User Interface Paradigms for

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User Interface Paradigms for Describing Pathway
Models Cliff ShafferDepartment of Computer
ScienceVirginia Tech
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Fundamental Questions

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

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Who are the Users?
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Who are the Users?

• Modelers
• Expert users
• Observation Not biologists
• Chemists, Physicists, Engineers

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What is the Task?

• Primary Tasks
• Preparing a model for the purpose of simulation
• Figuring out the model
• Verifying the model

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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

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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

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Modelers Lifecycle
Data Notebook
Wiring Diagram
Differential Equations
Parameter Values
Simulation
Analysis
Comparator
Data Notebook
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The Cell (Modeler) Cycle

• Outer Loop
• Define Reaction Equations
• Inner Loop
• Adjust parameters, initial conditions

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Tysons Frog Egg Model
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Simulation of the budding yeast cell cycle
mass
Sic1
Cln2
Clb2
Cdh1
Cdc20
Time (min)
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Designing an Interface
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Designing an Interface

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

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Designing an Interface

• Observation Rational human beings can have
  widely divergent opinions on what interface
  paradigm makes them productive.
• Ex LaTeX vs. MS Word

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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.

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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

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What is Pathway Model Building Like?
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What is Pathway Model Building Like?

• Photography?

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What is Pathway Model Building Like?

• Photography?
• Programming?

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What is Pathway Model Building Like?

• Photography?
• Programming?
• Writing?

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What is Pathway Model Building Like?

• Photography?
• Programming?
• Writing?
• Drawing/Painting?

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What is Pathway Model Building Like?

• Photography?
• Programming?
• Writing?
• Drawing/Painting?
• Bridge designing?

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Existing Paradigms

• Graphical
• Virtual Cell, BSP, JDesigner
• Wizards
• Gepasi
• Equations or Scripts
• JigCell, Jarnac
• No implementation is pure

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BSP
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JigCell
Tysons Frog Egg Model
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A Characteristic of our Models

• We cant get away from the fact that there is
  mathematics to describe
• Parameter/initial condition values
• Rate laws

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How to Compare Interfaces

• Time required to complete task
• Errors committed during task
• Learning curve

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Application-Specific Issues

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

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Graphical vs. Equation

• Pros
• Better intuitive grasp of overall model
• Cons
• Low information density
• Poor support for mathematical details

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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