Introduction to computational cell biology

Professor Greg Buzzard MATH 402, 4-1937 buzzard at math dot purdue dot edu

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Resources

There are many resources available on the web and in the library.  A few are listed below.  Remember that any source may contain errors, so check more than one source and/or ask your professor!

Textbook website

Models – systems and models linked to the text by Fall, et al

General explanation

	Cardiovascular system - description and examples of models
	Hearts Gone Wild - news article about fibrillation and modeling
	Wikipedia - generally reliable, user-maintained encyclopedia.  Has fairly clear explanations for many common cardiac and general biology terms.
	Nonlinearity in the heart - an introductory article describing some interesting dynamical behavior in the heart.
	ECG Library - examples and explanations for many types of ECG patterns
	Cardiovascular physiology – very readable introduction

Models and modeling projects

	CellML cardiac models - a repository of models written in CellML - look for the maths.pdf file to get the equations for a model
	Heart Simulation Project - open source ion channel models

Course web sites

	Computational Models of the Cardiac Myocyte - course web site from Johns Hopkins biomedical engineering
	Cardiovascular System Dynamics and Modeling - course web site from University of Pittsburgh bioengineering
	Mathematical and Computer Modeling of Physiological Systems - course web site from University of Wisconsin-Madison biomedical engineering

Software

	winpp (basic introduction and locbif tutorial)
	ODE plotter - simple interface for graphing solutions of 2 variable ODEs
	Dynamical systems software - links to many programs that can be used for analyzing dynamical systems

Some Centers and Researchers Focusing on Cardiac Modeling:

Centers:

	Center for Cardiovascular Bioinformatics and Modeling - Johns Hopkins
	US FDA
	Oxford Cardiac Electrophysiology Group
	Cardiac Bioelectricity and Arrhythmia Center, Washinton University in St. Louis
	Cardiac Mechanics Research Group, UCSD
	Cardiovascular Research Laboratory, UCLA
	Center for Arrhythmia Research - includes several demo applets (see the left side bar)

Individuals: See also N. Trayanova's list.

Use the jump index:
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, R, S, T, V, W, Y, Z

A:	Aguel, Felipe, Ph.D.	US FDA
	Aliev, Rubin, Ph.D.	Medical University of South Carolina
B:	Bahar, Sonya, Ph.D.	University of Missouri at St. Louis
	Barkley, Dwight, Ph.D.	University of Warwick, Coventry, England
	Barr, Roger C., Ph.D.	Duke University, NC,
	Beaumont, Jacques, Ph.D.	SUNY, Syracuse, NY,
	Biktashev, Vadim, Ph.D.	University of Leeds, UK
	Boyett, Mark, Ph.D.	University of Manchester, UK
	Bub, Gil, Ph.D.	McGill University, Montreal, Quebec, Canada
C:	Cherry, Elizabeth M., Ph.D.	Cornell University
	Chialvo, Dante R., Ph.D.	Northwestern, UCLA
	Christini, David J., Ph.D.	Cornell University, NY, NY
	Clancy, Colleen, Ph.D.	Cornell University, NY, NY
	Clayton,Richard H. Ph.D.	University of Sheffield, UK
	Colli Franzone, piero, Ph.D.	Università di Pavia, Italy
	Cytrynbaum, Eric Ph.D.	University of British Columbia, CA
D:	Delmar Mario, M.D., Ph.D.	SUNY, Syracuse, NY,
	Demir, Semahat S., Ph.D.	University of Tennessee, Memphis, TN
	Dössel, Olaf Ph.D.	Universität Karlsruhe
E:	Eason, James C., Ph.D.	Washington and Lee University, Virginia
	Efimov, Igor R., Ph.D.	Washington University in St. Louis
	Entcheva, Emilia, Ph.D.	SUNY Stony Brook
F:	Fast, Vladimir G., Ph.D.	University of Alabama at Birmingham
	Fenton, Flavio H., Ph.D.	Cornell University, NY
	Fox, Jeff,	Gene Network Sciences, Ithaca, NY
G:	Garfinkel, Alan, Ph.D.	UCLA, Cardiovascular Research Lab. Los Angeles, CA
	Gauthier, Dan, Ph.D.	Duke University, NC
	Giles, Wayne R., Ph.D.	University of Calgary, Calgary, Canada
	Gilmour, Robert F., Jr., Ph.D.	Cornell University, Ithaca, NY
	Glass, Leon, Ph.D.	McGill University, Montreal, Quebec, Canada
	Golding, Simon, Ph.D.	Formerly of Oxford University, UK
	Gray, Richard A., Ph.D.	University of Alabama at Birmingham
	Greenside, Henry S., Ph.D.	Duke University, NC
	Guevara, Michael R., Ph.D.	McGill University, Montreal, Quebec, Canada
H:	Hagberg, Aric, Ph.D.	Los Alams, NM
	Hakim, Vincent, Ph.D.	École Supérieure de Physique, Paris Fr
	Henriquez, Craig S., Ph.D.	Duke University, NC
	Holden, Arun, Ph.D.	University of Leeds, Leeds, UK
	Hunter, Peter J.,Ph.D.	Auckland University, NZ
I:	Ideker, Raymond E., Ph.D.	University of Alabama at Birmingham
J:	Jalife, Jose, M.D.	SUNY Syracuse, NY
	Johnson, Christopher R., Ph.D.	University of Utha, Salt Lake City, UT
	Jones, Janice, Ph.D.	Georgetown Univeristy, DC
K:	Karma, Alain S., Ph.D.	Northeastern University
	Keener, James P., Ph.D.	University of Utah, Salt Lake City, UT
	Kleber, Andre G., M.D.	University of Bern, Switzerland
	Knisley, Stephen B., Ph.D.	University of North Carolina
	Krassowska, Wanda, Ph.D.	Duke University, NC
L:	Leon, L. Joshua, Ph.D.	University of Calgary, Calgary, Canada
	Levine, Herbert, Ph.D.	UCSD, La Jolla, CA
	Lin, Shien-Fong (Marc) Ph.D.	Cedars-Sinai Heart Center
	Lines, Glenn Ph.D.	Simula Research Laboratory, Norway
M:	MacLeod, Rob Ph.D.	University of Utha, Utha
	Malkin, Robert A., Ph.D.	Duke University, NC
	McCulloch, Andrew D., Ph.D.	University of California, San Diego, CA
	McQueen, David M., Ph.D.	Courant Institute of Mathematical Sciences, NY
	Müller, Stefan C., Ph.D.	Universität Magdeburg, Deutschland
N:	Nash, Martyn P., Ph.D.	University of Auckland, New Zealand
	Noble, Denis, Ph.D.	Oxford University, UK
	Nygren, Anders, Ph.D.	University of Calgary, Calgary, Canada
O:	Otani, Niels F., Ph.D.	Cornell University, NY
P:	Panfilov, Alexander, Ph.D.	Utrecht University, Utrecht, The Netherlands
	Paterson, David J., Ph.D.	Oxford University, UK
	Pertsov, Arkadii M., Ph.D.	SUNY Syracuse, NY
	Peskin, Charles S., Ph.D.	Courant Institute, NY
	Plonsey, Robert, Ph.D.	Duke University, NC
	Pollard, Andrew E., Ph.D.	University of Alabama at Birmingham
	Pullan, Andrew	Auckland University, NZ
Q:	Qu, Zhilin, Ph.D.	UCLA, Cardiovascular Research Lab. Los Angeles, CA
R:	Rappel, Wouter J., Ph.D.	UCSD La Jolla, CA
	Riccio, Mark e-mail	Cornell University, NY
	Rogers, Jack M., Ph.D.	University of Alabama at Birmingham, AL
	Rohr, Stephan, Ph.D.	University of Bern, Stwitzerland
	Roth, Bradley, Ph.D.	Oakland University, Michigan
	Rudy, Yoram, Ph.D.	Case Western Resrve University, Cleveland, OH
S:	Salama, Guy, Ph.D.	University of Pittsburgh, PA
	Shrier, Alvin, Ph.D.	McGill University, Montréal, Québec, Canada
	Starmer, Frank C., Ph.D.	Medical University of South Carolina, SC
T:	Thakor, Nitish, Ph.D.	Johns Hopkins University, MD
	Titomir, Leonid, Ph.D.	IITP, Russian Academy of Sciences, Moscow, Russia
	Trayanova, Natalia A., Ph.D.	Tulane University, New Orleans, LA
	Tung, Leslie, Ph.D.	Johns Hopkins University, MD
V:	Vetter, Frederick Ph.D.	University of Rhode Island, RI
	Vigmond, Edward J., Ph.D.	University of Calgary, Calgary, Canada
	Vinet, Alain, Ph.D.	Université de Montréal, Montréal, Québec, Canada
W:	Weiss, James N., M.D.	UCLA, Cardiovascular Research Lab. Los Angeles, CA
	Wikswo, John P., Ph.D.	Vanderbilt University, Nashville, TN
	Winslow, Raimond L., Ph.D.	Johns Hopkins University, Baltimore, MD, USA
	Wolf, Patrick D., Ph.D.	Duke University, NC
	Woods, Marcella, Ph.D.	Vanderbilt University, Nashville
Z:	Zaritski, Roman Ph.D.	Montclair State University, NJ
	Zhabotinsky, Anatol M., Ph.D.	Brandeis University, Waltham, MA
	Zykov, Vladimir, Ph.D.	Institut für Experimentelle PhysiK, Magdeburg Germany