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

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

Who are the Users?

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

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

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

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

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

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

Tyson’s Frog Egg Model

synthesisdegradationsynthesis degradation binding activationinactivation

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

Designing an Interface

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

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

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.

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

What is Pathway Model Building “Like”?

Photography?

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

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

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

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

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

BSP

JigCell Tyson’s Frog Egg Model

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

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

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

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

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