SCI X, November 16th, 2016

Posters and Demos

Scientific Visualization

• Platform-Independent Genome-Wide Pattern of DNA Copy-Number Alterations Predicting Astrocytoma Survival and Response to Treatment Revealed by the GSVD Formulated as a Comparative Spectral Decomposition: Katherine A. Aiello and Orly Alter
• A Novel Tensor GSVD Predicting Ovarian Serous Cystadenocarcinoma Survival and Response to Platinum-Based Chemotherapy: Theodore E. Schomay, Katherine A. Aiello, and Orly Alter
• SVD Identifies Transcript Length Distribution Functions from DNA Microarray Data and Reveals Evolutionary Forces Globally Affecting GBM Metabolism: Nicolas M. Bertagnolli, Justin A. Drake, Jason M. Tennessen and Orly Alter
• Detecting copy-number variation using dNTP limited PCR and high-resolution melting: Luming Zhou, Robert Palais and Carl T. Wittwer
• In Situ Visualization of Particle Simulations: Will Usher, Ingo Wald, Aaron Knoll, Michael Papka, Valerio Pascucci
• Grassmannian Atlas: A General Framework for Exploring Linear Projections of High-Dimensional Data: Shusen Liu, Peer-Timo Bremer, Jayaraman J. Thiagarajan, Bei Wang, Brian Summa, and Valerio Pascucci
• PIDX: Scalable I/O for Massive Simulations: Sidharth Kumar, Steve Petruzza, Duong Hoang, Valerio Pascucci
• Brain Source Localization Pipeline: Ally Warner, Chris Johnson, Moritz Dannhauer
• OpenSpace: Charles Hansen, Gene Payne, Matthew Territo
• Parallel processing of non-human primate brain data: Steve Petruzza, Aniketh Venkat, Attila Gyulassy, Frederick Federer, Alessandra Angelucci, Peer-Timo Bremer and Valerio Pascucci
• Data Exploration for Nuclear Safety Analysis: Dan Maljovec, BeiWang, Paul Rosen, Diego Mandelli, Andrea Alfonsi, Giovanni Pastore, Cristian Rabiti, Valerio Pascucci
• Interactive Analysis of Petascale Climate Datasets: Cameron Christensen, Shusen Liu, Peer-Timo Bremer, Valerio Pascucci
• Direct Multifield Volume Ray Casting of Fiber Surfaces: Kui Wu, Aaron Knoll, Benjamin J Isaac, Hamish Carr, Valerio Pascucci
• Interactive Visualization and Exploration of Tracking Graphs for Understanding Evolution of Features: Wathsala Widanagamaachchi, Peer-Timo Bremer, Valerio Pascucci
• Interactive Topological Exploration of Particle Ensembles: Harsh Bhatia, Pavol Klacansky, Shusen Liu, Wathsala Widanagamaachchi, Attila Gyulassy, Valerio Pascucci, Peer-Timo Bremer
• ViSOAR Ag Explorer: Amy A. Gooch, Giorgio Scorzelli, Attila Gyulassy, Peer-Timo Bremer, Valerio Pascucci
• Telemedicine: ViSOAR Share: Luis Carlos Antola, Amy A. Gooch, Giorgio Scorzelli, Attila Gyulassy, Valerio Pascucci
• Data Acquisition, Management and Computation for Neuroscience: Aniketh Venkat, Frederick Federer, Steve Petruzza, Attila Gyulassy, Alessandra Angelucci and Valerio Pascucci
• Robust Feature Simplification of Vector Fields: Bei Wang, Primoz Skraba, Paul Rosen, Guoning Chen, Harsh Bhatia and Valerio Pascucci 
• Analysis and Visualization of ALMA Data Cubes: Paul Rosen, Bei Wang, Chris Johnson, Jeff Kern, Betsy Mills, Anil Seth
• Finding Hidden Shapes: Topology for Feature-Based Reasoning: Attila Gyulassy, Harsh Bhatia, Aaron Knoll, Bei Wang, Peer-Timo Bremer, Valerio Pascucci

Demos:

• FluoRender: Yong Wan
• Neuron Microscopy Data Tracing in Virtual Reality: Pavol Klacansky and Will Usher
• Intel’s OSPRay Renderer on a Displaywall: Laura Lediaev
• OpenSpace: Gene Payne, Matthew Territo

Infovis

• Visually Comparing Weather Features in Forecasts: P. Samuel Quinan and Miriah Meyer
• Visualization for Reverse Engineering the Retina: Ethan Kerzner and Miriah Meyer
• Pathfinder: Visual Analysis of Paths in Heterogeneous Graphs: Christian Partl, Samuel Gratzl, Marc Streit, Anne Mai Wasserman, Hanspeter Pfister, Dieter Schmalstieg, and Alexander Lex
• BubbleNet: A Cyber Security Dashboard: Sean McKenna, Diane Staheli, Cody Fulcher, Miriah Meyer
• Distributed Indoor Air-quality Sensing (DIAS): Jimmy Moore, Miriah Meyer
• DragonView: Toward Understanding Network Interference in Dragonfly-based Supercomputers: Yarden Livnat, Abhinav Bhatele, Nikhil Jain, Peer-Timo Bremer, Valerio Pascucci

Imaging

• Biomedical Image and Data Analysis Core - BIDAC: Josh Cates, Clement Vachet
• Connectomics Empowered By Deep Learning: Mehran Javanmardi, Mehdi Sajjadi, Tolga Tasdizen
• Magnetic Resonance Imaging Uses: Eleanor Wong and Blake Zimmerman
• MRI and CT Basis for SCI Imaging Projects: Markus Foote and Blake Zimmerman
• Motion Estimation in Medical Images: Markus Foote, Caleb Rottman, Sarang Joshi
• Generalized Data Depth and Applications: Mukund Raj, Mahsa Mirzargar, Robert M. Kirby and Ross T. Whitaker
• Quantitative Analysis of Femoral Cortical Bone Thickness using Shape Analysis: Praful Agrawal, Shireen Y. Elhabian, Penny Atkins, Ross T. Whitaker, Jeff Weiss, and Andrew E. Anderson
• Objective Severity Metric for Craniosynostosis: Riddhish Bhalodia, Ladislav Kavan, Ross Whitaker

Demos:

• ShapeWorks: Praful Agrawal
• Shape Variation Animation: Rhiddish Bhalodia

Biomedical Computing

• Virtual Neurophysiology Workbench: Alberto Fuentes, Christopher R. Butson PhD
• Patient-Specific Computational Modeling Aids Deep Brain Stimulation Therapies: Andrew Janson, Johannes Vorwerk PhD, Christopher R. Butson PhD
• Mobile Decision Support System for Nurse Management of Neuromodulation Therapy: Gordon Duffley, Jens Krueger PhD,AnikoSzabo PhD, Barbara Lutz PhD, Daniel Martinez-Ramirez MD, Michael S. OkunMD, Christopher R. ButsonPhD
• Which anatomical regions are activated by Deep Brain Stimulation as elucidated by high field diffusion weighted MRI?: Katherine G. Warthen, Dr. Chris R. Buston, Dr. Justin D. Hilliard, Dr. Kelly D. Foote
• FEBio: Finite Elements for Biomechanics: Steve A. Maas, David S. Rawlins, Gerard Ateshian, Benjamin J. Ellis, Jeffrey A. Weiss
• Effect of Focal Chondral Defects in the Hip: A Framework for Understanding Degradation and Developing Treatment Strategies: Jocelyn N. Todd, Travis G. Maak, Jeffrey A. Weiss
• Data Tools for ECGI: ECG Forward/Inverse Toolkit and EDGAR Database: Computational Electrocardiology Group
• Noninvasive Electrical Diagnosis of Cardiac Abnormalities: The Computational Electrocardiology Group
• The International Neuromodulation Registry: Butson Lab: Kara Johnson, Gordon Duffley, Andrew Janson, Daria Anderson, Katie Warthen, Shana Black, Corinne Garcia, Theresa Lins, Johannes Vorwerk, PhD, Andrea Brock MD, Christopher R. Butson, PhD. Development: Clement Vachet, Josh Cates of the Biomedical Image and Data Analysis Core (BIDAC), Wayne Bradford, David Richardson, Tom Cheatham, Anita Orendt of the Center for High Performance Computing (CHPC)
• Electrocardiographic Imaging (ECGI): Computational Electrocardiology Group
• Consortium for ECG Imaging: Advancing ECGI Through Collaboration: Computational Electrocardiology Group

Scientific Computing

• Modelling Electrochemical Devices: Chris Gritton, James Guilkey, Justin Hooper, Dmitry Bedrov, Robert M. Kirby, Martin Berzins
• Preparing Uintah for Intel Xeon Phi-based Supercomputers: John Holmen, Damodar Sahasrabudhe, Daniel Sunderland, Alan Humphrey, and Martin Berzins
• The WRF Single-Moment 6-Class Microphysics’ (WSM6) Performance Optimization: Timbwaoga Aime Judcael Ouermi (TAJO), Aaron Knoll, Robert M Kirby, Martin Berzins
• Improving Clean Coal Technologies: Martin Berzins
• Physically Constrained Ensemble Kalman Filter: Erin Linebarger, Akil Narayan, Dongbin Xiu

Demos:

• Uintah: Allen Sanderson

SCI X, November 13th, 2012

Posters and Demos

Visualization

• Visualization of Biological Data - Miriah Meyer
• Visual Analytics for Situational Awareness - Yarden Livnat
• Interactive Exploration of Large Tractography and EEG Data for Source Localization - Erik Anderson
• Uncertainty Visualization at SCI - Kristi Potter
• Visualization Approaches for Performance Analysis of Massively Parallel Applications - Paul Rosen
• BioVis Software demo - Kris Zygmunt
• CompreheNGSive, a Tool for Exploring Next-generation Sequencing Variants - Alex Bigelow
• A Story of Reanimating An Embryonic Mouse Limb - Yong Wan
• Using Depth Perception to Enhance Volume Rendering - Pascal Grosset
• ImageVis3D software - James Hughes

Simulation

• The Uintah Framework: A Unified Heterogeneous Task Scheduling and Runtime System for Energy Applications
• Uintah Framework Hybrid Task-based Parallelism Algorithm - Alan Humphrey
• Scalable Linear Solvers for the Next Generation: Applications in Oxy-coal Clean Energy Boiler Design - John Schmidt
• Mesoscale Reaction Modeling of Granular Beds of Explosives Subject to Impact - Joseph Peterson and Charles Wight, Dept. of Chemistry
• Unconventional and Renewable Energy Research Utilizing Advanced Computer Simulation
• Architecting the Finite Element Method Pipeline for the GPU - Zhisong Fu
• Army Collaborative Research Alliance (CRA): MSME :Electronic Materials by Design

Center for Extreme Data Management, Analysis and Visualization (CEDMAV)

• ViSUS: Visualization Streams for Ultimate Scalability demos - Giorgio Scorzelli
• Analysing Performance at Exascale Using Intuitive Visualizations - Aaditya Landge
• Interactive Digital Photography at Scale - Brian Summa
• A Static Load Balancing Scheme for Parallel Volume Rendering on Multi-GPU Clusters - Shusen Liu
• Visualization and Exploration of High Dimensional Data - Dan Maljovec
• Topological Analysis of Neural Circuitry - Cameron Christensen, Attila Gyulassi
• Feature-Based Analysis of Large-Scale Data using Limited Resources and Interactive Techniques for Exploration - Wathsala Widanagamaachchi, Peer-Timo Bremer
• Scalable Visualization and Processing of High Resolution Data - Sidharth Kumar, Brian Summa
• Visualizing Robustness of Critical Points for Time-Varying Vector Fields - Bei Wang
• Hybrid Parallel Computing - Sujin Philip
• Visualization of Large Scale Microscopy Data - Shusen Liu, Cameron Christensen
• Flow Analysis for Scientific Discovery - Harsh Bathia

Microscopy

• Fluorender, an Interactive Rendering Tool for Confocal Microscopy Visualization - Hideo Osuna , Dept. of Neurobiology and Anatomy
• NCR Toolset
• Light Microscopy Image Process - Nisha Ramesh, Luke Hogrebe
• Neural Circuit Reconstruction from Electron Microscopy Images - Cory Jones, Ting Liu, Mojtaba Seyedhosseini

Image Processing

• Down Syndrome: Bridging Genes, Brain and Cognition - Clement Vachet
• Automatic Geological Feature Detection in Seismic Volumes - Danny Perry
• Polynomial Regression on Riemannian Manifolds - Jacob Hinkle
• Meshing for Multimaterial Biological Volumes - Jonathan Bronson
• An Optimal Graph-cut Method for Atrial Wall Segmentation from Delayed Contrast MRI - Gopal Veni
• White Matter Maturation in Early Brain Development - Neda Sadeghi, Anuja Sharma
• Real Time Image Denoising of Fluoroscopy Images for Dose Reduction - Caleb Rottman
• Characterization of Regional Appearance Changes in Early Brain Development - Avantika Vardhan

Shape Analysis

• Quantitative Analysis of Time Series of MR Images of TBI Patients - Bo Wang
• Analysis of Longitudinal Shape Variability vis Subject-Specific Growth Modeling - James Fishbaugh
• Shape Analysis for Orthopedics - Manasi Datar
• Analysis of Human Brain Connectivity from Multi-modal Imaging - Wei Liu, Xiang Hao
• Shape Analysis in Kernel Space - Yen-Yun Yu
• Relating Brain Shape with Neurological Disorders - Prasanna Muralidharan, Nikhil Singh

Center for Integrative Biomedical Computing (CIBC)

• SCIRun, Seg3D, BioMesh3D demos - Ayla Kahn, Dan White
• ImageVis3D Demos - James Hughes
• White Matter Structure Assessment from Reduced HARDI Data using Low-Rank Polynomial Appoximations - Yaniv Gur

Cardiac and Neuro Electrophysiology

• Improving Defibrillator Use in Pediatrics using Computer Simulation
• Electrocardiographic Characterisation of Acute Myocardial Ischemia
• Tailored Atrial Fibrillation Management via Image Processing
• Precise Electrical Stimulation of the Human Brain
• Epilepsy - Identifying Epileptical Sources in the Human Brain

Genomic Signal Processing

• Global Copy-Number Alterations Predicting Glioblastoma Multiforme Survival from Comparative Modeling of Patient-Matched Tumor and Normal aCGH Profiles - Benjamin Alpert, Preethi Sankaranarayanan
• Cross-Platform Validation of a Genomic Pattern for the Prognosis and Assessment of GBM Brain Cancer - Katie Aiello
• Similarities and Differences between Normal Brain and GBM Tumor Metabolism Uncovered by SVD of Transcript Size Distributions - Nicolas Bertagnolli, Jason Tennessen
• Capacitive Model of Optically Induced Cell Stimulation May Be Incomplete - Ted Schomay

Computational Biomechanics

• Subject-Specific Computational Modeling of Normal, Dysplastic and Retroverted Hips - Corinne Henak
• FEBio: Finite Elements for Biomechanics, software demo - David Rawlins, Steve Maas, Benjamin Ellis
• AngioFE: Simulation of the Mechanical Regulation or Angiogenesis - Lowell Edgar

SCI X, November 4th, 2011

Posters and Demos

Imaging Research

• Neural Circuit Reconstruction using Electron Microscopy - Seyed Mojtaba Seyedhosseini Tarzjani
• Long Range Digital Neural Circuit Reconstruction - Luke Hogrebe
• Long Range Axon Tracing with Neurotracker - Cameron Christensen, in collaboration with Valerio Pascucci

• On Relating Brain Shape with Neurological Disorders - Prasanna Muralidharan, Nikhil Singh, in collaboration with Sarang Joshi 
• Analysis of Human Brain Connectivity from Mutli-Model Imaging - Wei Liu, Xiang Hao 
• Heritability of Facial Appearance - Yen-Yun Yu

• Continuous Trajectories from discrete Anatomical Shapes - James Fishbaugh
• Analysis of White Matter Maturation in Early Brain Development - Neda Sadeghi
• Brain Changes in Traumatic Brain Injury - Bo Wang, Marcel Prastawa
• Segmenting the Invisible: Processing of 4D Image Data - Avantika Vardhan, Sylvain Gouttard
• Brain Imaging Studies: High Throughput by Automatic Processing Pipeline - Xiaoyue Huang
• Down Syndrome: Bridging Genes, Brain and Cognition - Sylvain Gouttard

• DTI Building and Statistical Analysis - Gopalkrishna Veni
• Meshing for Multimaterial Biological Volumes -  Jonathan Bronson
• Fast Shape-based Nearest-Neighbor Search for Brain MRIs - Peihong Zhu
• Brain Population Analysis with Manifold Models - Sam Gerber
• Solving Eikonal Equations - Zhisong Fu, in collaboration with Mike Kirby
• Image Registration - Jihwan Kim

• Modeling Respiratory and Cardiac Organ Motion - Jacob Hinkle
• Real-time Image Denoising of Fluoroscopy Images for Dose Reduction - Caleb Rottman, in collaboration with Ross Whitaker

Scientific Computing

• Cardiac Position Sensitivity using Stochastic Collocation -  Darrell Swenson, in collaboration with Rob Macleod
• Interactive Visualization of High-Order Finite Element Fields using a GPU-based Ray Tracer - Blake Nelson
• A Fast Iterative Method for Solving the Eikonal Equation on Triangulated Surfaces - Zhisong Fu, James Lewis, in collaboration with Ross Whitaker
• Filtering for Visualization - Hanieh Mirzaee

• Image based Modeling Pipeline - Darrell Swenson, Dafang Wang
• Noninvasive Diagnosis and Localization of Heart Ischemia from Body-Surface Electrocardiography
• Volume conductor modeling of the human head for electroencephalography (EEG) used in epilepsy
• Myocardial Ischemia - Kedar Aras, Brett Burton
• Cardiac Arrhythmias - Greg Gardner, Josh Blauer, Jess Tate
• Epilepsy investigated non-invasively using Elecroencephalography (EEG) and Magnetoencephalography (MEG), Volume conductor modeling of the human head for electroencephalography (EEG) used in epilepsy - Moritz Dannhauer

• Uintah Software - John Schmidt, John Davison de St-Germain

• Patient-specific Modeling of Hip Dysplasia - Corinne Henak, Ben Ellis, Andy Anderson
• FEBio: Finite Elements for Biomechanics, Software Demo - Steve Maas

• Medical Prediction from Comparison of Patient-Matched Genomic Profiles - Benjamin O. Alpert
• Novel Cancer Drug Targets from Comparison of Patient-Matched Genomic Profiles - Preethi Sankaranarayanan
• A Higher-Order Decomposition for Comparison of Multiple Large-Scale Datasets - Sri Priya Pannopalli, Michael A. Saunders (Stanford University), Charles F. Van Loan (Cornell University)
• Principles of Nature form Integration and Comparison of Large-Scale Molecular Biological Data - Orly Alter

Scientific Visualization

• FluoRender: an Interactive Visualization System for 3D and 4D Confocal Microscopy data in Neurobiology Research  - Yong Wan
• Medical Prediction from Comparison of Patient-Matched Genomic Profiles - Pascal Grosset
• Massively Parallel Ray Tracing in Scientific Visualization - Carson Brownlee
• Dynamic Particle System on the GPU - Mark Kim

• Adaptive Samplng with Topological Scores - Dan Maljovec, Bei Wang, Peer-Timo Bremer
• Topology based feature extraction and tracking - Shusen Liu, Attila Guylassy,  Peer-Timo Bremer
• Vector Field Analysis - Harsh Bhatia, Josh A. Levine, Peer-Timo Bremer
• Scalable visualization and processing of high resolution data - Brian Summa, Sidharth Kumar
• Performance analysis and Visualization - Aaditya Landge, Josh Levine, Peer-Timo Bremer - Winner, SCIx Best Poster
• Hybrid computing for HPC Applications - Sujin Philip, Brian Summa

• Dynamic Particle System on the GPU - Alex Bigelow

• Uncertainty Visualization - Kristi Potter
• Vector Field Topological and Advanced Analysis - Guoning Chen
• Visualization and Analysis Tools for Assisting In Evaluating Fusion Simulations - Allen Sanderson, Scott Kruger, Stephane Ethier
• Abstract Visualization of Runtime Memory Behavior - Roni Choudhury, Paul Rosen
• Unconventional Mappings for Visual Analysis of Large Data - Paul Rosen
• Uncertainty Analysis and Visualization of Diffusion Tensor Magnetic Resonance Imaging - Fangxiang Jiao, Yaniv Gur
• Using EEG to Investigate the Visual Properties of Images - Erik Anderson
• Epinome - Yarden Livnat
• ImageVis3D - Tom Fogal
• Seg3D, SCIRun - Ayla Khan

The Software Development Center

• Asthma Tracker - Dillon Lee
• Western Innovation Network - Josh Small, Nathan Galli
• Vutara - Steve Callahan
• Millsoft3D: 3D Mining Simulation - John Schreiner