User Interface Paradigms forDescribing Pathway Models

Cliff ShafferDepartment of Computer Science

Virginia Tech

Fundamental Questions

• Who are the users?

• What are the tasks?• What are the key bottlenecks?

Who are the Users?

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 LifecycleModeler’s Lifecycle

Data NotebookData Notebook

Wiring DiagramWiring Diagram

Differential EquationsDifferential Equations Parameter ValuesParameter Values

AnalysisAnalysis SimulationSimulation

ComparatorComparator

Data NotebookData Notebook

ExperimentalExperimentalDatabasesDatabases

The Cell (Modeler) Cycle

• Outer Loop:– Define Reaction Equations

• Inner Loop:– Adjust parameters, initial conditions

Tyson’s Frog Egg Model

'1 1 2

d[Cln2][SBF] [Cln2]

dk k k

t

' '3 3 4 4 5

d[Clb2][Mcm1] [Cdh1] [Clb2] [Sic1][Clb2]

dk k k k k

t

' '6 6 T 7 7

6 T 7

[Cdc20] [Cdh1] [Cdh1] [Clb5] [Cdh1]d[Cdh1]

d [Cdh1] [Cdh1] [Cdh1]

k k k k

t J J

synthesis degradation

synthesis degradation binding

activation inactivation

0 50 100 150

0.0

0.5

1.0

1.5

0.0

0.5

0.0

0.5

1.0

1

2

Time (min)

Sic1

mass

Clb2

Cln2

Cdh1

Simulation of the budding yeast cell cycle

G1 S/M

Cdc20

Designing an Interface

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”?

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