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Friday, March 18, 2011

Support for SBGN-ML

The recent release of SBW 2.8.2 adds support for SBGN-ML to the Systems Biology Workbench. This has been implemented using the SBML Layout Library, a .NET library that reads layout and rendering information from SBML models. This library is available separately and is used in many projects for example:

Of course it can also be used directly in any .NET application. The easiest way to get started is this:

  • install SBW (this will install the latest version of the layout lib)
  • start Visual Studio
  • add a reference to the SBMLExtension.dll as can be found in C:\Program Files (x86)\KGI\SBW\Layout to a new project (any .net language can be used).

Before we get started let us make sure we have some SBGN-ML files available, so at this point you would download a couple .sbgn files from the SBGN-ML repository.

The SBML Layout library converts all layout annotation it understands into the SBML Layout and Rendering Annotations. This is done by using:

var layout = Util.readLayoutFromFile(@”path/filename”);

where the  filename could be an SBML file with layout annotations (JDesigner / JDesigner 2 annotations, SBML Layout / SBML Rendering information, CellDesigner annotations (experimental)) or an SBGN-ML file.

So if you wanted to convert SBGN-ML to a PNG file all you would need is a bit of code like this:

var layout = Util.readLayoutFromFile(filename);
var name = Path.GetFileNameWithoutExtension(filename);
var outname = Path.Combine(outDir, name + ".png");


At this point the library does not allow to write out SBGN-ML, if that is a feature that is important to you, please let me know.

Systems Biology Workbench (SBW) 2.8.2 Released

We are pleased to announce the a release of the Systems Biology Workbench 2.8.2, 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 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.

The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages.

Major changes in this release:

  • Updated JDesigner
  • Improved event support in RoadRunner,
  • Support of SBGN-ML (from SBML Layout)
  • Support of SED-ML L1V1 (from the Simulation Tool)

For a full list of changes see:

As always we appreciate any feedback from users send to:


- Frank