The Computable Plant software web site contains most of our recent disseminated software. The link is here. Further software is available at some of the PhD thesis pages, and/or below.
Cellerator and xCellerator, Shapiro and Mjolsness, together with related packages: here. A Mathematica package designed to aide biological modeling via the automated conversion of chemical reactions into ODEs and/or stochastic processes, their subsequent solution via numerical integration, and analysis thereof.
ERleap, David Orendorff thesis software: [ERleap]
Hierleap, David Orendorff thesis software: [Hierleap.]
Graph-Constrained Correlation Dynamics, Todd Johnson thesis software: [Graph-Constrained Correlation Dynamics.] This also requires: Dependency Diagrams, Todd Johnson thesis software: [Dependency Diagrams]
Stochastic Gradient descent software for parameter estimation in stochastic biochemical models, by Yuanfeng Wang: here.
Cambium intermediate modeling language for morphodynamics: This page.
Dynamical Grammars: Guy Yosiphon thesis software [ “Plenum” Dynamical Grammar implementation software site ]