Research Software – Computational Biology

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 ]

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