copper: a performance curve generator for building energy simulation - Published in JOSS (2023)
oxDNA
oxDNA: coarse-grained simulations of nucleic acids made simple - Published in JOSS (2023)
AirTrafficSim
AirTrafficSim: An open-source web-based air traffic simulation platform. - Published in JOSS (2023)
Utopia
Utopia: A Comprehensive and Collaborative Modeling Framework for Complex and Evolving Systems - Published in JOSS (2020)
WorldDynamics.jl
WorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Models - Published in JOSS (2024)
PAS
PAS: a Python Anesthesia Simulator for drug control - Published in JOSS (2023)
DE-Sim
DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python - Published in JOSS (2020)
CancerSim
CancerSim: A Cancer Simulation Package for Python 3 - Published in JOSS (2020)
polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories
polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories - Published in JOSS (2021)
QMix
QMix: A Python package for simulating the quasiparticle tunneling currents in SIS junctions - Published in JOSS (2019)
GPUE
GPUE: Graphics Processing Unit Gross--Pitaevskii Equation solver - Published in JOSS (2018)
MACE
MACE: a Machine-learning Approach to Chemistry Emulation - Published in JOSS (2025)
tightbinder
tightbinder: A Python package for semi-empirical tight-binding models of crystalline and disordered solids - Published in JOSS (2024)
pylattica
pylattica: a package for prototyping lattice models in chemistry and materials science - Published in JOSS (2024)
FIPS
FIPS: An R Package for Biomathematical Modelling of Human Fatigue Related Impairment - Published in JOSS (2020)
Learning Simulator
Learning Simulator: A simulation software for animal and human learning - Published in JOSS (2021)
directChillFoam
directChillFoam: an OpenFOAM application for direct-chill casting - Published in JOSS (2023)
Oetqf: A Julia package for quasi-dynamic earthquake cycle simulation
Oetqf: A Julia package for quasi-dynamic earthquake cycle simulation - Published in JOSS (2025)
GORILLA
GORILLA: Guiding-center ORbit Integration with Local Linearization Approach - Published in JOSS (2023)
skijumpdesign
skijumpdesign: A Ski Jump Design Tool for Specified Equivalent Fall Height - Published in JOSS (2018)
pyelli
An open source ellipsometry analysis tool for reproducible and comprehensible building of optical models.
BiGGer
BiGGer: A Model Transformation Tool written in Java for Bigraph Rewriting in GrGen.NET - Published in JOSS (2024)
POMDPStressTesting.jl
POMDPStressTesting.jl: Adaptive Stress Testing for Black-Box Systems - Published in JOSS (2021)
The MOOSE Thermal Hydraulics Module
The MOOSE Thermal Hydraulics Module - Published in JOSS (2024)
dispersiveshallowwater.jl
A Julia library of structure-preserving numerical methods for dispersive wave equations
PathSim - A System Simulation Framework
PathSim - A System Simulation Framework - Published in JOSS (2025)
SOAP
SOAP: A Python Package for Calculating the Properties of Galaxies and Halos Formed in Cosmological Simulations - Published in JOSS (2025)
dia
dia: An R package for the National Oceanic and Atmospheric Administration dam impact analysis - Published in JOSS (2025)
KeepDelta
KeepDelta: A Python Library for Human-Readable Data Differencing - Published in JOSS (2025)