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.

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

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:

Matlab Export Anyone?

SBW for a long time had facilities for exporting SBML models to Matlab and a slew of other formats. I have to admit I never really used the Matlab Export before, and so it came as a surprise when I heard that the export of SBML Assignment rules was broken. But good news, at least this export is now working just fine.

So let us look at some examples on how we would use it. For this let us construct a very simple model, a 3 step linear chain:

Here we set Node0 and Node2 to be a Boundary (fixed) Species, as they are not really part of the system. And we want Node0 to be controlled by an Assignment Rule, which sets the value of Node0 to ‘5’ starting at 1 second for 2 seconds. Outside this window Node0 should be close to zero (and I say close to zero and not zero so that the integrators will pick up the change). So this translates into a piecewise function:

Node0 = 5 if 1 < time < 3 and 0.1 otherwise

in SBML infix speak this translates into:

Node0 = piecewise(5, and(geq(time,1), leq(time, 3)), 0.1)

here of course piecewise, stands for the piecewise operation, note that you can have as many pieces as you’d want … for every piece you would add two terms, the value and a Boolean expression. The Boolean expressions supported are:

Name	Argument type	Explanation
and	n-ary	n-ary and like in the example above, it is 1iff all arguments are 1
xor	n-ary	n-ary xor, is 1 iff not all arguments are 1 or all arguments are 0
or	n-ary	n-ary or, is 1 if at least one of the arguments is 1
not	unary	is 1 if argument is 0 and 0 otherwise
gt(a,b)	binary	greater: is 1 if a > b
lt(a,b)	binary	less than: is 1 if a < b
geq(a,b)	binary	greater or equal: is 1 if a >= b
leq(a,b)	binary	less or equal: is 1 if a <= b
eq(a,b)	binary	equal: is 1 iff a == b
neq(a,b)	binary	not equal: is 1 iff a != b
piecewise( value, condition, otheriwse)	n-ary	piecewise function: each piece is defined with a value, condition pair and concluded with an value for the otherwise clause. all values and conditions can of course be function expressions as well.

So let us look at the complete model in the JarnacLite language (this will allow you to just paste it into JarnacLite without you having to download the SBML model):

p = defn AsssignmentExport

var Node1;
ext Node0,Node2;

J0: Node0 -> Node1; J0_k*Node0;
J1: Node1 -> Node2; J1_k*Node1;

Node0 = piecewise(5, and(geq(time,1), leq(time, 3)), 0.1);

end;

p.Node0 = 0;
p.Node1 = 0;
p.Node2 = 0;
p.J0_k = 0.1;
p.J1_k = 0.1;

When in JarnacLite, a click on SBW\Translate SBML –> Any will bring up the SBML Translators, and a click on the Matlab tab shows you the newly translated model:

As you can see this model is complete with instructions on how to use it in Matlab. And here the good news it works in Octave as well! (you’d just download ode23.m and put it in the same directory and you should be good to go!) So all that is left is to save the file as .. say … AsssignmentExport.m into your Matlab work directory and run:

x0 = AsssignmentExport
[t, x] = ode23s(@AssignmentExport, [0 20], AssignmentExport);
plot(t,x);

and you should see a graph like this:

And here the disclaimer, I do know that you’d normally implement these sort of things as SBML Events, but so far we don’t export SBML events to Matlab, but you can always use roadRunner to have them simulated correctly.

So if you want to give this new version of the Matlab export a try, download a new Installer, or select Systems Biology Workbench\Utilities\Update SBW from an existing SBW installation.