Utah P41 Renewal Site Visit 2015
Introduction
Schedule
Start End
Dur
Topic
8:00
8:15 15 Shuttle to Campus
8:15
8:30 15 Continental Breakfast
8:30
8:40 10 Motivation and Goals of the Center
8:40
8:50 10 Comments and Feedback
8:50
9:00 10 Image Processing and Geometric Analysis
9:00
9:10 10 Comments and Feedback
9:10
9:20 10 Visualization
9:20
9:30 10 Comments and Feedback
9:30
9:40 10 Simulation and Estimation
9:40
9:50 10 Comments and Feedback
9:50 10:00 10 Collaboration and Service
10:00 10:10 10 Comments and Feedback
10:10 10:25 15 Break
10:25 10:35 10 Infrastructure
10:35 10:45 10 Comments and Feedback
10:45 10:55 10 Training, Dissemination, and Administration
10:55 11:05 10 Comments and Feedback
11:05 12:05 60 Posters and Demos
12:05 13:05 60 Lunch
13:05 13:10
5 DBP Intro
13:10 13:20 10 Comments and Feedback
13:20 13:30 10 DBP Example: Microscopy
13:30 13:40 10 DBP Example: Cardiac Arrhythmias
13:40 13:50 10 DBP Example: Biomechanics and Blood Flow
13:50 14:00 10 DBP Example: Neural Modulation
14:00 14:20 20 Comments and Feedback
14:20 15:00 40 Exec Meeting
15:00 16:00 60 Discussion with PIs
17:30
19:30 120 Optional Pub DInner
Introduction
Presenter(s)
EAB Members
EAB Members
Chris J
EAB Members
Ross
EAB Members
Chris J (Chuck Hansen)
EAB Members
Dana (Rob and Chris Butson)
EAB Members
Rob
EAB Members
All
Liz
EAB Members
Greg
EAB Members
All
Rob
EAB Members
Liz/Rob for Rai Winslow, PhD
Rob for Nassir Marrouche, MD
Ross for Jeff Weiss, PhD
Chris B for Kelly Foote, MD
EAB Members
EAB Members
All
Center Strategy
Introduction
Center History
Introduction
Center for Bioelectric Field Modeling, Simulation
and Visualization established in 1999.
Renewed as the Center for Integrative Biomedical
Computing (CIBC) established in October 2005.
Submitted Renewal in September 2009 (end date
is July 31, 2010)
Renewed until July 31, 2015
Center Moves to NIGMS in 2012
New Program Officer – Fred Friedman
Center Renewal Proposal – September 25, 2014
Center Renewal Site Visit – February 18, 2015
Center Impact
Introduction
NIH/NCRR Center
Awarded for 3 years.
Sept, 1999
NIH/NCRR Center
Renewal for 3 years.
Sept, 2002
46 Publications
First Workshop
map3d v3.0 - 6.2
BioPSE/SCIRun v1.0.0 - v1.6.0
NIH/NCRR CIBC
Renewal for 5 years
Feb. 2005
49 Publications
Second Workshop
map3d v6.4 - 6.5
BioPSE/SCIRun v1.20.0
First release:
BioFEM
BioTensor
BioImage
NIH/NCRR CIBC
Renewal for 5 years,
July 2010
159 Publications
5 Workshops
BioPSE/SCIRun v1.20.0 - v4.2
BioFEM
BioTensor
BioImage
New BioMesh3D
map3d v6.4 - 6.5
ImageVis3D v1.0
Seg3D v1.12
ShapeWorks
2015
132 Publications
13 Workshops
NIH/BTR Portal
BioPSE/SCIRun v4.2 - v4.7
SCIRun v5.0 alpha
BioMesh3D
BioMesh3D Client v1.0
BrainStimulator
Forward/Inverse Toolkit
map3d v7.1
ImageVis3D v2.0.1 - v3.1
Seg3D v2.15
ShapeWorks v0.3.0 - v1.2
Cleaver v2.0
Research Impact
Introduction
Software – Downloads >165,000
Total&downloads
Downloads&in&2014
44,531&(since&2004)
3,372
44,436&(since&2007)
5,724
27,077&(since&2008)
4,981
Mobile&(App&Store)&&40,795&
(since&2009)
7,040
7,799
790
3,625&(since&2009)
475&(w/o&NITRC&dowloads)
Introduction
Software Wikipedia Pages
Introduction
Software Videos
Introduction
http://vimeo.com/85177018
CIBC Software Development
Introduction
Training Impact: Since 2005
Postdoctoral Fellows:
Introduction
• Jeroen Sinstra—Research Staff Scientist, Numira Biosciences, Inc.
• Xavier Tricoche—Associate Professor, Computer Science, Purdue University
• Jens Krueger—Professor of Computing Science, University of Duisberg
• Josh Levine—Assistant Professor of Computing Science, Clemson University
• Erik Anderson—Research Scientist, EGI
Graduate Students—Ph.D.:
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Seok Lew—Massachusetts General Hospital, Dept. of Radiology
Fangxiang Jiao – TGS
Burak Erem – Postdoc, Boston Children’s Hospital
Suyash Awaite - Assistant Professor in the Department of Computer Science and Engineering at the
Indian Institute of Technology, Bombay.
Dafang Wang – Post Doctoral Fellow, Johns Hopkins University
Sarah Geneser—Post Doctoral Fellow, Stanford University
Alireza Ghodrati—Biomedian LLC
Saeed Babaeizadeh—Phillips Medical
Miriah Meyer—Post Doctoral Fellow, Harvard University, Assistant Professor of Computer Science and
SCI Institute
Jason Shepherd—Sandia National Laboratory
Chris Butson—Associate Professor, University of Utah
Sila Kurugol - Postdoc at BWH
Josh Cates—Research Staff CARMA
Darrell Swenson – L3
Training Impact (Cont.)
Introduction
Graduate Students—M.S.:
•
•
•
•
•
•
Anastasia Mironova—Conoco Phillips
Lee Roy Myers—Instructor, Eastern Wyoming College
P.J. Hawkes—Medical School, University of Utah
J.R. Blackham—Apple Computer
Andrew Keely—Nuance Communications
Jaume Coll Font – Ph.D. student at NEU (CIBC Supported)
Undergraduate Students:
• McKay Davis—Makai Ocean Engineering, Waimanalo, Hawaii
• Zachary Warnock—Medical School, University of Utah
• Lindsey Healy—Graduate Student, Bioengineering, Univ. of Utah
• Patrick Rasch
• Anatoliy Zharkikh
• Cory Shirts
Summary of Center Impact Assessment
Introduction
- Technology development/algorithms
• Papers published
• Citations to papers
- Software/dissemination
• New software products
• Software releases
• Downloads and citations/acknowledgements
- Scientific Impact
• Scientific results from DBPs (enabled by TRD)
• Training- Graduate students/fellows- Tutorials and workshops
- Mechanisms
- Weekly CIBC Executive Meetings
- Weekly Software Design and Evaluation Meetings
- Annual External Advisory Board Meetings
Center Vision
Introduction
Center Vision
Introduction
Center Vision
Introduction
Biomedical Research Clusters
Introduction
Driving Biological Partners
Introduction
Microscopy and Small Scale Imaging: Rai
Winslow, PhD, John’s Hopkins University,
Microscopy and Small Scale Imaging: Gabrielle
Kardon, PhD, University of Utah,
Biomechanics and Blood Flow: Alison Marsden,
PhD, University of California, San Diego,
Biomechanics and Blood Flow: Jeffrey Weiss
PhD, Andrew Anderson PhD, University of
Utah, Statistical and Biomechanical Analysis of
Hip Dysplasia
Driving Biological Partners
Introduction
Neuromodulation and Brain Source
Localization, Don Tucker, PhD, University of
Oregon and EGI
Neuromodulation and Brain Source Localization,
Michael Okun, MD and Kelly Foote, MD,
University of Florida
Cardiac Arrhythmias and Ischemia: Natalia
Trayanova, PhD, John’s Hopkins University,
Simulation of Cardiac Defibrillation
Cardiac Arrhythmias and Ischemia: Nassir
Marrouche MD, University of Utah, Imagebased Management of Atrial Fibrillation
Center Impact
Introduction
SINCE OUR LAST RENEWAL IN 2009:
NIH/NIGMS CIBC
Renewal, 2009
Software Impact
• Over 15,000 downloads of SCIRun, (all from outside the Center and our affiliate institutions)
• Over 15,000 downloads of Seg3D,
• Over 7000 downloads of the CIBC data sets.
• Over 23,800 downloads of ImageVis3D and ImageVis3D Mobile.
(Average 250% increase in software downloads)
Publication Impact
• Over 300 papers published by scientists outside the Center referencing CIBC software (33% increase)
• Center members have authored over 140 publications related to biomedical computing in a wide range of technical
and biomedical journals and conference proceedings.
2015
Schedule
Start End
Dur
Topic
8:00
8:15 15 Shuttle to Campus
8:15
8:30 15 Continental Breakfast
8:30
8:40 10 Motivation and Goals of the Center
8:40
8:50 10 Comments and Feedback
8:50
9:00 10 Image Processing and Geometric Analysis
9:00
9:10 10 Comments and Feedback
9:10
9:20 10 Visualization
9:20
9:30 10 Comments and Feedback
9:30
9:40 10 Simulation and Estimation
9:40
9:50 10 Comments and Feedback
9:50 10:00 10 Collaboration and Service
10:00 10:10 10 Comments and Feedback
10:10 10:25 15 Break
10:25 10:35 10 Infrastructure
10:35 10:45 10 Comments and Feedback
10:45 10:55 10 Training, Dissemination, and Administration
10:55 11:05 10 Comments and Feedback
11:05 12:05 60 Posters and Demos
12:05 13:05 60 Lunch
13:05 13:10
5 DBP Intro
13:10 13:20 10 Comments and Feedback
13:20 13:30 10 DBP Example: Microscopy
13:30 13:40 10 DBP Example: Cardiac Arrhythmias
13:40 13:50 10 DBP Example: Biomechanics and Blood Flow
13:50 14:00 10 DBP Example: Neural Modulation
14:00 14:20 20 Comments and Feedback
14:20 15:00 40 Exec Meeting
15:00 16:00 60 Discussion with PIs
17:30
19:30 120 Optional Pub DInner
Introduction
Presenter(s)
EAB Members
EAB Members
Chris J
EAB Members
Ross
EAB Members
Chris J (Chuck Hansen)
EAB Members
Dana (Rob and Chris Butson)
EAB Members
Rob
EAB Members
All
Liz
EAB Members
Greg
EAB Members
All
Rob
EAB Members
Liz/Rob for Rai Winslow, PhD
Rob for Nassir Marrouche, MD
Ross for Jeff Weiss, PhD
Chris B for Kelly Foote, MD
EAB Members
EAB Members
All