| |
|
| Monday |
Topics/Session,
Instructor: Raquell Holmes |
| |
|
|
| 9:00 |
Welcome
* Participant introductions
* Overview of workshop
* Resources, Handouts
|
| 9:45 |
Overview
of Computational biology
* Biological models and computational
approaches
|
| 10:30 |
Break
- 15 mins |
| 10:45 |
Working with Stella and the Goldbeter
model
* Presentation
* Concept mapping and simulation
* Introduction to Stella (Univ.
of Georgia page)
* Exercise1 create your own version
of the cell cycle statements in Stella Demo. Discussion
of units.
* Exercise 2, playing with
existing model.
|
| 12:00 |
Lunch
1 hour |
| 1:00 |
Cell
Cycle Models: Research papers
* Goldbeter, Sha et al.,Tyson,
* Group work:
* Recognizing components, reactions, testable hypothesis,
math
*Worksheets
|
| 3:00 |
Break
15 mins |
| 3:15 |
Group
work: Design and prepare for Tuesday presentation
* Sketch initial model of interest
* Identify related models resources.
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|
|
|
| Tuesday |
Topics/Session,
Instructors: Jill Sible, Raquell Holmes |
| |
|
|
| 9:00 |
Practical
and personal considerations in collaborations between
experimentalists and theoreticians. |
| |
*Presentation (PDF)
*The cell cycle as case: Novak-Tyson,
1993 and Sha
et al, 2003 |
| 10:15 |
Break
30 mins |
| 10:45 |
Designing
experiments for numerical modeling
* Redesigning data: Exercise
|
| 12:00 |
Lunch
1 hour |
| 1:00 |
Group
work time
* Prepare for group presentation
on initial model
* Investigate potential tools or topics
|
| 3:00 |
Break
15 mins |
| 3:15 |
Participant
Group Presentations-5 minutes each
Preview of JDesigner, Virtual Cell…
*other
tools presented by participants. |
|
|
|
| Wednesday |
Topics/Session,
Instructor: Herbert Sauro |
| |
|
|
| 9:00 |
Introduction
to Modeling
Presentation
* Signal cascades and other biological systems
|
| 9:45 |
Introduction
to JDesigner
* Exercises in creating simple reaction
models
|
| 10:30 |
Break
15 mins |
| 10:45 |
Important
considerations in constructing models
* Conservation analysis and scales
|
| 12:00 |
Lunch
1 hour |
| 1:00 |
Project
exercises:
* Stochastic models in excel
* Starting your own
* relaxation oscillators
* Hysterises
|
| 3:00 |
Break
15 mins |
| 3:15 |
Additional
model exploration
* Tutorial 3 of JDesigner Tutorial
Manual
(PDF)
|
| 4:45 |
Group
discussion 15 mins |
|
|
|
| Thursday |
Topics/Session,
Instructors: Ann Cowan, Ion Moraru |
| 9:00 |
Review
of calcium dynamics and studies using Virtual
Cell |
| 9:45 |
Introduction
to Virtual Cell |
| 10:30 |
Break
15 mins |
| 10:45 |
Hands
on with Virtual Cell:
* Existing models in database
|
| 12:00 |
Lunch
1 hour |
| 1:00 |
Implementing
your own model in Virtual Cell |
| 3:00 |
Break
15 mins |
| 3:15 |
Work
time and wrap up |
|
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