graphsim
graphsim: An R package for simulating gene expression data from graph structures of biological pathways - Published in JOSS (2020)
SimuPy
SimuPy: A Python framework for modeling and simulating dynamical systems - Published in JOSS (2017)
AdditiveFOAM
AdditiveFOAM: A Continuum Multiphysics Code for Additive Manufacturing - Published in JOSS (2025)
macpan2
Tools for building and calibrating compartmental models of infectious disease.
pydesrap_mms
Reproducible analytical pipeline (RAP) for Python discrete-event simulation (DES) implementing an M/M/s queueing model.
rdesrap_mms
Reproducible analytical pipeline (RAP) for R discrete-event simulation (DES) implementing an M/M/s queueing model.
https://github.com/ami-iit/jaxsim
A differentiable physics engine and multibody dynamics library for control and robot learning.
transit-lab-simmetro-docs
TransitLab SimMETRO is an urban heavy-rail operations simulation model developed at the MIT Transit Lab, built upon decades of research. This repository contains a comprehensive documentation. While the full package may not be open-sourced soon, the documentation provides valuable insights into the capabilities of the simulation model.
helipad
An agent-based modeling framework for Python with a shallow learning curve and powerful visualization capabilities.
ghosts
GHOSTS is a realistic user simulation framework for cyber experimentation, simulation, training, and exercise
https://github.com/austinjhunt/petrinet-webgme-designstudio
A custom design studio for modeling and simulating distributed systems as Petri (place/transition) Nets, built with JointJS, WebGME, and NodeJS.
desirna
State of the art software for RNA sequence design. The first to solve the Eterna benchmark!
cultural_evolution_abm_tutorial
This tutorial shows how to create very simple simulation or agent-based models of cultural evolution in R
warteschlangensimulator
Warteschlangensimulator is a free, platform independent, discrete-event, stochastic simulator which allows to model queueing systems in form of flowcharts.
https://github.com/ravenexp/pyplanetarium
Python bindings for Planetarium sub-pixel precision light spot rendering library
phgasnets
Port-Hamiltonian Model for Gas Networks with Compressors (mirror repository)
physicell
PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch. Thanks!
https://github.com/danielvartan/logoscope
🖍️ NetLogo Syntax Highlighting for Visual Studio Code
https://github.com/exabyte-io/esse
JSON schemas and examples representing structural data, characteristic properties, modeling workflows and related data about materials standardizing the diverse landscape of information
