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BioUML development kit
BioUML Development Kit (BDK) allows to Java developer implement their own
plug-ins for
BioUML workbench and BioUML server.
Download (35 Mb).
We have started to write BioUML developer guide that should help a developer in
his work:
Developer guide
Other useful information:
Compilation
To compile BioUML workbench from source files you need to use Ant (http://ant.apache.org/).
Build.xml file located in bdk/src directory.
Main targets are:
- ant plugin.all - creates jars (compile if necessary) for all BioUML plugins.
- ant run - starts BioUML workbench. Alternatively you may use bdk/run.bat (Windows) or
bdk/run.sh (Linux)
"Out of memory exception"
With default ant settings you can get "Out of memory exception" during BioUML compilation.
One of the solution of this problem is following:
- find ../bin/ant.bat file (for Linux ../bin/ant) in directory where Ant is
installed
- add line below in the beginning of the file
SET ANT_OPTS=%ANT_OPTS% -Xmx256m
BDK content
We have tried to make BDK
distributive compact as possible, thus documentation and source code for third
party libraries are not included in the distributive. Developers can download
them from corresponding web sites, listed below.
BioUML development kit includes:
- BioUML workbench sources (biouml package)
They are available under GNU LGPL license.
(c) Copyright Institute of Systems Biology 2002-2008. All rights reserved.
- Java libraries from Biosoft.Ru.
These libraries (ru.biosoft packages) are essential part of BioUML Development
Kit.
They are available under GNU LGPL license.
(c) Copyright Biosoft.Ru 2002-2008. All rights reserved.
http://www.biosoft.ru
- Java libraries from (package com.developmentontheedge)
These library are used for BioUML framework UI.
Copyright © 2001-2008 DevelopmentOnTheEdge.com. All Rights Reserved.
http://www.developmentontheedge.com
- BeanExplorer(TM)
New methodology for rapid development of application
user interface.
Copyright © 2001-2008 DevelopmentOnTheEdge.com. All Rights Reserved.
http://www.BeanExplorer.com.
- Eclipse platform runtime
(c) Copyright IBM Corp. and others 2000-2004. All rights reserved.
http://www.eclipse.org
- Java libraries from Jakarta project (LOG4J, CLI)
Copyright © 1999-2005 The Apache Software Foundation. All Rights Reserved.
http://www.apache.org
- Systems Biology Workbench
Copyright 2001-2007 California Institute of Technology and Japan Science and
Technology Corporation.
http://www.sbw-sbml.org
- Rhino: JavaScript for Java
Copyright © 1998-2003 The Mozila Organization.
http://www.mozilla.org
- MySQL AB's JDBC Driver for MySQL
Copyright (c) 2002/2003 MySQL AB
http://www.mysql.com
- JGraph, JGraph-Addons
Copyright (c) 2000-2004 Copyright JGraph, Ltd. All Rights Reserved.
http://www.jgraph.com
- SBML semantic test suite
Slightly modified version of original
SBML Semantic Test Suite - Beta Release developed by Andrew Finney.
- JUnit
http://www.junit.org
- build.xml - makefile for Ant to compile and run BioUML
workbench or it
parts.
Other modules can include additional software developed by third parties.
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BioUML tutorial
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October 10, 8.30-12.30 a.m - tutorial
"BioUML - integrated platform for building virtual cell and virtual physiological human"
on ICSB 2010 conference.
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Development roadmap was updated
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It outlines of the future releases that the BioUML project hopes to accomplish.
More...
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SBML tests passed 100%
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BioUML version 0.9.0 have passed all tests from SBML test suite version 2.0 (SBML L1v2, L2v1-4, L3v1)
Test details.
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Demo - flash movies
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We have created 7 flash movies that demonstrate main BioUML features.
Movies
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BioUML forum
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The forum aims to co-ordinate a community effort towards
of development of BioUML and its application for modelling
of biological systems. Here you can ask your questions as well as
post your comments and suggestions.
More...
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