| Package Name | Access | Summary | Updated |
|---|---|---|---|
| PyDAS | public | A Python wrapper to several differential algebraic system solvers | 2025-03-25 |
| cupsoda | public | cupSODA is a black-box deterministic simulator of biological systems for NVIDIA graphics cards (GPUs), using the CUDA framework. | 2025-03-25 |
| stochkit-lite | public | StochKit is an extensible stochastic simulation framework developed in C++ that aims to make stochastic simulation accessible to practicing biologists and chemists, while remaining open to extension via new stochastic and multiscale algorithms. | 2025-03-25 |
| atomizer | public | Project for the translation of SBML files into BNGL files | 2025-03-25 |
| stochkit | public | StochKit is an extensible stochastic simulation framework developed in C++ that aims to make stochastic simulation accessible to practicing biologists and chemists, while remaining open to extension via new stochastic and multiscale algorithms. | 2025-03-25 |
| kappa | public | Kappa is a rule-based language for modeling systems of interacting agents. | 2025-03-25 |
| graphviz | public | Graphviz is open source graph visualization software | 2025-03-25 |
| pygraphviz | public | PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. | 2025-03-25 |
| pysb | public | PySB (pronounced "Pie Ess Bee") is a framework for building rule-based mathematical models of biochemical systems. It works nicely with scientific Python libraries such as NumPy, SciPy and SymPy for model simulation and analysis. | 2025-03-25 |
| nfsim | public | NFsim is a network-free stochastic simulator for biochemical reaction networks | 2025-03-25 |
| bionetgen | public | BioNetGen is software for the specification and simulation of rule-based models of biochemical systems | 2025-03-25 |
