Category Archives: Software & Databases

StochSS: Stochastic Simulation Service | A Cloud Computing Framework for Modeling and Simulation of Stochastic Biochemical Systems

This software was easy to install and very intuitive.  If you are interested in doing stochastic simulations, you might give it a try.


Bayesian modeling

Dr. Ma provides quite comprehensible explanation of Bayesian modeling in the following link. This type of modeling has recently become very popular in some biological fields.

The Golly “John Conway’s Game of Life” Simulator




This is a link to state-of-the-art software for ODE continuation and bifurcation problems.


An introduction to AUTO.

Printer Information

If the color printer in the back of the room does not appear as “BushPrint”, you may also find it as   “HershyPrintW”.  The IP address is

XPPAUT Documentation

XPP Documentation – ODE File Syntax

XPP Documentation – The Entire Manual

Printer Information

The printer in the back of the room is “bushprint” with IP address

XPPAUT – X-Windows PhasePlane plus Auto


VCell – The Virtual Cell

VCell – The Virtual Cell.