graphsim
graphsim: An R package for simulating gene expression data from graph structures of biological pathways - Published in JOSS (2020)
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.
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.
cultural_evolution_abm_tutorial
This tutorial shows how to create very simple simulation or agent-based models of cultural evolution in R
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!
desirna
State of the art software for RNA sequence design. The first to solve the Eterna benchmark!