Module modelmage

source code

Contains the main function and the modelMaGe class that start the program.

Due to multiple changes in the development process, the code has become ugly and not well structured. Until I have fixed and refactored it, I will give a short description of the dependencies and the order of a program call: modelmage.py: main():

• parses the input and hands the arguments -r and -k to initializer
  • initializer returns a normalized format of the arguments in the form of a comma separated string and the macros which are used to name the generated models
• instantiates the ModelMage class and sets a master model
• calls the ModelMage.generate() method with the suitable arguments
  • instantiates the RemoveHandler and KineticsHandler class to retrieve the correct logical combinations of species and reactions
  • instantiates Generator and calls generator.generate(), which returns the newly created sbml documents
  • writes the documents to sbml and copasi files
  • calls update_tasks_cps()
    • instantiates CPShandler and imports the tasks from the master model into the newly created cps files
  • calls estimateParameters and discriminate