Systems Biology Software Project / News: Recent posts

We are pleased to announce the a release of the Systems Biology Workbench 2.8.1, available from:

http://sys-bio.org

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 other's 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. ... read more

We are pleased to announce a release of the Systems Biology Workbench 2.8.0,
available from:

http://sys-bio.org

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. ... read more

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.... read more

This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.

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

available from:

http://sys-bio.org

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. ... read more

We are pleased to announce a release of the Systems Biology Workbench 2.7.8,

available from:

http://sys-bio.org

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. ... read more

We are proud to inform you about this latest release of the Systems Biology Workbench. In SBW 2.7.7 we focused on optimization and usability improvements for various modules. Details below:

Changes in Version 2.7.7

- Installer
- set working directory for shortcuts

- Jarnac
- replaced CVODE dll
- Relaxed restriction on Gillespie to use arbitrary rate laws

- RoadRunner
- fixed bug in event interpretation
- performance optimizations... read more

We are proud to release SBW 2.7.6 for Win32, Linux and OSX ... here is what is new in this version:

New Modules in 2.7.6

- Jacobian Viewer
- visualizes the Jacobian during a time-course simulation
- BioModels Importer
- Import models from Biomodels.NET and analyze them within SBW

Changes in Version 2.7.6

- SBML Translators
- the Matlab / Mathematica / XPP translator have been updated to resolve an issue with
some SBML Id's ... also fractional stoichiometries are now taken into account
- the XPP translator now also contains compartment definitions
- added C / C# / Java / MathematicaTranslators ... feedback welcome... read more

Changes in Version 2.7.5

Aug 2007

- Jarnac
- Fixed missing search feature from Jarnac editor
- Harmonising use of cvode between Jarnac and roadRunner
- added SBW menu to roadRunner, run a model first, then select the module it will be sent to ...
- Fixed parameter error in SBML generation

- JDesigner
- Background colour is now transparent when saving image in png format.... read more

With this new Release, the SBW Java bindings now work also with Windows VISTA. Apart from that minor glitches with SBML handling have been resolved. Also the C# bindings have been revised again ...

this new version of SBW 2.7.3 brings along Python bindings for Python 2.5, as well as updated C# bindings, that will work also on Windows 2000

A new release of the Bifurcation discovery tool was needed, so it would work on Windows 2000.

SBW 2.7.1 released, currently the release is for windows only ... the OSX & linux release will be made soon ...

We are pleased to announce that a new version of SBW has been released. The new version contains major changes to all included modules.

We finally released SBW 2.5.5. This release contains updates of all components. Also the auto start feature is finally working as it should.

Furthermore we changed our libraries on OSX so that we should be save regarding software updates from apple.

For installation instructions see:

http://jdesigner.sourceforge.net/Installer.html

Finally the confusion of the whereabouts of SBW should have an end ... henceforth

sourceforge.net/projects/sbw

will be used for development of the SBW Core and the binding Libraries while

sourceforge.net/projects/jdesigner

will be used to develop SBW modules. General information on SBW will be provided at:

http://ww.sys-bio.org

Cheers
Frank

A new binary release of SBW has been made for all supported platforms.

Finally the SBW Core compiles with gcc 4.0. To compile it get the source code from CVS, and use the scons build tooll (http://scons.sf.net) to build.

Finally a binary Release for any Linux system is available. The installer was created using the BitRock installer: http://www.bitrock.com. In order to install it just download the bin-file, change it to be executable and run it ...

This installer has been tested with FC 4, FC3 and Suse 9.2