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sys-bio / SBstoat

Parameter optimization using Tellurium
MIT License
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Create test suite using BioModels #6

Closed joseph-hellerstein closed 3 years ago

joseph-hellerstein commented 3 years ago

Create a framework that does the following for an SBML file (e.g., from BioModels):

  1. Finds the parameters and chooses a subset (based on an argument supplied to the test)
  2. Constructs lmfit.params for the selected parameters with a value range that includes the value of the parameter in the model. The initial value is set to something different from the value in the simulation (again, controlled by an argument supplied to the test)
  3. Does parameter fitting. (May have to control the compute cycles.)
  4. Checks if the fitted parameter and bootstrap CIs are close enough to the original value.
joseph-hellerstein commented 3 years ago

Done