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2006 Program on Development, Assessment and Utilization of Complex Computer
Models
Biosystems Modeling Workshop
March 5-7 at the Radisson RTP
General Information
Application
Schedule
General Information
This Workshop forms part of the Biological Modeling Subprogram of the SAMSI program on the
Development, Assessment and Utilization of Complex Computer Models. The workshop focuses in
particular the development, calibration and validation of computational systems biology models.
Models used in systems biology range from small biochemical networks modeled with a set of coupled
ODEs that can be simulated quickly on a standard PC, through to large spatio-temporal models of
whole cell (or cell population) behaviour run on large computing facilities. Some models are
deterministic, while others are intrinsically stochastic, giving different output on each run.
All typically contain uncertain parameters that must be estimated from sparse, noisy experimental
data. Additionally, there is often uncertainty regarding model structure. Particular problems that
arise in the context of systems biology models include: estimating large numbers of parameters
from sparse data, parameter estimation using complex multivariate data, simultaneous estimation of
model parameters and structure, and estimating parameters of complex stochastic models.
The workshop aims to stimulate the formation of working groups on a small number of key
mathematical and statistical challenges in computational systems biology modeling.
Workshop Committee: Darren Wilkinson (Newcastle, UK), Greg Rempala (Louisville), Ralph Smith
(SAMSI).
REGISTRATION IS CLOSED
Schedule
Monday, March 5, 2007
Radisson RTP, Room H, 3rd Floor
Presentation Abstracts
| 8:00-8:50 |
Registration and Continental Breakfast |
| 8:50-9:00 |
Welcome
Jim Berger, SAMSI |
| 9:00-10:00 |
Tutorial on Biochemical Network Modelling
Eberhard Voit, Georgia Institute of Technology |
| 10:00-10:30 |
Break |
| 10:30-11:30 |
Tutorial on Stochastic Kinetic Models
Greg Rempala, Univ. of Louisville
|
| 11:30-12:30 |
Tutorial on Drawing Together Aspects of Systems Engineering and Systems Biology
Herschel Rabitz, Princeton
|
| 12:30-1:45 |
Lunch, Room FG |
| 1:45-2:45 |
Maya Mincheva, Univ. of Wisconsin
Dynamical Properties of Biochemical Reaction Networks |
| 2:45-3:45 |
Thomas Kepler, Duke
Computational Systems Immunology |
| 3:45-4:15 |
Break |
| 4:15-5:00 |
Poster Presentation Introduction Session |
| 6:30-8:30 |
Poster Session and Reception, Room AB, 2nd Floor
(Please have your
poster set up by 6:15)
SAMSI will provide poster presentation boards and tape. The board dimensions
are 4 ft. wide by 3 ft. high. They are tri-fold with each side being 1 ft. wide and the center
2 ft. wide. Please make sure your poster fits the board. The boards can accommodate up to 16
pages of paper measuring 8.5 inches by 11 inches. |
Tuesday, March 6, 2007
Radisson RTP, Room H, 3rd Floor
| 8:30-9:00 |
Registration and Continental Breakfast |
| 9:00-10:00 |
Adrian Dobra, Univ. of Washington
Efficient Stochastic Search Algorithms for "Large p" Regression with
> Dependent Covariates |
| 10:00-11:00 |
Guillaume Bonnet, U.C. - Santa Barbara
On Some Stochastic Oscillator Problems Related to Biological Rhythms |
| 11:00-11:30 |
Break |
| 11:30-12:30 |
Panel Discussion - Top-down Versus Bottom-up Approaches to Biosystems Modelling
John Yin, Univ. of Wisconsin
Tom Knudsen, Univ. of Louisville |
| 12:30-1:45 |
Lunch, Room FG |
| 1:45-3:50 |
New Researcher Session (20 minutes each)
John Fricks, Penn State, Diffusion Ratchets and Molecular Motors
Sam Isaacson, Univ. of Utah, The Reaction-Diffusion Master Eq. is an Asymptotic Approximation of
Diffusion to a Small Target
Khuloud Jaqaman, Scripps, Phenotypic Clustering of Yeast Mutants Based on Kinetochore Microtubule Dynamics
Hye-Won Kang, Univ. of Wisconsin, Multiscale Methods in Heat Shock Model
Sotiria Lampoudi, U.C.-Santa Barbara, The Effect of Reactant Size on Stochastic Chemical Kinetics
Richard Yamada, Cornell, A Chemical Kinetic Model for Transcriptional Elongation |
| 3:50-4:20 |
Break |
| 4:30-5:30 |
SAMSI Distinguished Lecture
Daniel Gillespie, Gillespie Consulting
Stochastic Chemical Kinetics |
| 5:30-6:30 |
Lecture Reception, Room FG |
Wednesday, March 7, 2007
Radisson RTP, Room H, 3rd Floor
| 8:30-9:00 |
Registration and Continental Breakfast |
| 9:00-10:00 |
Kevin Brown, Harvard
Sophisticated Statistical Mechanics of Sloppy Models |
| 10:00-11:00 |
Lea Popovic, Cornell
Model Reduction Techniques for Biochemical Networks |
| 11:00-11:30 |
Break |
| 11:30-12:30 |
Panel Discussion - Key Mathematical and Statistical Challenges in Computational Systems Biology
Linda Petzold, U.C. - Santa Barbara
Mike Reed, Duke
Darren Wilkinson, Univ. of Newcastle, U.K. |
| 12:30-1:45 |
Lunch, Room FG |
| 1:45-2:45 |
Samuel Kou, Harvard
Stochastic Challenges in Single-Molecule Biophysics |
| 2:45-3:00 |
Break |
| 3:00-4:30 |
Discussion of Working Groups Projects and Activities |
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