Rob's Links to Research Groups/Resources

"A new chapter has been opened in the study of heart diesease, not by the work of a single investigator, but by that of many talented men, who have not been influenced in their work by political boundaries and, distributed over the whole surface of the heart, have devoted their powers to an ideal purpose, the advance of knowledge by which, finally, suffering mankind is helped."
Wilhem Einthoven from his Nobel Lecture, December 11, 1925.

In this wonderful spirit, links to other research groups and resources.

Bioelectric Field Electrophysiology and Simulation Research

Groups we have worked with

Center for Interative Biomedical Computing at Utah/SCI Institute.
Dana Brooks and his group at Northeastern University (and my main collaborator).
Virtual Physiological Human Intitute, an international non-profit organisation incorporated in Belgium, whose mission is to ensure that the Virtual Physiological Human is fully realised, universally adopted, and effectively used both in research and clinic.
University of Auckland Bioengineering Institute, host of the CellML project and a Physiome site, directed by Peter Hunter.
Institute of Biomedical Engineering> at the University of Karlsruhe, directed by Olaf Doessel.
Duke Computational Electrophysiology Group, Duke University.
Institute for Computational Medicine at Johns Hopkins University directed by Rai Winslow.
Center for Cardiovascular Bioinformatics and Modeling at Johns Hopkins University directed by Rai Winslow.
Cardiocascular Research Grid at Johns Hopkins University directed by Rai Winslow.
Computational Cardiology Electrophysiology Lab at Johns Hopkins University, directed by Natalia Trayanova.
The Lausanne Heart Group headed by Adriaan van Oosterom.
Oxford University Computing Lab and the Chaste software.
Department of Medical Physics and Biophysics at the University of Graz.
The University of Nijmegen Bioelectricity Group The Netherlands.
NeuroImaging Research Group at the University of Southern California
Frank Sachse at the CVRTI, University of Utah.
SimBio project in Germany.
- The SimBio Wiki page
- Some of the code for SimBio was based on the CAUCHY project
SIMULA: Simulating the electrical activity of the heart at the University of Oslo, Norway.

Groups we know about

University of Alabama Cardiac Electrophysiology Group
Cell Electrophysiology Simulation Environment (CESE) by Sergey Missan at Dalhousie University.
Cellular Open Resource (COR) from Oxford Univeristy.
Cardiac Mechanics Research Group Andrew McCulloch at UCSD.
Cardiac mechanics from University of Iowa Radiology.
DynAmo project Tampere University, Finnland.
LabHeart from Don Bers at Loyola University.
Institute for Medical Signal Processing and Imaging at the University fo Health Informatics and Technology Tyrol, Autria.
INRIA: Simulations of biomechanical heart from Maxime Sermesant of the Epidaure research project at INRIA Sophia Antipolis in France.
Forschungszentrum Juelich Institute of Medicine in Juelich, Germany.

Bioelectricity Tutorials and Resources

Bioelectromagnetism text by Jaakko Malmivuo and Robert Plonsey.
Inverse Problem of Electro- and Magnetocardiography: Review and Recent Progress from Olaf Dössel, University of Karlsruhe.
Bioelectricity and Excitable Tissue from Donald C. Mikulecky at Virginia Commonwealth University
Bioelectricity summary as a project from North Carolina State students.
Mathtools a technical computing portal for all scientific and engineering needs
BEM for Laplace Problems

Electrocardiography/Cardiology Sites

Wilhelm Einthoven information from the Nobel Prize site.
Physionet NCRR resource Research Resource for Complex Physiologic Signals and Harvard.
Overview of Cardiovascular Physiology fairly simple and high level but well organized and pretty clear.
Nice set of cardiology simulation links from Suzanne Shontz.
NASPE Electrophysiology information for patients and practitioners.
American Heart Association
Encyclopedia of cardiovascular pharmacology from the University of Utah.
ECG's: The ECG Library Homepage , including the History of Electrocardiography by Dean Jenkins.
Tutorial guide to Reading ECGs from New York University Medical School
Animation of the heart cycle medstat.med.utah.edu/kw/pharm . This animation requires the Shockwave Flash plugin, and you can download the player plug-in from www.macromedia.com/software/flash.
HeartInfo site a general purpose cardiology site.
Premier Heart a company marketing the Multifunction Cardiogram (MCG) approach to analyzing ECGs for myocardial ischemia.
BSP Medical Inc, a company marketing the HyperQ method of analysis of QRS morphology for detection of myocardial ischemia.

Basic and Clinical Electrophysiology Links

Joseph F. Spear at University of Pennsylvania, project in experimental models of LQTS.
Order and Disorder a training program for clinical electrophysiology with lots of great product links.

Other Electrophysiology Groups

Inistitute of Medical Physics and Biophysics, Graz University of Graz, Austria.
Oxford University Electrophysiology Group
The CARMA Center for research and management of atrial arrhtymias.
The Utah Brain Institute

Heart Related Organizations

Electric Impedance Tomography

EIT.org! This contains links to all the other groups and good background material.
EIT group at RPI
Jennifer Mueller at CSU
Dartmouth College group
Kuppio University group, Finnland

Forward and Inverse Problems

Finnish Center of Excellence in Inverse Problems
Discrete Ill-posed problem papers from Daniella Calvetti's web site.
Multimodal integration of EEG, MEG and fMRI Special issue of International Journal of Bioelectromagnetism

NIH NCBC Centers

NCBC web site
Main portal for NCBCs
Simbios: Stanford Center for Biomedical Computation headed by Russ Altman.
National Alliance for Medical Image Computing at Harvard, Ron Kikinis.
Center for Computational Biology at UCLA, Art Toga.
Informatics for Integrated Biology and the Bedside Partners Health Care, Boston
National Center for Integrative Biomedical Informatics Brian D. Athey.
National Center for Multi-Scale Study of Cellular Networks Andrea Califano, Columbia University.
National Center for Multi-Scale Study of Cellular Networks Andrea Califano, Columbia University.

Other Simulation Groups/Centers

Cardiac Mechanics Research Group Andrew McCulloch at UCSD.
NBCR P41 Center at UCSD National Biomedical COmputation Resource.
Cardiac simulation wabsite a nice and comprehensive list of simulation groups and software.
Simbios: Stanford Center for Biomedical Computation headed by Russ Altman.
The Virtual Cell from the University of Connecticut Health Center. Also linked to the Center for Biomedical Imaging Technology
Biomedical Computation Review a new (2005) magazine about biomedical computing from Standford University.
Digital Human Project
Living Human Project (LHP) Here is also a link to a pdf file describing the project.
University of Utah research institutes
Charles Peksin at the Courant Institute, simulations of heart mechanics.
Cardiac Biomechanics Group at Columbia University
Montana State's Computational Biology Center
National Simulation Resource from the University of Washington. (Check the software link for XSIM and JSIM) (Jim Bassingthwaighte, Zheng Li)
CenSSIS Center for Subsurface Sensing and Imaging Systems ERC at Northeastern University.
Boundary Element Resources Network A resource for BEM.
Stanford Biocomputing Center
Systems Biology Workbench Development Group including the Systems Biology Markup Language (SBML).
The Weierstrass Institute for Applied Analysis and Stochastics in Berlin.
Dwayne Westneskow

Simulation/Mapping Software

SCIRun/BioPSE/map3d and other SCI Institute software.
Ecgsim from the University of Nijmegen (Van Oosterom and Oostendorp).
CardioInsight a company with a commercial mapping/inverse solution system.
CardioWave from Duke Computational Electrophysiology Group , Duke University.
Cell Electrophysiology Simulation Environment (CESE) by Sergey Missan at Dalhousie University.
CMISS from the University of Auckland.
Continuity from the Cardiac Mechanics Group at UCSD.
Web based map data viewer from Raymond Bond in Northern Ireland. Very clever app.
ECGSYN a program to simulate the ECG time signals.
Luo-Rudy Simulation model of mammalian ventricular cells.
iCell web based simulation model for electrophysiology from
Semahat S. Demir, Dept. of Biomedical Engineering, University of Memphis (and the NSF).
Use preview mode to avoid the need for password or contact Semahat for one.
2D Fitzhugh-Nagumo model from Northeastern University
Obituary of Jin-Ichi Nagumo
Don Bers model of a cardiac cell (in Labview).
Open EEG an open source EEG software project maintained at sourceforge.
NEURON
GENESIS from Jim Bower and Matthew Wilson.
Brainstorm from the USC NeuroImaging Research Group.
Brain Voyager
Netsolve at University of Tennessee's Innovative Computing Laboratory.
Summary of linear algebra software freely available on the Internet from Jack Dongarra.
Mathtools a technical computing portal for all scientific and engineering needs.
SoftMCG Software a commercial MCG processing software.
Matlab Links

Mapping Hardware and Data Acquisition and Processing

BioSemi, a commerical mapping system for bioelectric fields.
Heartscape Technologies, makers of the Prime ECG system for BSPM. Latest news from 2010 is that Verathon Inc, has purchased the technology and related assets for the PRIME ECG Product from HeartScape Technologies (Columbia, Maryland), where it seems to have disappeared.

Visualization and Problem Solving Environments

MGL Tools from the molecular Graphics Lab and Scripps Research Institute. Vis package is PMV for molecular vis, Vision is the PSE.
Center for the Representation of Multi-Dimensional Information (CROMDI) at the University of Utah.
The Pad++ zooming user interface.
Javaview adds three-dimensional graphics to web pages.
Electronic Geometryt Models an archive of geometric models.

BioMedical Imaging and Image Processing

Utah Center for Advanced Imaging Research (UCAIR) , including Medical Imaging Research Lab (MIRL) at the University of Utah.
University of Utah small animal imaging facility
Duke Center for In Vivo Microscopy
NA-MIC NCBC Center at Harvard Link to their Wiki.
National Biomedical Resource Center in Image-guided Therapy (IGT)
Statistical Parametric Mapping, a course on image manipulation from the Wellcome Department of Cognitive Neurology, UK.
Current Density Imaging with MRI cool idea...
NRRD library from Gordon Kindlmann. See also here for UNRRDU
The AIR package for automated image registration.
OSIRIX a Mac based system for image processing and viewing.

Simulation Techniques and Tutorials

Finite and Boundary Element Methods tutorial from Peter Hunter.
Notes on Bioengineering course from University of Auckland.
Albert, an adaptive FEM toolkit. The manual (PDF) is also available and includes a lot of good background on FEM methods in general.
Summary of linear algebra software freely available on the Internet from Jack Dongarra.
BEM Primer from Yousef Rashed.

Model/Mesh Generation and Computational Geometry

TetGen mesh generater from Hang Si. at the WIAS in Berlin
VGrid mesh generator
Generation of Surface Models from Segmented, Medical Image Data cd from the Visualization Group at the University of Magdeburg
Mesh generation software
Mesh generation primer from Jonathan Shewchuk Excellent place to start learning about mesh generation.
Robert Schneider's comprehensive mesh generation page
MIchael Float's web page with links to the Siscat software home page for representing scattered data. University of Oslo.
GRUMMP GRUMMP --- Generation and Refinement of Unstructured, Mixed-Element Meshes in Parallel. University of British Columbia.

Biomagnetics Links

SQUID AD, a company in Germany promoting MEG and MCG.
Biomagnetism Resource Site
SoftMCG a commerical MCG software. Hardware (up to 9-channel systems) also available from the same company.

Expermental Links

Fixation of tissue samples by formalin

Teaching Materials and Resources

Rob's Teaching background page for materials related to courses I teach.
Richard Felder's home page Resources in Science and Engineering Education.
Cardiology Page from Dalhousie University.
Heart Images from Bristol Biomed.
Mathworld a great math resource site from Eric Weisstein
Journal Watch Cardiology, a summary of current articles on Cardiology.
Heart Disease Resource Guide from the Pacific Online ACLS Course.
Kid's guide to the CV system (from the same ACLS site).

Miscelaneous Academic Links/Information

Suggestions for new faculty on lab budgets from NatureJobs, a business perspective for young faculty when setting up their first labs.

Miscelaneous Cool Stuff

Genomes to Life project funded by DOE.
Nobel Prize web site, including lists of all Nobel laureates.
Mathworld a great math resource site from Eric Weisstein
Utah Science Center
The Access Grid, a collaborative communications system, and a list of existing nodes
How Stuff Works a web site for the terminally curious.
Powers of ten.
Related link to the originators of the ideas in the power of 10 sequence.
Reference Desk Good place for general searches.
Math on the web
Utah Outdoors, with some links to good local hikes.
Mac TeX/LaTeX web site a complete reference to all the tools for doing LaTeX on the Mac.
PC-versions of Emacs, LaTeX, etc. for those poor souls who have to use Windoze.

Last update: Fri Jul 4 15:22:31 2003 by Rob MacLeod