1. User Interface Paradigms for Describing Pathway Models Cliff Shaffer Department of Computer Science Virginia Tech

2. Fundamental Questions Who are the users? What are the tasks? What are the key bottlenecks?

3. Who are the Users?

4. Modelers –Expert users Observation: Not biologists –Chemists, Physicists, Engineers

5. What is the Task? Primary Tasks –Preparing a model for the purpose of simulation –Figuring out the model –Verifying the model

6. What is the Task? Primary Tasks –Preparing a model for the purpose of simulation –Figuring out the model –Verifying the model Other tasks are secondary –Describing the model to others –Exchanging models –Teaching

7. What is the Task? Primary Tasks –Preparing a model for the purpose of simulation –Figuring out the model –Verifying the model Other tasks are secondary –Describing the model to others –Exchanging models –Teaching Fundamental Problem: Modelers are at the limit

8. Modeler’s Lifecycle Data Notebook Wiring Diagram Differential Equations Parameter Values Analysis Simulation Comparator Data Notebook ExperimentalDatabases

9. The Cell (Modeler) Cycle Outer Loop: –Define Reaction Equations Inner Loop: –Adjust parameters, initial conditions

10. Tyson’s Frog Egg Model

11. synthesisdegradationsynthesis degradation binding activationinactivation

12. Time (min) Sic1 mass Clb2 Cln2 Cdh1 Simulation of the budding yeast cell cycle G1S/M Cdc20

13. Designing an Interface

14. Observation: Rational human beings can have widely divergent opinions on what interface paradigm makes them productive.

15. Designing an Interface Observation: Rational human beings can have widely divergent opinions on what interface paradigm makes them productive. –Ex: LaTeX vs. MS Word

16. Designing an Interface Observation: Rational human beings can have widely divergent opinions on what interface paradigm makes them productive. –Ex: LaTeX vs. MS Word Observation: Pathway modeling is a creative process.

17. Designing an Interface Observation: Rational human beings can have widely divergent opinions on what interface paradigm makes them productive. –Ex: LaTeX vs. MS Word Observation: Pathway modeling is a creative process. –Flow state

18. What is Pathway Model Building “Like”?

19. Photography?

20. What is Pathway Model Building “Like”? Photography? Programming?

21. What is Pathway Model Building “Like”? Photography? Programming? Writing?

22. What is Pathway Model Building “Like”? Photography? Programming? Writing? Drawing/Painting?

23. What is Pathway Model Building “Like”? Photography? Programming? Writing? Drawing/Painting? Bridge designing?

24. Existing Paradigms Graphical –Virtual Cell, BSP, JDesigner Wizards –Gepasi Equations or Scripts –JigCell, Jarnac No implementation is “pure”

25. BSP

26. JigCell Tyson’s Frog Egg Model

27. A Characteristic of our Models We can’t get away from the fact that there is mathematics to describe –Parameter/initial condition values –Rate laws

28. How to Compare Interfaces Time required to complete task Errors committed during task Learning curve

29. Application-Specific Issues Unavoidable text Total keystrokes required Density of information Support for abstraction Cognitive match for user Ability to grasp the overall structure

30. Graphical vs. Equation Pros: –Better intuitive grasp of overall model Cons: –Low information density –Poor support for mathematical details

31. A Usage Scenario Modeler is struggling with setting the fundamental structure of the model –Graphical sketch Modeler needs to fill in the details –Fill in skeleton on spreadsheet Modeler is in verification mode –Alternate simulation runs with tweaking the spreadsheet Modeler wants to explain to others –Show a diagram