BioUML workbench

• Windows: download (3.5 mb)
• other platforms: will be available soon.

Requirements

• Java 1.3 (or later) virtual machine. You can download it from Sun's Java web site.
• Processor: Pentium II 500 or higher
• Memory: 128 mb or more
• Disk space: 10 mb
• MATLAB 5.3 or later
  BioUML framework can work without MATLAB, however possibility of biological systems simulation will be disabled.

BioUML modules

KEGG/pathways

• complete module (1.4 mb) contains Java code and main data from KEGG/pathway database.
• activated module (30 kb). You need KEGG/pathway database that is installed on your computer or local network.

TRANSPATH module (32 kb)
This module contains only Java code to incorporate TRANSPATH^® database into BioUML framework. You need TRANSPATH database to use this module. We test this module for TRANSPATH 2.4.

GeneNet module (58 kb)

This module contains only Java to incorporate GeneNet database into BioUML framework. During installation this module allows you to download GeneNet database from official GeneNet server (wwwmgs.bionet.nsc.ru).

BioUML development kit

BioUML Development Kit (BDK) should allow you to develop your own modules for BioUML as well as modify and improve BioUML framework for your own needs.

BioUML development kit includes:

• All BioUML sources (biouml package).
  They are available under GNU LGPL license.
• Java libraries from Biosoft.Ru
  These libraries (ru.biosoft package) are essential part of BioUML Development Kit and also available under GNU LGPL license.
• Java libraries from Jakarta project (LOG4G, Xerces, Xalan).
  We include only binary files while anybody can download sources from Jakarta project web site: http://jakarta.apache.org
• Java libraries from DevelopmentOnTheEdge.com.
  These library are used for BioUML framework UI.
• BeanExplorer - a new methodology for rapid development of application user interface.
• Miscellaneous:
  • Automatically generated documentation
  • UML diagrams (as gif images and as part of Together project)
  • build.xml - makefile for ant to compile and run BioUML framework or it parts
  • examples - several diagrams as an example.