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

2. 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

3. 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

4. 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

5. 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

6. 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)

7. 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)

8. Run Manager

9. 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

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

11. 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!

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

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