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Wednesday, September 25, 2013

Systems Biology Workbench 2.10.0 - RC2

We are still working on the next release for SBW. Some users commented, that the last release candidate did not work for them, having issues in JDesigner. As of right now a new Windows build is available, from the Update tool or:


Thank you again for all the reports so far, please keep them coming.

Monday, September 16, 2013

SED-ML Level 1 Version 2–Release Candidate

The COMBINE meeting has just started, and we finally made the release candidate for the SED-ML Level 1 Version 2 specification available. SED-ML L1V2 finally extends the simulation experiments covered by SED-ML to include any kind of repeat and perturbation experiment. Apart from that it also includes the possibility to fully parameterize simulations, by specifying algorithm specific parameters like relative and absolute tolerances of integrators. The specification is available online from:

On my end I’ve updated the libSedML, and the SED-ML Script editor and of course SBW to be able to simulate L1V2. Another major change has been applied to the SED-ML Web Tools that now also support L1V2, and are now also capable of simulating the repeatedTask concept with CellML additionally to SBML.

As always any feedback is appreciated.

SED-ML Logo 5

Sunday, September 1, 2013

Systems Biology Workbench 2.10 (RC1)

As hinted at, a couple of days ago, we are shortly before the release of the next version of SBW with enhancements for all associated programs. Today I want to announce a new release candidate. On SourceForge you will find installers for Windows, OSX as well as Linux (x86 & x64). You can download them from:

I’ve also created virtual machines & live images with SUSE studio, that are available online:

32bit OpenSUSE 12.3,
64bit OpenSUSE 12.3

Any feedback is appreciated.