COMPUTATIONAL CELL BIOLOGY
July 24 - August 13, 2012
Application Deadline: May 16, 2012

Instructors:

Reka Albert, Pennsylvania State University
Leslie Loew, University of Connecticut Health Center
Suzanne Scarlata, Stony Brook University Medical Center
Gregory Smith, College of William and Mary

Course website

Computational cell biology is the field of study that applies the mathematics of dynamical systems together with computer simulation techniques to the study of cellular processes. The field encompasses several topics that have been studied long enough to be well established in their own right such as calcium signaling, molecular motors and cell motility, the cell cycle, and gene expression during development. In addition to providing a recognizable larger community for topics such as these, this course will provide a base for the development of newer areas of inquiry – for example the dynamics of intracellular second-messenger signaling, of programmed cell death, of mitotic chromosome movements, and of synthetic gene networks. Unlike computational genomics or bioinformatics, computational cell biology is focused on simulation of the molecular machinery (genes-proteins-metabolites) that underlie the physiological behavior (input-output characteristics) of living cells.

The three week course in Computational Cell Biology will incorporate a series of didactic lectures on the mathematics of dynamical systems, computational simulation techniques, cell biology and molecular biology. Practicing theoreticians and experimentalists will rotate in for 1-3 day visits during the course to give lectures and interact with the students. Midway through the course, students will select an area for independent study, and the focus of the last week of the course will largely be on these projects, supplemented by continued visiting lecturers.

Speakers for 2011 included:
Reka Albert, Pennsylvania State University
Avrama Blackwell, George Mason University
Sarah Day, College of William and Mary
Leah Edelstein-Keshet, University of British Columbia
James Faeder, University of Pittsburgh
Jeff Hasty, University of California, San Diego
Michael Hucka, Caltech
Oleg Igoshin, Rice University
Ravi Iyengar, Mount Sinai School of Medicine
James Keener, University of Utah
James Lechleiter, University of Texas Health Sciences Center
Avi Ma'ayan, Mount Sinai School of Medicine
Pedro Mendes, University of Manchester
Ion Moraru, University of Connecticut Health Center
Robert Phair, Integrative BioInformatics
Karen Sachs, Stanford University School of Medicine
James Schaff, University of Connecticut Health Center
Arthur Sherman, National Institutes of Health
David Terman, Ohio State University
Heather Wellman, Mathworks
Verena Wolf, Saarland University
Lingchong You, Duke University

Visiting faculty will change from year to year, and the specific topics covered will vary. Potential areas include:

Fundamentals
-Cell biology (signaling, differentiation, motility, cell cycle,
apoptosis)
-Molecular biology (gene expression, posttranslational modification,
proteolysis)
-Mathematical biology (dynamical systems, phase plane, elementary
bifurcations)
-Computational tools (numerical simulation, software, SBML)

Advanced Topics
Sniffers, buzzers, toggles and blinkers
Practical bifurcation theory
Reaction-diffusion-advection
Stochastic modeling
Physical chemistry of aggregation/polymerization
Mechano-chemical dynamics
Sensitivity & robustness
Optimization, parameter estimation

Case Studies
calcium signaling
cancer modeling
cardiac modeling
signal transduction networks
gene expression
apoptosis
cell cycle regulation
cytoskeletal dynamics
neural models
intracellular trafficking & molecular motors
cell motility & chemotaxis
mechanics of mitosis & cell division
oscillations & bursting in neurosecretion
fertilization phenomena
development
mitochondrial function
cell differentiation
synthetic gene networks
circadian modeling
computational modeling in drug discovery

This course is supported with funds provided by the National Science Foundation