Updated SED-ML Web Tools (now with editing of SED-ML descriptions)

I’ve just released a new version of the SED-ML Web Tools they as always available from:

http://sysbioapps.dyndns.org/SED-ML Web Tools/Home/

The new version allows to edit the loaded model either by directly manipulating the XML, or by altering the model using the SED-ML Script Language.

Here a simple tutorial of creating a new SED-ML description from an SBML model and then modifying it using SED-ML Script.

As always I look forward to your feedback. To make it easier to collect I’ve signed up with idea informer, so there is now an orange feedback button right there on the page. That makes it easy to request your feature requests:

Creating SED-ML for SBML models

I have just released a new version of the SED-ML Web Tools. This version creates SED-ML models for SBML files. Have a look here:

http://sysbioapps.dyndns.org/SED-ML%20Web%20Tools/Home/Create

All that is needed is to fill out this form:

After that the SED-ML description can be executed, or downloaded. More advanced options (such as creating SED-ML descriptions for CellML models) is available in the SED-ML Script Editor:

sf.net/projects/libsedml/files/

SED-ML Web Tools, SED-ML Script Editor & CellML Simulation Support

I’ve just upgraded the SED-ML Web Tools to a newer version.

http://sysbioapps.dyndns.org/SED-ML%20Web%20Tools/Home/

This version includes several bug fixes, as well as an experimental version of CellML simulation support. The CellML simulation support is thanks to an executable based on the CellML API provided by David Nickerson.

To accommodate this there have been several changes to the LibSedML API, where previously the API would have properties like .SBML or functions like GetSBMLId(), now these functions are hidden behind a native interface IModelingLanguage that will be populated based on the Model source URN as provided in the SED-ML file. This should make it easy to provide support for other languages such as NeuroML and VCellML as well.

I have also released a new version of the SED-ML Script editor. It now allows to open SBML or CellML files directly, for which then a rudimentary SED-ML file will be generated. Later it can be modified for more complex experiments. It also provides SED-ML validation capabilities. This time it is a windows only release (since I only have the CellML simulator as windows binary). It is available from SourceForge:

sf.net/projects/libsedml/files/

Introducing the SED-ML Web Tools

I’ve spend the weekend working on a new set of tools for simulating and Validating SED-ML files. They are online now under:

• http://sysbioapps.dyndns.org/SED-ML Web Tools

Let us first take a brief tour around the site:

Let me point just a couple of things.

Simulation

The current implementation will only simulate SBML files, using RoadRunner. As soon as I find time to update it I will add additional simulators. Currently 3D plots won’t work either. And of course simulation will only work if the model files are either:

• accessible via URNs
• accessible via WEB
• included in the archive.

Simulation already implements the Nested Simulation Proposal.

Validation

The new thing about the validation is that it also provides an option to fix common errors. This feature can be used to upgrade SED-ML files that were created before SED-ML L1V1 was released! Simply click on ‘Fix common errors’, and then download the file again.

Stay tuned for further updates, the next steps will be to Create and Edit simulation experiment descriptions. Also planned are web services that make it easy to create SED-ML files!

Flux Balance Constraints for libSBML 5.0.0

In time for todays session on SBML at HARMONY 2011 below a set of windows binaries that include libSBML 5.0.0 with the first beta version of the Flux Balance Constraints package. This time the package is implemented using the libSBML 5 extension API, which allows easy interaction with SBML Level 3 extensions.

For more information about the Flux Balance Constraints package, please have a look at the proposal page. On that page you find a detailed description about the current proposal, as well as links to examples.

Below you find full installers (including C#, Java, Perl and Python bindings) as well as python bindings for specific versions of Python.

• libSBML 5.0.0 + FBC full installer (Win32)
• libSBML 5.0.0 + FBC full installer (Win64)
• libSBML 5.0.0 + FBC python 2.5 (Win32)
• libSBML 5.0.0 + FBC python 2.6 (Win64)
• libSBML 5.0.0 + FBC python 2.6 (Win32)
• libSBML 5.0.0 + FBC python 2.7 (Win64)
• libSBML 5.0.0 + FBC python 2.7 (Win32)

If you don’t use Windows and still would like to try out the FBC package on your platform, I have a source package. In order to use this, download the libSBML 5 source distribution, as well as the fbc-package, then extract the fbc-package into the libsbml 5 source tree. Next, use CMake to configure the program to your needs, ensuring to set ENABLE_FBC=ON (or in the UI check the ENABLE_FBC option).

1. libSBML 5.0.0 source release
2. fbc-package-beta-1

Please let me know how the package is working for you.

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:

• Auto Layout
• Layout Web Application
• Layout Web Service
• BenZaiTen (no public release)
• Simulate 3D

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");
layout.ToImage().Save(outname);

Limitations

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:

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.

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:

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

As always we appreciate any feedback from users send to:

sbwteam@gmail.com

Enjoy

- Frank