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ISBJava Overview

CompBio Group, Institute for Systems Biology

Version 2.4.4, Released 2006/09/28

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


The ISBJava project is a library (collection) of classes written in the Java programming language, that are intended to be used for research in computational biology. ISBJava was written by Stephen Ramsey in the laboratory of Hamid Bolouri at ISB. For more information, please refer to the ISBJava home page.

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 the ISBJava library is included with the library installer. You can find the code in the "src" subdirectory of the installation directory for this program.

External Libraries and Credits

Certain packages in the ISBJava library make use of external libraries. In order to successfully compile the ISBJava library, you will need to have these external libraries installed on your computer. 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.


For documentation on how to use the ISBJava program, please consult the ISBJava User Manual. For detailed documentation of the application programming interface (API) to the ISBJava library, please consult the ISBJava home page. When ISBJava is installed, a PDF version of the API documentation "APIDocumentation.pdf" can be found in the "docs" subdirectory of the installation directory.

Contact Information

The initial version of ISBJava was implemented by Stephen Ramsey. Many people 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:

isbjava NOSPAM at NOSPAM

Last updated: 2006/01/30 20:19:24

Please e-mail comments or corrections regarding this document to: isbjava NOSPAM at NOSPAM