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Dizzy Overview

CompBio Group, Institute for Systems Biology

Version 1.11.4, Released 2006/09/28

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Contents

  1. Introduction
  2. License and Disclaimer
  3. Supported Platforms
  4. Source Code
  5. External Libraries and Credits
  6. Documentation
  7. Screenshot
  8. Contact Information

Introduction

Dizzy is a chemical kinetics stochastic simulation software package written in Java. It provides a model definition environment and an implementation of the Gillespie, Gibson-Bruck, and Tau-Leap stochastic algorithms. The software is based on the ISBJava library. An article describing Dizzy is available. Dizzy was written by Stephen Ramsey in the laboratory of Hamid Bolouri at ISB.

License and Disclaimer

This software is licensed under the GNU Lesser General Public License (LGPL), which is a standard "free software" and "open source" license. A copy of the license agreement is available online, as well as in the "docs/License.html" file in the installation directory for this software.

This version is alpha (experimental) software. Please be patient while we fix bugs, add new features, and add (much needed) documentation. Your patience is appreciated. Please be advised that the Institute for Systems Biology and the authors disclaim any liability stemming from the use of this software, as stated in the license agreement.

Supported Platforms

This software requires a Java Runtime Environment (JRE) version 1.4 or newer, because it uses Java 1.4 language features and extensions. It has been tested on Windows XP Professional, Fedora Core 1 Linux, and Mac OSX. The software should function properly on most platforms for which the Sun Java Runtime Environment is available.

Source Code

The source code for this application is included with the application installer. You can find the code in the file "ISBJava-src.tar.gz" that is installed in the "src" subdirectory of the installation directory for this program.

External Libraries and Credits

The Dizzy system relies upon a number of external libraries, all of which are supplied with the Dizzy installer. For a list of external library dependencies and pointers to the web sites where the source code for these libraries can be obtained, please refer to the external libraries section of the user manual.

Documentation

For documentation on how to use the Dizzy program, please consult the Dizzy User Manual. When Dizzy is installed, a PDF version of the manual "UserManual.pdf" can be found in the "docs" subdirectory of the installation directory. For detailed documentation of the application programming interface (API) to the Dizzy system, please consult the ISBJava home page. In addition, the Dizzy system provides a set of sample model definition files.

Screenshot

screenshot
Screen shot of the Dizzy program

Contact Information

Dizzy was developed by Stephen Ramsey. Many people have provided help and resources. If you have questions about this software, or if you have a bug report that you would like to submit, please contact the CompBio Group at Institute for Systems Biology by sending email to:
dizzy NOSPAM at NOSPAM systemsbiology.org.

Last updated: 2006/01/30 20:19:25

Please e-mail comments or corrections regarding this document to: dizzy NOSPAM at NOSPAM systemsbiology.org