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Wednesday, August 19, 2009

SBW 2.7.10 Released

Finally, the  new version of SBW is released, just in time for this years ICSB. Here the full release announcement:

SBW-Logo We are pleased to announce the a release of the Systems Biology Workbench 2.7.10,

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.

There are a number of significant changes in this release:

  1. Event support in Jarnac Lite, improved event support in roadRunner (and support for delayed events), improved display of discrete events in the Simulation Tool.
  2. Improved support for SBML Layout and proposed Render Extension, changes in auto layout module, adding of a SBGN style sheet based on SBO terms.
  3. Numerous bug fixes and usability improvements

For a full list of changes see:

For a list of modules included with the Systems Biology Workbench and a description of what they do please have a look at

In case you are interested in instruction in how to use the Systems Biology Workbench join our tutorial at this year’s ICSB, for more information see:

As always we appreciate any feedback from users send to:

- Frank (for the SBW Development Team)

Monday, August 17, 2009

Almost there – Next SBW Release

I’m finally in the final phase of testing the next SBW installer. Here the list of operating systems tested so far: Win 2000, Win XP, Vista, Windows 7, Windows Server 2003, Windows Server 2008, Fedora 11, Centos 4.6, Centos 5, Debian 5.0, Ubuntu 5, Ubuntu 9.04, openSUSE 11.1, Slackware 12.2 and of course OS X 10.5. All seems to be well and ready to go.

SBW-Logo So here the links to the current installers let me know if things need to change:

Of course things go sometimes horribly wrong, especially with … shall we say … not quite up-to-date linux installations. So here a couple of things to keep in mind:

  • get a new-ish MONO, it will help a lot the current version of MONO 2.4.2 is just amazing and it seems to be feature complete. Thus there is no real reason not to use it. Alas, for some distros it is really hard to get to a working MONO installation. If your system belongs to this category, have a look here, and download the 1.9.2 binary installer.
  • Some linux distros forsake a good and working Java installation with a gnu compiler, unfortunately our java modules do not play nice with it, in fact the post installation step is likely to fail if you have it as first java in your path. You’d be better of getting a nice JDK, like the one from SUN, or even the OpenJDK from your linux distro.
  • If you still have trouble with the post installation step, you don’t have to uninstall SBW, just run the post installation step manually as in:

    <sbw-2.7.10 dir>/ <full path to sbw 2.7.10 dir> or 

    ./ /home/fbergmann/SBW-2.7.10

    that usually works and if a step takes too long a friendly ps-ef followed by a kill –9, or even simply a

    killall –9 java, killall –9 mono, killall –9

    Broker works wonders. 

Cheers and on to more testing.