Release of the Systems Biology Workbench 2.10.0

We are proud to finally announce a new release of the Systems Biology Workbench 2.10.0. You can download this release directly from SourceForge. This version provides updates to all components:

• Jarnac comes up with an altered front-end, that will make it easier to work with it. It features also additional script commands .
• JDesigner has been updated to work on newer Windows versions (7-8.1). It also can now load and save model parameters from / to external files. And it features a new plugin system.

Since our last official release, the SBML Level 3 Layout Package has finally been officially accepted, this release supports that final version as well. Similarly, SED-ML Level 1 Version 2 has been released, and with the Simulation Tool those files can be executed. Broken down into individual applications we have:

• Layout Viewer / SBW Auto Layout: Support for SBML Level 3 Layout Package.
• SBW Simulation Tool: Support for all SBML levels, and SED-ML Level 1 Version 2. First experiments such as Parameter Scans can also be exported. It also automatically displays targets of SBML Events / Rules in the list of selected elements, when loading models. The Simulation Tool also supports loading files from the COMBINE archive.
• SBML Support Library: SBML models using the Hierarchical Model Composition package will be automatically flattened, when possible (The file has to be valid, and all submodels have to be reachable.).
• JarnacLite / RoadRunner / SBML Support Library / JDesigner: A number of custom annotations have been added to allow the specification / simulation of distribution functions, or referencing the rate of change of a species. I've written about that before: distribution and rateOf.

As some of you know, Frank has joined the COPASI team. This made it possible to write a translator for COPASI, and now there is a new SBW import category that enables calling modules, to have a specific format converted into SBML, which can then be consumed. Current bidirectional translators are available for COPASI and JARNAC format. Practically that means that COPASI and JARNAC files can now be directly imported into: Simulation Tool, Auto Layout and others.

Of course there have been many more changes, bug fixes and improvements, so have a look at our full changelog.

Preparing the next SBW release (2.10)

It has been some time since the last release. Of course we never stopped working, as you can tell if you look at the change log:

SBW Change log

Apart from major upgrades to JDesigner and Jarnac, there is full support for the newly released Layout package. Additionally, Level 3 models using the Hierarchical Modeling (i.e. comp) Package can be automatically flattened for use in our simulators. Also an import option has been added to many modules, so that COPASI files can be opened.

The new windows installer can be downloaded from:

Windows Installer

Or obtained from the update program.

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:

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.

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: http://sys-bio.org/changelog.

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

http://jdesigner.sourceforge.net/

More details can also be found on my blog at:

http://frank-fbergmann.blogspot.com/

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:

sbwteam@gmail.com

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:

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.

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: http://shrinkster.com/14xc

For a full list of changes see: http://sys-bio.org/research/sbwChangelog.htm

As always we appreciate any feedback from users send to: sbwteam@gmail.com

Thanks

- the SBW Development Team