Dynetica - A Simulator of Dynamic Networks

(written in Java; needs JDK1.3 or above)
Copyright © 2000-2003 by Lingchong You.

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Installation

Download the current version of Dynetica 1.2 Beta (Sourceforge).

Unzip this file to a directory, say DyneticaDirectory. In DyneticaDirectory you should have two items, one is a jar file: Dynetica.jar, the other is a subdirectory called "examples", which holds some example models built in Dynetica.

To run Dynetica, you can type the following command in a command window (in Unix or Windows):

java -classpath Dynetica.jar Dynetica // NOTE: if you're in the directory "DyneticaDirectory"

java -classpath <DyneticaDirectory>/Dynetica.jar Dynetica //NOTE: if you're anywhere else

Previous version:

Download previous version

Screenshots

The main window showing a simplified model of phage T7 intracellular growth cycle

A figure window showing the simulated time-courses for selected components.

Click here for the User's guide of Dynetica (PDF). You may also check out a preprint (PDF) describing this software.

Features

Graphic construction of kinetic models of various biological systems.
The user needs only specify the components in the system and their interactions. The program automatically generates the ordinary differential equations.
Time course simulations using either deteriministic algorithms or stochastic algorithms (currently only the Gillespie algorithm has been implemented).
Basic sensitivity analysis