SIAM Conference on Computational Sciene and Engineering 
Feb 10--13 2002 
Hyatt Regency Islandia Hotel San Diego CA 
Minisymposia on Bioinformatics and Computational Biology 

For more information visit, http://www.siam.org/meetings/cse03/index.htm


Tuesday, February 11
MS25 Computational Modeling in Proteomics
10:30 AM - 12:30 PM
Room: Regency Ballroom A



Now that the genomes of many organisms have been sequenced, a major
challenge is the characterization of the proteins (numbering in the
hundreds of thousands) and protein complexes that drive cellular function.
High-throughput technologies such as mass spectrometry and NMR are being
developed to characterize the sequence, structure, and function of
proteins. A related
computational effort is the study of which proteins interact with each
other, and the characterization of protein interaction networks. The
Department of Energy's new Genomes to Life program is an active sponsor of
this work. The speakers in this session will discuss some of the
developments in the newly emerging field of computational proteomics.
Related work on how protein interaction data is used in cell-level 
modeling
will be discussed by speakers in mini-sympoium MS61.
Organizers: Alex Pothen, Old Dominion University and Sandia National
Laboratories
Steve Plimpton, Sandia National Laboratories

10:30-10:55 Hybrid Methods for Protein Structure Determination:
Application of Computational Methods and Sparse Experimental Data
   Ying Xu, Oak Ridge National Laboratory
11:00-11:25 Enumerating and Counting Protein Folds using Distance
Information
   Jean-Loup Faulon, Alex Slepoy, Malin Young, and Mark Rintoul,
   Sandia National Laboratories
11:30-11:55 Enhancing Protein Secondary Structure Prediction by
Sequence-to-Structure Alignments
   Rafal Adamczak, Aleksey Porollo, and Jarek Meller, University of 
 Cincinnati
12:00-12:25 Graph and Hypergraph Models of Protein Interaction
Networks
   Alex Pothen, Old Dominion University and Sandia National Laboratories




Tuesday, February 11
MS37 Computational Cell Biology
3:15 PM - 5:15 PM
Room: Regency Ballroom A
For Part II, see MS61


This mini-symposium concentrates on the relatively new and emerging
discipline of computational cell biology, where quantitative computer
models are used to simulate various aspects of the structure and function
of Eucaryotic and Procaryotic cells. Several levels of complexity exist in
generating these "virtual" cell models that progress from simulating well
mixed, time-dependent, reaction kinetics to fully 3-D, spatially resolved,
time-dependent, reaction/diffusion/advection models. The seminars within
this mini-symposium will cover computational cell biology models, codes 
 and
environments for simulating
either intra- and extra-cellular processes. Specific subjects to be 
 covered
include models, algorithms, data management, code development, parallel
computing, and biologist/code interfaces relevant to computational cell
biology.

Organizer: Petri Fast, Lawrence Livermore National Laboratory
Harold E. Trease, Pacific Northwest National Laboratory
Steven J. Plimpton, Sandia National Laboratories

3:15-3:40 The Virtual Microbial Cell Simulator (VMCS): A
Computational Simulation Hierarchy for Modeling the Systems Biology of
Microbial Cells
   Harold E. Trease, Pacific Northwest National Laboratory
3:45-4:10 Optimized Monte Carlo Methods for Large-scale
Microphysiological Modeling
   Thomas M. Bartol, The Salk Institute; Joel Stiles, Pittsburgh
   Supercomputing Center
4:15-4:40 A Three-dimensional Overset Grid Model of Ca$^{2+}$
Waves in {\em Xenopus Laevis} Eggs
    Petri Fast, Lawrence Livermore National Laboratory
4:45-5:10 The Virtual Cell Project
    Les Loew, University of Connecticut



Wednesday, February 12
MS61 Computational Cell Biology
3:15 PM - 5:15 PM
Room: Regency Ballroom A
For Part I, see MS37
This mini-symposium concentrates on the relatively new and emerging
discipline of computational cell biology, where quantitative computer
models are used to simulate various aspects of the structure and function
of Eucaryotic and Procaryotic cells. Several levels of complexity exist in
generating these "virtual" cell models that progress from simulating well
mixed, time-dependent, reaction kinetics to fully 3-D, spatially resolved,
time-dependent, reaction/diffusion/advection models. The seminars within
this mini-symposium will cover computational cell biology models, codes 
and environments for simulating either intra- and extra-cellular processes.
Specific subjects to be covered include models, algorithms, data
management, code development, parallel computing, and biologist/code
interfaces relevant to computational cell biology.

Organizer: Petri Fast, Lawrence Livermore National Laboratory
Harold E. Trease, Pacific Northwest National Laboratory
Steven J. Plimpton, Sandia National Laboratories

3:15-3:40 Studying the Alpha Pathway in Yeast with Moleculizer
   Larry Lok, The Molecular Sciences Institute
3:45-4:10 The Impact of Spatial Realism on Microphysiological Models
   Joel Stiles, Pittsburgh Supercomputing Center; Thomas M.
   Bartol, The Salk Institute
4:15-4:40 Mesh Generation and Modeling of Biological Systems Using Cubit
   Jason Shepherd, Sandia National Laboratories
4:45-5:10 Application of Continuum, Unstructured Finite Element Numerical
Methods to Spatial Models of Intracellular Calcium Dynamics
   Shawn Means, Sandia National Labor