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Monday, March 16, 2009

Re-release of SBW 2.7.9

Just a follow up on last weeks entry about Installation Problem of SBW 2.7.9 on Windows XP machines. The problem has now been resolved (by recompiling all C++ modules using VS 2003). And SBW 2.7.9 R2 is available for download from SourceForge.

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Here the full change log:

Changes in Version 2.7.9 R2

This release is a re-release of SBW 2.7.9, that was necessary because some windows machines
had problems running the new version due to problems with the C++ Runtime. In this version:

- all C++ modules and libraries have been recompiled with MSVC7

- JacobianViewer: The JacobianViewer was recompiled to run on 64bit systems in the 32bit
  sub system.
- C# Inspector: BugFix: some UI-controls would not align properly when the window was resized.

FluxBalance Analysis with SBW

Herbert came across the LPsolve, a LPGL library for solving linear programming questions. Steady state flux balance analysis can be stated as linear programming question. This is what the new SBW FluxBalance module does:


You can load an SBML file, specify all flux constraints and your objective that is to be minimized / maximized and the module will solve the LP problem.

The prototype is available for download. In the near future this functionality will also be included in LibStructural.

Sunday, March 8, 2009

Installation problems of SBW 2.7.9 on Windows XP

SBW Logo-blackWhile away on conference I have heard of several issues installing SBW 2.7.9. I’m terribly sorry for the problem. A new installer will be issued end of next week, this will give me time to sort out the issue.

In order to make the current SBW 2.7.9 working all that is needed is to install the Visual Studio 2008 SP1 Runtime in fact the installer is attempting to install the runtime, but in the cases where the installation fails, this obviously did not work. To use this version of SBW 2.7.9 :

Again I’m sorry for the inconvenience.  The new version next week, will re-use an older version of the runtime, resulting in some loss of functionality, however it does not require the separate runtime installation.

Tuesday, March 3, 2009

Join us at SIGCSE 2009

I’ll be presenting new developments for the Systems Biology Workbench, as well as Athena, our CAD / CAM Software for Synthetic Biology at the 40th ACM Technical Symposium on Computer Science Education or short SIGCSE 2009. You can find us in Exhibit Hall A, at the Microsoft booth #201.

Systems Biology Workbench 2.7.9 released

We finally have a new release of the Systems Biology Workbench. Here the release announcement:

We  are pleased  to announce  a release  of the  Systems Biology  Workbench 2.7.9,

available from:

The  Systems  Biology  Workbench   (SBW), is  a  software   framework  that allows   heterogeneous   application    components-written   in     diverse programming   languages  and   running   on  different   platforms   -   to communicate  and use  each  others' capabilities via a fast binary  encoded -message system. Our goal was  to create  a simple, high  performance, open -source   software  infrastructure  which   is   easy  to  implement    and understand.  SBW enables  applications  (potentially  running on  separate, distributed computers) to communicate via a simple network protocol.

The interfaces  to the  system  are  encapsulated in  client-side libraries that we provide for different programming languages.

Of  primary focus  for this  release was  to improve  performance for  core SBW components.  Now roadRunner  as well  as all  AutoLayout procedures are much  faster than before. The ‘Simulation Tool’ now also allows  performing frequency  analysis experiments.  Much effort  has  gone  into making  sure that this release works  on the Win64 architecture. This release   includes also fixes for  Jarnac,  JDesigner and  most other applications  we deliver with the framework.

For  this Windows  release we  switched  to  a new  compiler. Thus  it  is recommended to uninstall  the previous version  of SBW prior  to installing this  release. It  is also    recommended   to    install   the    compiler runtime   components  from:

For a full list of changes see:

As always we appreciate any feedback from users send to:


- the SBW Development Team

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