Schedule

July 22 – August 12, 2013
Bush Hall

7:30 AM to 9:00 AM – Breakfast
9:00 AM to 12:00 PM – Morning session (w/ 30 min break)
12:00 PM to 1:30 PM – Lunch
1:30 PM to 4:30 PM – Afternoon session (w/ 30 min break)
5:30 PM to 7:00 PM – Dinner
7:00 PM to 10:00 PM -Evening session

Monday, July 22nd, evening, 7pm
Wine and cheese reception

Tuesday, July 23rd, morning
[ Welcome and announcements – Andrea Stephenson ]
Robert Phair, Integrative Bioinformatics
“ODEs from molecular cell biology to physiology and pharmaceutical R&D”
“Molecular Cell Biology and ODEs; Fluorescent proteins kinetics and model diagrams”

Tuesday, July 23rd, afternoon
Gregory D. Smith, The College of William & Mary
“Cellular biophysics and modeling with ordinary differential equations (ODEs)”

Tuesday, July 23rd, evening
Student research presentations

Wednesday, July 24th, morning & afternoon
Gregory D. Smith, The College of William & Mary
(see above)

Wednesday, July 24th, evening
Exercises (Phair & Smith)

Thursday, July 25th, morning
Gerda DeVries, University of Alberta
“Michaelis-Menten Enzyme Kinetics: Modeling and Approximations”

Thursday, July 25th, afternoon, evening
Les Loew, University of Connecticut
“Virtual Cell and ODEs”
[ Exercises before and/or after. ]

Friday, July 26th, morning
Gerda DeVries, University of Alberta
“Biochemical and Genetic Networks: Thresholds and Switches”

Friday, July 26th, afternoon
Ion Moraru & Les Loew, University of Connecticut
“Virtual Cell and Pathway Modeling”

Friday, July 26th, evening
Exercises (w/ DeVries & Moraru)

Sunday, July 27th, morning
[ Introduction to student project objectives ]
Gregory D. Smith, The College of William & Mary
“Cellular biophysics and modeling: ionic channels and excitable membranes”

Saturday, July 27th, afternoon
David Terman, The Ohio State University
“Dynamical Systems – Part 1”

Saturday, July 27th, evening
Exercises (Terman)

Sunday, July 28th, morning
David Terman, The Ohio State University
“Dynamical Systems – Part 2”

Sunday, July 28th, afternoon
Gregory D. Smith, The College of William & Mary
“Calcium excitability, bistability and oscillations”
“Stochastic gating of ion channels: the basics”

Sunday, July 28th, evening
Exercises / Projects

Monday, July 29th, morning
Student Projects

Monday, July 29th, afternoon
John Tyson, Virginia Polytechnic Institute and State University
“Network dynamics and physiology”
“Network dynamics and cell cycle controls (derministic models)”

Monday, July 29th, evening
Exercises (w/ Tyson)

Tuesday, July 30th, morning
Student Projects

Tuesday, July 30th, afternoon
John Tyson, Virginia Tech
“Stochastic models of cell cycle regulation”

Tuesday, July 30th, evening
Exercises (w/ Tyson)

Wednesday, July 31, morning
James Lechleiter, University of Texas at San Antonio
“The Biology of Calcium signaling”

Wednesday, July 31, afternoon
Asawari Samant, The Mathworks, Inc.
“An overview of MATLAB and the SimBiology toolbox”

Wednesday, July 31, evening
Projects / Exercises
[Abstracts of proposed projects due @ 10pm.]

Thursday, August 1, morning
James Keener, University of Utah
“Cardiac models”

Thursday, August 1, afternoon
Gregory D. Smith, The College of William & Mary
“Random walks and diffusion”
James Schaff, University of Connecticut
“Virtual cell and PDEs”
Les Loew, University of Connecticut
“Actin and dendritic nucleation”

Thursday, August 1, evening
Exercises (w/ Loew, Moraru, Schaff)

Friday, August 2, morning
Eric Sobie, Mount Sinai Medical College
“Local control of cardiac Ca release: biological importance and modeling approaches.”

Friday, August 2, afternoon
[ Course photograph @ 4:30pm-ish ]
Ion Moraru & James Schaff, University of Connecticut
“Virtual cell, stochastic reaction networks, and stochastic spatial modeling”

Friday, August 2, evening
Exercises (w/ Moraru and Schaff)

Saturday, August 3, morning
Student projects

Saturday, August 3, afternoon
[ Sailing trip 1-3pm ]
[ Course Picnic @ Airslie Beach (if rain, then Blackford Hall) ]
[ 4:00pm – 5:00pm Bar & Raw Bar / 5:00pm – 7:00pm Bar & Buffet ]

Saturday, August 3, evening
Exercises / Projects

Sunday, August 4
[ Day Off ]

Monday, August 5, morning
Leonard Harris, University of Pittsburg
“Rule-based modeling”

Monday, August 5, afternoon
Pedro Mendes, University of Manchester
“Optimization and Parameter Estimation with COPASI – Part I”

Monday, August 5, evening
Exercises (w/ Mendes)

Tuesday, August 6, morning
Pedro Mendes, University of Manchester
“Optimization and Parameter Estimation with COPASI – Part II”

Tuesday, August 6, afternoon
Martin Feinberg, The Ohio State University
“Chemical Reaction Network Theory”

Tuesday, August 6, evening
Exercises (w/ Feinberg)

Wednesday, August 7, morning
Student Projects

Wednesday, August 7, afternoon
Reka Albert, Pennsylvania State University
“Graph theoretical analysis of intra-cellular networks”
“Linking the structure and dynamics of intra-cellular networks”

Wednesday, August 7, evening
Exercises (w/ Albert)

Thursday, August 8, morning
Reka Albert, Pennsylvania State University
“Discrete dynamic modeling of signal transduction networks”

Thursday, August 8, afternoon
Exercises (w/ Albert) from 1:30-2:30
[ Plate race @ 3pm near Dulbruck ]

Thursday, August 8, evening
Student Projects

Friday, August 9, morning
Student Projects

Friday, August 9, afternoon
Jeff Hasty, University of California at San Diego
“Gene networks and synthetic biology”

Friday, August 9, evening
Karen Sachs and Tiffany Chen, Stanford
“Baysian analysis of reaction networks”

Saturday, August 10, morning
Student Projects

Saturday, August 10, afternoon
Tiffany Chen & Karen Sachs, Stanford
“Cell cycle modeling”
“Machine Learning and Network Analysis”

Saturday, August 10, evening
Exercises (w/ Sachs and Chen)

Sunday, August 11, morning
Michael Hucka, Caltech
“SBML, Model Databases and Translation”

Sunday, August 11, afternoon
Project Presentations

Sunday, August 11, evening
[ Course Banquet ]
6:00-6:45pm, Cocktails in Blackford Hall Bar
6:45pm, Dinner in Clarkson Dining Room
(Lower Level of Blackford Hall)

Monday, August 12, morning
Wrap up

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