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:

http://precedings.nature.com/documents/4257/version/2

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.

Examples

Just a brief overview of the examples:

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

 

Availability

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:

Doc:            http://precedings.nature.com/documents/4257/version/1
Examples:   http://frank-fbergmann.blogspot.com/2010/03/nested-simulation-experiments.html