Mesa 3
Mesa 3: Agent-based modeling with Python in 2025 - Published in JOSS (2025)
SimuPy
SimuPy: A Python framework for modeling and simulating dynamical systems - Published in JOSS (2017)
Utopia
Utopia: A Comprehensive and Collaborative Modeling Framework for Complex and Evolving Systems - Published in JOSS (2020)
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.
HELICS
Hierarchical Engine for Large-scale Infrastructure Co-Simulation (HELICS)
wifi-based-landmark-estimation
Research project files concerning non-stationary landmark localization
https://github.com/cloudsimplus/cloudsimplus
State-of-the-art Framework 🏗 for Cloud Computing ⛅️ Simulation: a modern, full-featured, easier-to-use, highly extensible 🧩, faster 🚀 and more accurate ☕️ Java 24+ tool for cloud computing research 🎓 Examples: https://github.com/cloudsimplus/cloudsimplus-examples
cbdc-offline-sim
A CBDC simulation framework, designed to simulate an offline implementation with a barabasi albert graph and fradulent nodes. Markov processes are used for up and down states as well as transaction frequency.
helipad
An agent-based modeling framework for Python with a shallow learning curve and powerful visualization capabilities.
simobility
simobility - light-weight mobility simulation framework. Best for quick prototyping
https://github.com/bluebrain/coreneuron
Simulator optimized for large scale neural network simulations.
https://github.com/bluebrain/multiscalerun
Python package to run brain cells simulation at different scales
shapespyer
The project provides Python tool-chain and shell scripts for molecular simulation workflows: preparation, running and analysing molecular dynamics (MD) simulations of bio- and organic soft condensed matter.
PathSim - A System Simulation Framework
PathSim - A System Simulation Framework - Published in JOSS (2025)
traversecraft
TraverseCraft is a versatile Python library for creating static, animated, and interactive visualizations, enabling robust simulations for AI, RL, and ML. Ideal for students, educators, and researchers, it allows real-time observation of algorithm behaviors with an intuitive interface.
proteus
Coupled atmosphere-interior framework to simulate the temporal evolution of rocky planets.
https://github.com/bvieth/powsimr
Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
PyBullet Industrial
PyBullet Industrial: A process-aware robot simulation - Published in JOSS (2023)
physicell
PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch. Thanks!