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Wednesday, January 18, 2012

SED-ML Nested Simulation Proposal v2

With the start of the new year it is time to get the Nested Simulation Proposal for SED-ML ready for wide-spread adoption. I believe nested simulations are vital for SED-ML so that we can cover a much larger variety of simulation experiments. I think it is especially important NOT to create a new simulation class for every single different simulation we perform on a model. By just defining two simulation classes:

  • One Step: which brings the model to the next desired output step.
  • Nested Simulation: which allows running over another simulation task, while changing multiple models parameters with computed values from ranges.

it is possible to construct a large number of simulations that are currently carried out.  I’ve taken these past weeks to fully flesh out all the details and the document is now available from Nature Proceedings:

The new version describes in detail all attributes and elements and features a number of examples (see below)

All features have been implemented in libSedML. The major change is that internally libSedMLRunner no longer produces a simple 2d array of data, but a NuML result set.

NOTE: This proposal only covers the generation of the data, not the visualization. In other words this proposal allows to generate n-dimensional data sets, while currently our DataGenerators can not access the values. I believe the two issues should be handled in different proposals.


Just a brief overview of the examples:

Steady state scan image
Pulsing a parameter during a simulation image
Multiple Stochastic Traces image
Timecourse scan image
2D Steady State scan image



As indicated above, the proposal is implemented in libSedML, a also released a new version of the SED-ML Web Tools, that can simulate all of the above examples.

Just for completeness sake: here the link to the old version:


FBC Package & SBMLToolbox 4.1.0 Getting Started

Today the SBML Team released version 4.1.0 of the SBML Toolbox. The news? It can be used with the SBML Level 3 Flux package. So what do you need to get it set up?

  1. Grab the beta FBC package for your system from:
  2. Grab SBML Toolbox 4.1.0:
  3. unzip / start Matlab / change into the toolbox directory, run the ‘install’ command.
  4. run the tests to be sure all is working fine for you:
    cd Test

Please let us know how things are going for you!