1. Model Composition Andrew Finney No relevant affiliation

2. Overview Review existing proposal New Stuff figured out at Newcastle Hackathon Late Breaking - Proposal for new ‘module’: –Model Inclusion How the various Level 3 ‘modules’ interact Short Hand for Level 3 Conclusions

3. The proposal prior to Newcastle Submodels –SBML document contains multiple models Instances –Copies of models appearing inside a referencing model Direct Links –Most references to object inside a model can be replaced with a path to an object inside an instance Example: a species reference can refer to a species inside an instance –This means you can create a reaction linking species in different instances Overloading Links –Explicit arc between a pair of objects Directed: One overloads or replaces the other Any reference to the overloaded object is acquired by the overloading object Example: –a species in one model replaces a species in another. –the species ends up with the union of all the species references Ports –Optional –Exposed name for internal object in model –Links can refer to Port instead of internal object

4. Model Composition Example of Direct Links Instance A of Model ZInstance B of Model Z f g h h f g i

5. Model Composition Example of Direct Links Flattened a/f a/g a/h b/h b/f b/g i

6. Model Composition Example of Link Overloading Instance A of Model ZInstance B of Model Z f g h h f g i

7. Model Composition Example of Link Overloading Flattened a/f a/g a/h b/g i

8. Model Composition Example of Link Overloading with Interfaces Instance A of Model ZInstance B of Model Z f g h h f g i F H G H F G

9. Ideas from Newcastle Explicit ‘Must Be Overloaded’ field on Port N to M links The semantics of Overloading Reactions Garbage Collection

10. N to M Overloading Links From overloads To From can be either present or not present –Not present indicates that the To set is deleted from the resulting model –How do we handle ‘remaining’ references to the To object? cascaded deletion: –any referencing object is also deleted its an error –other overloads must be present to create a tidy flattened model explicitly More than one object in To –simply indicates that the To set is replaced by the From object More than one object in From –flattened model has all the from objects and none of the to objects Nice for reactions but what about other objects?

11. Example: Species removed Instance B of Model Z f Composed Model g g Flattened Model

12. Reaction Overloading Consider reaction network to be bi-partite graph –arcs (species references) link species nodes to reaction nodes Overload on species –Flattened species node acquires union of incident edges Overload on reaction –Flattened reaction node retains incident edges of the overloading reaction node only

13. Reaction Overloading: Example Composed Model Instance A of Model Z Instance B of Model Y f g h n m i

14. Reaction Overloading: Example Flattened Model g n m i

15. Reaction Overloading: Example Garbage Collected Model n m i

16. What Next? (Model Composition building on L2 only) Establish overloading rules for all objects –Reactions only type to support N to M? –Species, Compartment can support 1 to M –Species Type, Compartment Type, Instance, Parameter can only support 1 to 1 Instance overload is fun!!! –Requires Ports to match?? Species Type overload in Multi-component context problematic

17. Model Inclusion New Module –separate from Model Composition covers combining separate XML documents into a single larger model Ideal for solving problems of reusing systems of multi-components

18. Model Inclusion: Implications Model Inclusion –Have a list of simple elements that pair a name field value with a URL value for another model –Name value, the Inclusion Name, is in global namespace in including model –Objects in these models can be referenced using ObjectRef using the Inclusion name and the name of the object in the referenced model Model Composition –retain model instances that are instances of model referenced by URL semantics are different

19. How the Level 3 Modules Interact Model Composition Arrays Multi-component Species Arrays of Instances Overloading Arrays Arrays of binding sites Observables referenced from Ports Spatial and Model Inclusion are orthogonal to these modules (or the there would be too many lines)

20. We need to be careful If we want to have formal modularisation of Level 3 –leads to separate XML namespaces We need to –Explore in outline all the likely extensions identify common elements identify pathological interactions Otherwise –Common elements repeated in different namespaces –Other embarrassing nastiness Suggestion/Example –Core Level 3 contains ObjectRef element

21. We need a short hand Actual Level 3 models will be very verbose Short hand for email discussion Adapt Darren W’s tool ??

22. Conclusions Newcastle meeting enabled us to identify useful improvements –N to M overloading links –Reaction overloads Tactical work required on Model Composition –Rules for overloading Strategic Work required on Level 3 –Establish Model Inclusion as separate module –Interactions between ‘modules’ –Development of Short hand