Runs, Parameter Sets, Outputs and Projects Beyond SBML Runs, Parameter Sets, Outputs and Projects

What is a Model? SBML includes: Reactions Parameter/IC values Events Conservation relations Etc. Aside from parameter/IC values, all is part of the “structural” definition

Parameter Sets One can view parameter sets as an integral part of the model Alternative view: The modeling process Outer loop: setting the framework (reactions) Inner loop: setting the parameters Breaking the parameter sets from the structure allows easy replacement of whole sets

Parameter Estimation What does a parameter estimation tool “create”? A parameter set Where does it go? If a parameter set is a separate entity, life will be simpler

What is a model? For us, its not just one structure with one parameter set (even after parameter estimation) “Wild Type” and mutants 120+ mutant forms for the Budding Yeast model

What is a Mutant? Most often, an alteration in a small number of parameter (or initial condition) values Occasionally, an alteration to the structural part of the model (reactions)

What about simulation? Each mutation requires its own simulation Simulation parameter settings might be an important feature in even a simple “wild type” model Each mutant might require its own simulation settings (initial time, length)

Run Manager

What about simulation output? Each simulation run outputs (for example) time course data that we might wish to save Where? Not in the SBML file

What else? Experimental data Transformations between simulation output and experimental data Objective functions

Projects Programming Integrated Development Environments have developed the concept of a “project” A collection of files that collectively define a “program” (more than just source code) We suggest that complex pathway models are far more than just the pathway!

What do we have? Structure (SBML file) Parameter sets (multiple) Simulation settings Runs Experimental data Transforms Objective functions Simulation outputs Project file

How do we keep it all together? A metafile? All files must be in a directory? Project file can reference files anywhere?