libSBML 5.6.0 Released

I’m glad to announce that we have just released libSBML 5.6.0. This new release comes with more binary installers. Among them Python 3 and R bindings in two flavors: with or without SBML package code. Main changes in this release are:

• An updated python 2.x binding, contributed by Gordon Ball, that makes the python API more python like. Here just one example on how this can look:

  Python 2.7.2 (default, Jun 12 2011, 14:24:46) [MSC v.1500 64 bit (AMD64)] on win32
  Type "help", "copyright", "credits" or "license" for more information.
  >>> from libsbml import *
  >>> doc = readSBML('/Development/libsbml/examples/sample-models/from-spec/level-3/membrane.xml')
  >>> doc.model
  <Model Model_1 "Reaction on membrane">
  >>> doc.model.compartments[0]
  <Compartment cyt "Cytosol">
  >>> doc.model.compartments[0].name
  'Cytosol'
  >>> 

  
  
• 
  
  Updated Layout package with GeneralGlyph / ReferenceGlyphs for those that want to represent other things than just compartments, species and reactions.
  
  
• 
  
  (experimental) Implementation of the QUAL package
  
  
• 
  
  (experimental) Updated Spatial package to make it easier dealing with ImageData as well as Spatial Parameters
  
  
• 
  
  (experimental) Updated Groups package that includes the ‘kind’ attribute.
  
  
• 
  
  (experimental) Updated FBC package that allows to set Operations and FluxBounds through enums.

All this is rounded up by bug fixes, with handling of MIRIAM annotations among others. The full release announcement is online.

Please grab the new version from SourceForge:

http://sourceforge.net/projects/sbml/files/libsbml/5.6.0/

SBML Spatial Extension & Simulation

As part of my new job at the University of Heidelberg I get to work again on spatial simulations. While trying to get my feet wet, I was able to experiment with a spatial simulator by Akira Funahasi’s group (see also his presentation at last years COMBINE). So today I just wanted to share the resulting video with you:

It always is fascinating watching these things. And the real amazing thing is that this is not a hard coded simulation, but one that is interpreted from an SBML file. And while it probably will take a while until we are regularly exchanging spatial models we are definitely on the right way!