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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:

Friday, July 30, 2010

JarnacLite – Helping with Kinetics!

The new version of JarnacLite, that is distributed with SBW 2.8.1 finally helps out in the arduous task of entering the kinetics. By using a customizable list of kinetic rate laws, it is now rather easy to construct models in this simple script format.

There are two steps to using this assistance:

  1. Enter the reaction scheme: In order to be able to filter the available rate laws, a reaction scheme needs to be present. Special note should be given to the reversible notation:

    S1 –> S2

    would mean that a species S1 is converted to S2, while

    S1 => S2

    would mean that this reaction is reversible. Different kinetics will be suggested.
  2. Once the reaction scheme is entered, pressing CTRL+SPACE or clicking the ‘Edit kinetic’ button will bring up the rate law selection dialog.
  3. All that is left to do after selecting a rate law is to adjust the parameters.

And here an example of how this looks in practice:

The SBW Simulation Tool – Part 4 – Parameter Scanning

It was always a bit cumbersome to perform parameter scans with our tools. Thus, with the new release of SBW a new plug-in was written that makes performing 1 or 2d parameter scans a snap. Be it steady state, or time course scans it should be easy to do. We support ranges (varying a parameter from a min to a max value in a number of steps), logarithmic ranges, or even just entering of specific parameter values to be used.

In order to be able to plot the scan results we interface with Gnuplot and allow users to tweak the gnuplot scripts. Resulting figures can then be exported as PDF or image.

Below a demonstration of the feature:

As you can see towards the end instead of just the floating species a wealth of output options is available.

The SBW Simulation Tool – Part 3 – The Script Plug-in

The new SBW Simulation Tool also features a script plug-in. By embedding IronPython, the popular python scripting language is available to power users. The script plug-in has access to the currently active Simulator (i.e.: RoadRunner) in its current state. Via simple programming one can influence all model variables and perform all kind of perturbation experiments. Also exposed are a Gillespie Simulator, the LibStructural Library. Of course access is granted to the host application, the plug-in itself and the graph panel. Finally, it is possible to programmatically access the BioModels database.

Admittedly the current implemented console is no substitute for a real Python editor, however, it is suited for inspections of the current state. For advanced use we recommend writing Python scripts in a separate editor and executing these scripts from the python console.

Below a short introduction to the script console. More documentation about the available methods is to come soon!

The SBW Simulation Tool – Part 2 – Signal Injection

The new simulation tool also comes with a couple of new interactive simulation experiments. The first one to be described here is the Signal injection plug-in as seen below.

It couldn’t be simpler to use. Simply load the model you want to experiment with, click the ‘add signal’ button, and choose parameter and signal type. Immediately the signal will be displayed in the graphing window and can be moved about with the mouse allowing you to directly see the influence this has.

For the sine  (or square wave) signal type it is possible to change the angular frequency by holding down the CTRL key and moving the mouse.

Here a video demonstrating this feature:

The SBW Simulation Tool – Part 1 – Look And Feel

The new release of the Systems Biology Workbench brings with it a largely rewritten version of the SBW Simulation Tool. Based on a new plug-in system, the Simulation Tool is now easily extendable. This allows not just to add new interactive simulation experiments, but also change the visual aspect of the Simulation Tool.

Changing the Look and Feel

By allowing the layout of the Simulation Tool customized by plug-ins it is now possible to find a layout that suits everyone. Here a the inbuilt examples:

image image image

But of course it would be easy to extend it … say by using a ribbon layout on windows:


I wonder what the simulation tool will look like tomorrow :)

In order to change the layout a user simply selects one of the options from the menu: