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User Interface Paradigms for

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Preparing a model for the purpose of simulation. Figuring out ... beings can have widely divergent opinions on what interface paradigm makes them productive. ... – PowerPoint PPT presentation

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Title: User Interface Paradigms for


1
User Interface Paradigms for Describing Pathway
Models Cliff ShafferDepartment of Computer
ScienceVirginia Tech
2
Fundamental Questions
  • Who are the users?
  • What are the tasks?
  • What are the key bottlenecks?

3
Who are the Users?
4
Who are the Users?
  • 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
Modelers Lifecycle
Data Notebook
Wiring Diagram
Differential Equations
Parameter Values
Simulation
Analysis
Comparator
Data Notebook
9
The Cell (Modeler) Cycle
  • Outer Loop
  • Define Reaction Equations
  • Inner Loop
  • Adjust parameters, initial conditions

10
Tysons Frog Egg Model
11
(No Transcript)
12
Simulation of the budding yeast cell cycle
mass
Sic1
Cln2
Clb2
Cdh1
Cdc20
Time (min)
13
Designing an Interface
14
Designing an Interface
  • 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
What is Pathway Model Building Like?
  • 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
Tysons Frog Egg Model
27
A Characteristic of our Models
  • We cant 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
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