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Sunday, November 11, 2012

SBW Flux Balance Analysis Tool … v2

Brett Olivier was here last week in HD, and we made quite some progress on the FBC specification. We also started with a test suite for tools implementing the FBC package. And as can be expected, these tests revealed quite some room in the original FBA Tool that from 2009.


The new version fully supports the SBML FBC package, will properly inform whether a solution was found or not, and sorts a number of problems (such as dealing with infinite bounds). The new version is still aimed as teaching tool, but now is much better suited as such. The list of changes:

  • fixed issue with infinite bounds
  • fixed issue accessing the results from the c library
  • added display of objective value and solution quality to status bar
  • added export of LP files
  • added import of COPASI / Jarnac files (if latest SBW is installed)

In any case I started a github page for the project, where the first windows installer is available for download:

Launch4j for 32bit

Launch4j is a great project, that can bundle java applications into an executable, so that starting these applications is no longer a problem. No batch files needed, no relying that the default extension for jars is starting them and no command line wizardry required. Launch4j would allow you to either bundle a JRE with your java application, or it could find it during runtime.

There was only one catch, you could not let it know that what you do want it to find is a certain architecture of JRE. See, when your project would use JNI and your native libraries are only available in 32 bit architecture, then running the project with a 64bit JVM would just not work.

Thanks to the wonders of open source, the full code for launch4j is publicly available from SF, so it was no problem to fork the project and add an option to the launcher that would allow it to find 32 bit JVMs first.

A new installer is available on github!, grab it here: