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Benchmarking
We wanted to verify that Tellurium/Roadrunner is faster than competing modeling software. This is a description of our methods to test the speeds of Tellurium and others under different circumstances.
This is a MATLAB extension, and although it has a GUI that can be used to create and test models, we need to use the console interface to benchmark it.
The timing tools we are using here are MathWorks' own commands tic and toc. Tic starts the timer, and toc displays the current time.
Another useful MATLAB tool is linspace(start,end,n) which generates a vector of n items starting from start until end evenly spaced
Sim Biology has a few important concepts, some of which are borrowed from another MathWorks modeling tool: Simulink.
The Model Object represents the species and reactions. It can be created in the GUI, in code, or by loading a file. We can load our SBML in with the sbmlimport command which will return to us the model object. Note that sbmlimport takes a character vector denoted by the apostrophes, not the quotation marks, which create a string.
modelObj = sbmlimport('C:\millard.xml')The Configuration Set is just as it sounds, a set of options that determines how the model will be performed e.g. start time, end time, integrator type, etc. The configuration set can be obtained from the model, and any changes to it will automatically be seen by the model.
cs = getConfigSet(modelObj, 'active')