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.]

Dependency Diagrams, Todd Johnson thesis software: [Dependency Diagrams]

Graph-Constrained Correlation Dynamics, Todd Johnson thesis software: [Graph-Constrained Correlation Dynamics.]

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 ]

Sigmoid model GUI and database: [Sourceforge software repository for Sigmoid]; [Project page ]; [ Ben Compani PhD thesis].