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Saturday, July 31, 2010

Systems Biology Workbench (SBW) 2.8.1 Released

We are pleased to announce the a release of the Systems Biology Workbench 2.8.1, 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. The SBW Simulation Tool has been largely rewritten to allow for a variety of interactive simulation experiments. Thanks to a new plug-in mechanism it is easy to extend the Simulation Tool.
  2. The script based modeling tool JarnacLite has been enhanced to make it easier to select Kinetic Laws to use.
  3. RoadRunner now supports SBML Level 3 (with the same restrictions that applied to Level 2, i.e.: no algebraic rules, no delays, no fast flag).
  4. Numerous bug fixes and usability improvements (such as a favorites menu bar, that allows to quickly edit / simulate SBML models in most applications).

For a full list of changes see:

With SBW 2.8.1 we have a new full release, with binaries for Windows, OSX (10.6) and Linux (tested with openSUSE 10.2 and Ubuntu Lucid). We are well aware that there are many more platforms available out there and regret not having the manpower to provide binaries for additional platforms. For this reason we have created a set of Virtual Machine (VMware/VirtualBox & Xen), hard drive image,  and Live CD image (running openSUSE 11.2). For all of these the username is ‘sbw’ and password is ‘linux’.

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

More details can also be found on my blog at:

In case you are interested in instruction in how to use the Systems Biology Workbench join our tutorial at this year's ICSB.

As always we appreciate any feedback from users send to:

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