Rob's Links to Research Groups/Resources

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

Bioelectric Field Electrophysiology and Simulation Research

• The Utah NCRR web page
• University of Auckland Group, host of the CellML project and a Physiome site.
• University of Alabama Cardiac Electrophysiology Group
• Dana Brooks and his group at Northeastern University (and my main collaborator).
• Cardiac Bioelectricity Research and Training Center at Case Western Reserve University.
• Cell Electrophysiology Simulation Environment (CESE) by Sergey Missan at Dalhousie University.
• Cellular Open Resource (COR) from Oxford Univeristy.
• Duke Computational Electrophysiology Group, Duke University.
• Oxford University Computing Lab and the Chaste software.
• Computational Cardiac Electrophysiology Group at Tulane University
• Cardiac Mechanics Research Group Andrew McCulloch at UCSD.
• Cardiac mechanics from University of Iowa Radiology.
• University of Aucklands Cardiac Mechanics Group
• DynAmo project Tampere University, Finnland.
• Center for Cardiovascular Bioinformatics and Modeling at Johns Hopkins University.
• LabHeart from Don Bers at Loyola University.
• The Lausanne Heart Group headed by Adriaan van Oosterom.
• Department of Medical Physics and Biophysics at the University of Graz.
• Institute for Medical Signal Processing and Imaging at the University fo Health Informatics and Technology Tyrol, Autria.
• Olaf Doessel Group at the University of Karslruhe.
• 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
• Simulating the electrical activity of the heart at the University of Oslo, Norway.
• 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.

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

• International Society of Electrocardiology
• The International Society for Computerized Electrocardiology
• International Society for Bioelectromagnetism
• Cardiac Electrophysiology Society
• American Heart Association
• International Society for Heart Research
• European Society of Cardiology
• North American Society for Pacing and Electrophysiology
• British Cardiac Society

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.
• Brainstorm from the USC NeuroImaging Research Group.
• Brain Voyager
• 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.
• Ecgsim from the University of Nijmegen (Van Oosterom and Oostendorp).
• 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.
• Netsolve at University of Tennessee's Innovative Computing Laboratory.
• The AIR package for automated image registration.
  
• 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

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.

BimdMedical 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
• 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.

Mesh Generation and Computational Geometry

• TetGen mesh generater from Hang Si. at the WIAS in Berlin
• VGrid mesh generator
• 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

• 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.

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.