Dynetica - A Simulator of Dynamic Networks
(written in Java; Java 1.7 preferred)
Copyright © 2000-2003 by Lingchong You.
Please contact Lingchong You (email@example.com) if you run into any problems or identify any bugs.
Download the current version of Dynetica 2.0 Beta
Unzip Dynetica2.0.zip. The unzipped folder will contain two subfolders: "Current Distribution" and "tutorial_models". Go into "Current distribution", you'll see a jar file, Dynetica.jar, which is the binary file of Dynetica. It depends on several libraries, which are put in the directory "lib". Do not change the name of the folder or make any changes to the .jar files in the folder.
In Windows (7 or 8) or MacOS (10.6 or above), double-clicking Dynetica.jar should run the program.
Alternatively,you can use a command window, go to the folder "Current Distribution", and then use the following command:
java -jar Dynetica.jar
This appears to be required in Linux (tested in Ubuntu)
When you first run Dynetica, no models are loaded. You can get a sense of how to run/build models by opening the input files in "tutorial_models". The documentation included here is somewhat outdated but is still useful to give the initial guidance for constructing and analyzing Dynetica models. This documentation will be updated in the near future.
Download previous version
The main window showing a simplified model of phage T7 intracellular growth cycle
A figure window showing the simulated time-courses for selected components.
- Graphic construction of kinetic models of various biological
- 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
Duke University ©2008