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NSF-CRI: A Hierarchical Data Storage System

March 15, 2006 - February 28, 2011

Investigators:
Charles Hansen
Steven Parker
Christopher Johnson

This project, acquiring a large-scale hierarchical storage management (HSM) system, provides access to the increasingly large datasets produced and analyzed by the members and collaborators of the Scientific Computing and Imaging (SCI) Institute at Utah. This institute creates new techniques, tools, and systems by which scientists may solve computational and imaging problems in many disciplines. The expertise utilized in addressing the problems include image and signal processing, modeling, simulation, and visualization. The work exploits the multidisciplinary mission of SCI. A large-scale HSM solution provides the ability to generate canonical datasets, accessible by researchers within SCI and many collaborators outside. The field of scientific computing is constrained by the problems posed by dataset management and storage. Dataset size and complexity has grown in parallel with available compute resource. Centralized, ready access to the modeling, simulation, and analysis data is fundamental to success. Dataset complexity grows as a product of compute resource and algorithm efficiency; while research in complex problems relies on this ever-increasing efficiency for its progress. Although computational speeds have increased dramatically, the complexity of the models produced has also increased, so that while models and simulations have improved their research effectiveness, the actual computation time needed to generate a given simulation has not declined. An advanced storage architecture helps in streamlining the workflow for a variety of data intensive research projects.


Broader Impact: The facility has a solid history of exporting its research via freely accessible datasets and software. Furthermore, SCI services many graduate and undergraduate students.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

Jeong, WK; Fletcher, PT; Tao, R; Whitaker, RT. "Interactive visualization of volumetric white matter connectivity in DT-MRI using a parallel-hardware Hamilton-Jacobi solver," IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, v.13, 2007, p. 1480. 

Adluru, G; Awate, SP; Tasdizen, T; Whitaker, RT; DiBella, EVR. "Temporally constrained reconstruction of dynamic cardiac perfusion MRI," MAGNETIC RESONANCE IN MEDICINE, v.57, 2007, p. 1027. 

Huang, X; Lee, YZ; McKeown, M; Gerig, G; Gu, H; Lin, W; Lewis, MM; Ford, S; Troster, AI; Weinberger, DR; Styner, M. "Asymmetrical ventricular enlargement in Parkinson's disease," MOVEMENT DISORDERS, v.22, 2007, p. 1657. 

Geneser, SE; Kirby, RM; Xiu, DB; Sachse, FB. "Stochastic Markovian modeling of electrophysiology of ion channels: Reconstruction of standard deviations in macroscopic currents," JOURNAL OF THEORETICAL BIOLOGY, v.245, 2007, p. 627. 

K. Damevski and K. Zhang and S. Parker. "Practical Parallel Remote Method Invocation for the Babel Compiler," Proceedings of the HPC-GECO/CompFrame'07 Workshop, 2007.

S. Gouttard and M. Styner and S. Joshi and R.G. Smith and H.C. Hazlett and G. Gerig. "Subcortical Structure Segmentation using Probabilistic Atlas Priors," Proceedings of The 10th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007), 2007.

O. Nemitz and T. Tasdizen and M. Rumpf and R.T. Whitaker. "Anisotropic Curvature Motion for Structure Enhancing Smoothing of 3D MR Angiography Data," Journal of Mathematical Imaging and Vision, v.7 (3), 2007, p. 217.

R. Palmer and M. DeLisi and G. Gopalakrishnan and R.M. Kirby. "An Approach to Formalization and Analysis of Message Passing Libraries," Proceedings of the 12th International Workshop on Formal Methods for Industrial Critical Systems (FMICS), 2007.

M. Styner and S. Xu and M. El-Sayed and G. Gerig. "Correspondence Evaluation in Local Shape Analysis and Structural Subdivision," Proceedings of ISBI 2007, 2007.

I. Wald and W.R. Mark and J. G{\'u}nther and S. Boulos and T. Ize and W. Hunt and S.G. Parker. "State of the Art of Real-Time Ray Tracing," Proceedings of Eurographics 2007, 2007.

E.W. Anderson, J. Ahrens, K. Heitmann, S. Habib, C.T. Silva. "Provenance in Comparative Analysis: A Study in Cosmology," Computing in Science and Engineering, v.10-3, 2008, p. 30.

J. Krueger, K. Potter, R. MacLeod, C.R. Johnson. "Unified Volume Format: A General System For Efficient Handling Of Large Volumetric Datasets," Proceedings of IADIS Computer Graphics and Visualization 2008 (CGV 2008, 2008.

F. Shepherd, C.R. Johnson.. "â??Hexahedral Mesh Generation for Biomedical Models in SCIRun,â??," Engineering with Computers,, v.25(1), 2009, p. 97.

M. Datar, J. Cates, P.T. Fletcher, S. Gouttard, G. Gerig, R.T. Whitaker.. "â??Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging,â??," Medical Image Computing and Computer-Assisted Intervention â?? MICCAI 2009, Lecture Notes in Computer Science LNCS,, v.5762, 2009.

T. Etiene, C.E. Scheidegger, L.G. Nonato, R. Kirby, C.T. Silva.. "Verifiable Visualization for Isosurface Extraction," IEEE Transactions on Visualization and Computer Graphics, v.15(6), 2009, p. 1227.

Henninger, HB; Maas, SA; Underwood, CJ; Whitaker, RT; Weiss, JA. "Spatial distribution and orientation of dermatan sulfate in human medial collateral ligament," JOURNAL OF STRUCTURAL BIOLOGY, v.158, 2007, p. 33. 

S. Boulos and D. Edwards and J.D. Lacewell and J. Kniss and J. Kautz and I. Wald and P. Shirley. "Packet-based Whitted and Distribution Ray Tracing," Proceedings of Graphics Interface 2007, 2007.

T.B. Terriberry and J.N. Damon and S.M. Pizer and S.C. Joshi and G. Gerig. "Population-Based Fitting of Medial Shape Models with Correspondence Optimization," Proceedings of Information Processing in Medical Imaging (IPMI '07), 2007.

H.T. Vo and S.P. Callahan and P. Lindstrom and V. Pascucci and C.T. Silva. "Streaming Simplification of Tetrahedral Meshes," IEEE Transactions on Visualization and Computer Graphics, v.13 (1), 2007, p. 145.

I. Wald. "On fast Construction of SAH based Bounding Volume Hierarchies," Proceedings of the 2007 Eurographics/IEEE Symposium on Interactive Ray Tracing, 2007.

G.-S. Li, X. Tricoche, D. Weiskopf, C.D. Hansen. "Flow Charts: Visualization of Vector Fields on Arbitrary Surfaces," IEEE Transactions on Visualization and Computer Graphics, v.14-5, 2008, p. 1.

Wald, I; Friedrich, H; Knoll, A; Hansen, CD. "Interactive isosurface ray tracing of time-varying tetrahedral volumes," IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, v.13, 2007, p. 1727. 

K. Damevski and A. Swaminathan and S. Parker. "Highly Scalable Distributed Component Framework for Scientific Computing," Proceedings of the 3rd International Conference on High Performance Computing and Communication (HPCC 2007), 2007.

M. Callahan, M.J. Cole, J.F. Shepherd, J.G. Stinstra, C.R. Johnson.. "â??A Meshing Pipeline for Biomedical Models,â??," Engineering with Computers,, v.25(1), 2009, p. 115.

T. Etiene, C.E. Scheidegger, L.G. Nonato, R. Kirby, C.T. Silva.. "â??Verifiable Visualization for Isosurface Extraction,â??," IEEE Transactions on Visualization and Computer Graphics, v.15(6), 2009, p. 1227.

Phatak, NS; Sun, Q; Kim, SE; Parker, DL; Sanders, RK; Veress, AI; Ellis, BJ; Weiss, JA. "Noninvasive determination of ligament strain with deformable image registration," ANNALS OF BIOMEDICAL ENGINEERING, v.35, 2007, p. 1175. 

Hamman, CW; Kirby, RM; Berzins, M. "Parallelization and scalability of a spectral element channel flow solver for incompressible Navier-Stokes equations," CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, v.19, 2007, p. 1403. 

Malik, M; Birnbaum, Y; MacLeod, RS; Shusterman, V. "Markers of impaired repolarization (vol 40, pg S54, 2007)," JOURNAL OF ELECTROCARDIOLOGY, v.40, 2007, p. 218. 

S. Yau, K. Damevski, D. Zorin, V. Karamcheti, S. Parker. "Result Reuse in Design Space Exploration: A Study in System Support for Interactive Parallel Computing," Proceedings of the 22nd International Parallel and Distributed Processing Symposium (IPDPS 2008),, 2008.

R.S. MacLeod, J.G. Stinstra, S. Lew, R.T. Whitaker, D.J. Swenson, M.J. Cole, J. Krueger, D.H. Brooks, C.R. Johnson.. "â??Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples,â??," Philosophical Transactions of The Royal Society A, Mathematical, Physical & Engineering Sciences,, v.367(189, 2009, p. 2293.

T. Ellkvist, D. Koop, J. Freire, C.T. Silva, L. Stromback.. "â??Using Mediation to Achieve Provenance Interoperability,â??," Proceedings of the IEEE International Workshop on Scientific Workflows,, 2009.

Younis Hijazi, Aaron Knoll, Mathias Schott, Andrew Lensler, Charles Hansen and Hans Hagen. "CSG Operations of Arbitary Primitives with Interval Arithmetic and Real-Time Ray Casting," DFU: Dagstuhl Followups: Scientific Visualization, Advanced Concepts, 2010, p. 78.

Weiss, JA. "Let us talk about it: Safe adolescent sexual decision making," JOURNAL OF THE AMERICAN ACADEMY OF NURSE PRACTITIONERS, v.19, 2007, p. 450. 

Malik, M; Birnbaum, Y; MacLeod, RS; Shusterman, V. "Markers of impaired repolarization," JOURNAL OF ELECTROCARDIOLOGY, v.40, 2007, p. S54. 

Kindlmann, G; Tricoche, X; Westin, CF. "Delineating white matter structure in diffusion tensor MRI with anisotropy creases," MEDICAL IMAGE ANALYSIS, v.11, 2007, p. 492. 

A. Ghodrati and D.H. Brooks and G. Tadmor and R.S. MacLeod. "Wavefront-Based Models for Inverse Electrocardiography," Proc. Int. Congress. on Electrocardiology, 2007.

C.B. Goodlett and P.T. Fletcher and W. Lin and G. Gerig. "Noise-Induced Bias in Low-Direction Diffusion Tensor MRI: Replication of Monte-Carlo Simulation with In-Vivo Scans," Proceedings of ISMRM 2007, 2007.

J. Daniels, T. Ochotta, L. Ha, C. Silva. "Spline-Based Feature Curves from Point-Sampled Geometry," The Visual Computer, v.24-6, 2008, p. 449.

Meyer, M; Nelson, B; Kirby, RM; Whitaker, R. "Particle systems for efficient and accurate high-order finite element visualization," IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, v.13, 2007, p. 1015. 

Newren, EP; Fogelson, AL; Guy, RD; Kirby, RM. "Unconditionally stable discretizations of the immersed boundary equations," JOURNAL OF COMPUTATIONAL PHYSICS, v.222, 2007, p. 702. 

Garth, C; Gerhardt, F; Tricoche, X; Hagen, H. "Efficient computation and visualization of coherent structures in fluid flow applications," IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, v.13, 2007, p. 1464. 

A. Knoll, I. Wald, C.D. Hansen. "Coherent Multiresolution Isosurface Ray Tracing," The Visual Computer, v.25(3), 2009, p. 209.

M. Meyer and B. Nelson and R.M. Kirby and R.T. Whitaker. "Particle Systems for Efficient and Accurate Finite Element Visualization," IEEE Transactions on Visualization and Computer Graphics, 2007, p. 1015.

D. Nain and M. Styner and M. Niethammer and J.J. Levitt and M.E. Shenton and G. Gerig and A. Bobick and A. Tannenbaum. "Statistical shape analysis of brain structures using spherical wavelets," Proceedings of ISBI 2007, 2007.

S.X. Vasquez, M.S. Hansen, A.N. Bahadur, M.F. Hockin, G.L. Kindlmann, L. Nevell, I.Q. Wu, D.J. Grunwald, D.M. Weinstein, G.M. Jones, C.R. Johnson, J.L. Vandeberg, M.R. Capecchi, C. Keller. "Optimization of Volumetric Computed Tomography for Skeletal Analysis of Model Genetic Organisms," The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology, v.291, 2008, p. 475.

T. Ize, I. Wald, S.G. Parker. "Ray Tracing with the BSP Tree," Proceedings of the IEEE Symposium on Interactive Ray Tracing, 2008, 2008.

Y. Wan, H. Otsuna, C.-B. Chien, C.D. Hansen.. "â??An Interactive Visualization Tool for Multi-Channel Confocal Microscopy Data in Neurobiology Research,â??," IEEE Transactions on Visualization and Computer Graphics,, v.15(6), 2009, p. 1489.

M. Callahan, M.J. Cole, J.F. Shepherd, J.G. Stinstra, C.R. Johnson.. "A Meshing Pipeline for Biomedical Models," Engineering with Computers,, v.25(1), 2009, p. 115.

A.N.M. Imroz Choudhury, M.D. Steffen, J.E. Guilkey, S.G. Parker. "Enhanced Understanding of Particle Simulations Through Deformation-Based Visualization," Computer Modeling in Engineering & Sciences, v.63(2), 2010, p. 117.

Luitjens, J; Berzins, M; Henderson, T. "Parallel space-filling curve generation through sorting," CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, v.19, 2007, p. 1387. 

J. Anderson, B. Jones, J. Yang, M. Shaw, C. Watt, P. Koshevoy, J. Spaltenstein, E. Jurrus, Kannan U.V., R.T. Whitaker, D. Mastronarde, T. Tasdizen, R. Marc.. "â??Ultra Structural Mapping of Neural Circuitry: A Computational Framework,â??," IEEE International Symposium on Biomedical Engineering (ISBI 2009)., 2009.

Ghodrati, A; Brooks, DH; MacLeod, RS. "Methods of solving reduced lead systems for inverse electrocardiography," IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, v.54, 2007, p. 339. 

Chisnall, D; Chen, M; Hansen, C. "Ray-driven dynamic working set rendering - For complex volume scene graphs involving large point clouds," VISUAL COMPUTER, v.23, 2007, p. 167. 

E.W. Anderson and S.P. Callahan and C.E. Scheidegger and J.M. Schriener and C.T. Silva. "Hardware-Assisted Point-Based Volume Rendering of Tetrahedral Meshes," Proceedings of SIBGRAPI 2007, 2007.

J. Cates and P.T. Fletcher and M. Styner and M. Shenton and R. Whitaker. "Shape Modeling and Analysis with Entropy-Based Particle Systems," Proceedings of Information Processing in Medical Imaging (IPMI) 2007, 2007, p. 333.

T. Ize and P. Shirley and S.G. Parker. "Grid Creation Strategies for Efficient Ray Tracing," Proceedings of the 2007 IEEE/Eurographics Symposium on Interactive Ray Tracing, 2007.

J. Daniels, C. Silva, J. Shepherd, E. Cohen. "Quadrilateral Mesh Simplification," ACM Transactions on Graphics (Proceedings of SIGGRAPH Asia 2008), 2008.

.R. Anderson, B.W. Jones, J.-H. Yang, M.V. Shaw, C.B. Watt, P. Koshevoy, J. Spaltenstein, E. Jurrus, Kannan U.V., R.T. Whitaker, D. Mastronarde, T. Tasdizen, R.E. Marc.. "A Computational Framework for Ultrastructural Mapping of Neural Circuitry," PLoS Biology, v.7(3), 2009, p. 74.

Y. Wan, H. Otsuna, C.-B. Chien, C.D. Hansen.. "An Interactive Visualization Tool for Multi-Channel Confocal Microscopy Data in Neurobiology Research," IEEE Transactions on Visualization and Computer Graphics,, v.15(6), 2009, p. 1489.

R.S. MacLeod, J.G. Stinstra, S. Lew, R.T. Whitaker, D.J. Swenson, M.J. Cole, J. Krueger, D.H. Brooks, C.R. Johnson.. "Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples," Philosophical Transactions of The Royal Society A, Mathematical, Physical & Engineering Sciences,, v.367(189, 2009, p. 2293.

C. Deitrich, C.E. Scheidegger, J. Schreiner, J. Comba, L.P. Nedel, C.T. Silva.. "Edge Transformations for Improving Mesh Quality of Marching Cubes," IEEE Transactions on Visualization and Computer Graphics,, v.15(1), 2009, p. 150.

C. Goodlett and P.T. Fletcher and W. Lin and G. Gerig. "Quantification of Measurement Error in DTI: Theoretical Predictions and Validation," Proceedings of The 10th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007), 2007.

K. Potter, J. Krueger, C.R. Johnson. "Towards the Visualization of Multi-Dimentional Stochastic Distribution Data," Proceedings of The International Conference on Computer Graphics and Visualization (IADIS) 2008, 2008.

K. Potter, J.M. Kniss, R. Riesenfeld, C.R. Johnson. "Visualizing Summary Statistics and Uncertainty," Computer Graphics Forum (Proceedings of Eurovis 2010), v.29(3), 2010, p. 823.

Lujan, TJ; Underwood, CJ; Henninger, HB; Thompson, BM; Weiss, JA. "Effect of dermatan sulfate glycosaminoglycans on the quasi-static material properties of the human medial collateral ligament," JOURNAL OF ORTHOPAEDIC RESEARCH, v.25, 2007, p. 894. 

G. Adluru and E. Hsu and E.V.R. DiBella. "Constrained Reconstruction of Sparse Cardiac MR DTI Data," Proceedings of FIMH 2007, 2007.

Yu Yang and Xiaofang Chen and Ganesh Gopalakrishnan and Robert M. Kirby. "Distributed Dynamic Partial Order Reduction Based Verification of Threaded Software," Proceedings of Model Checking Software: 14th International SPIN Workshop, 2007.

.R. Sanderson, M.D. Meyer, R.M. Kirby, C.R. Johnson. "A Framework for Exploring Numerical Solutions of Advection-Reaction-Diffusion Equations Using a GPU-Based Approach," Computing and Visualization in Science, 2008.

Aaron Knoll, Younis Hijazi, Rolf Westerteiger, Mathias Schott, Charles Hansen, Hans Hagen.. "Volume Ray Casting with Peak Finding and Differential Sampling," IEEE Transactions on Visualization and Computer Graphics,, v.15(6), 2009, p. 1571.

A.R. Sanderson, M.R. Meyer, R.M. Kirby, C.R. Johnson.. "A Framework for Exploring Numerical Solutions of Advection Reaction Diffusion Equations using a GPU Based Approach," Journal of Computing and Visualization in Science,, v.12, 2009, p. 155.

A.N.M. Imroz Choudhury, S.G. Parker.. "Ray Tracing NPR-Style Feature Lines," Proceedings of the 7th International Symposium on Non-Photorealistic Animation and Rendering (NPAR), 2009.

Thiago Ize, Carson Brownlee, Charles Hansen. "Real-Time Ray Tracer for Visualizing Massive Models on a Cluster," Eurographics Symposium on Parallel Graphics and Visualization, 2011, p. 61.

Carson Brownlee, Vincent Pegoraro, Siddharth Shankar, Patrick McCormick, Charles Hansen. "Physically-Based Interactive Schlieren Flow Visualization," IEEE Pacific Vis 2010, 2010, p. 145.

Awate, SP; Whitaker, RT. "Feature-preserving MRI denoising: A Nonparametric empirical Bayes approach," IEEE TRANSACTIONS ON MEDICAL IMAGING, v.26, 2007, p. 1242. 

Cascio, CJ; Gerig, G; Piven, J. "Diffusion tensor imaging: Application to the study of the developing brain," JOURNAL OF THE AMERICAN ACADEMY OF CHILD AND ADOLESCENT PSYCHIATRY, v.46, 2007, p. 213. 

Gribble, CP; Ize, T; Kensler, A; Wald, I; Parker, SG. "A coherent grid traversal approach to visualizing particle-based simulation data," IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, v.13, 2007, p. 758. 

Kirby, RM; Yosibash, Z; Karniadakis, GE. "Towards stable coupling methods for high-order discretization of fluid-structure interaction: Algorithms and observations," JOURNAL OF COMPUTATIONAL PHYSICS, v.223, 2007, p. 489. 

E.W. Anderson and G.A. Preston and C.T. Silva. "Towards Development of a Circuit Based Treatment for Impaired Memory: A Multidisciplinary Approach," Proceedings of IEEE EMBS Neural Engineering, 2007.

L. Bavoil and S.P. Callahan and A. Lefohn and J.L.D. Comba and C.T. Silva. "Multi-Fragment Effects on the GPU using the k-Buffer," {ACM} Symposium on Interactive {3D} Graphics and Games (i3D), 2007.

V. Pegoraro, I. Wald, S.G. Parker. "Sequential Monte Carlo Adaptation in Low-Anisotropy Participating Media," Proceedings of the 19th Eurographics Symposium on Rendering, 2008.

C. Deitrich, C.E. Scheidegger, J. Schreiner, J. Comba, L.P. Nedel, C.T. Silva.. "â??Edge Transformations for Improving Mesh Quality of Marching Cubes,â??," IEEE Transactions on Visualization and Computer Graphics,, v.15(1), 2009, p. 150.

V. Pegoraro, M. Schott, S.G. Parker. "A Closed-Form Solution to Single Scattering for General Phase Functions and Light Distributions," Computer Graphics Forum (Proceedings of the 21st Eurographics Symposium on Rendering, v.29(4), 2010, p. 1365.

Ellis, BJ; Debski, RE; Moore, SM; McMahon, PJ; Weiss, JA. "Methodology and sensitivity studies for finite element modeling of the inferior glenohumeral ligament complex," JOURNAL OF BIOMECHANICS, v.40, 2007, p. 603. 

Vasquez, SX; Kindlemann, G; Hansen, MS; Hockin, MF; Grunwald, D; Johnson, CR; Jones, GM; Cappechi, MR; Vandeberg, JL; Keller, C. "Volumetric computed tomography for skeletal analysis of model genetic organisms," BIRTH DEFECTS RESEARCH PART A-CLINICAL AND MOLECULAR TERATOLOGY, v.79, 2007, p. 421. 

G. Adluru and R.T. Whitaker and E.V.R. DiBella. "Spatio-Temporal Constrained Reconstruction of Sparse Dynamic Contrast Enhanced Radial MRI Data," Proceedings of the IEEE International Symposium on Biomedical Imaging, 2007, p. 109.

S. Pervez and G. Gopalakrishnan and R.M. Kirby and R. Palmer and R. Thakur and W. Gropp. "Practical Model Checking Method for Verifying Correctness of MPI Programs," Proceedings of EuroPVM-MPI 2007, 2007.

H.T. Vo and S.P. Callahan and N. Smith and C.T. Silva and W. Martin and D. Owen and D. Weinstein. "iRun: Interactive Rendering of Large Unstructured Grids," Proceedings of the 7th Eurographics Symposium on Parallel Graphics and Visualization (EGPGV 2007), 2007.

A. Baptista, B. Howe, J. Freire, D. Maier, C. Silva. "Scientific Exploration in the Era of Ocean Observatories," Computing in Science and Engineering, v.10-3, 2008, p. 53.

M. Schott, V. Pegoraro, C.D. Hansen, K. Boulanger, K. Bouatouch.. "A Directional Occlusion Shading Model for Interactive Direct Volume Rendering," Computer Graphics Forum, v.28(3), 2009, p. 855.

A.E. Anderson and B.J. Ellis and J.A. Weiss. "Verification, Validation and Sensitivity Studies in Computational Biomechanics," Computer Methods in Biomechanics and Biomedical Engineering, v.10, 2007, p. 171.

D.H. Brooks and A. Keely and A. Ghodrati and G. Tadmor and R.S. MacLeod. "Some Spatio-Temporal Approaches to Inverse Electrocardiography," Proc. Asilomar Conf. on Signals, Systems, and Computers, 2007.

K. Gorczowski and M. Stynera and J.Y. Jeonga and J.S. Marron and J. Piven and H.C. Hazlett and S.M. Pizer and G. Gerig. "Discrimination Analysis using Multi-Object Statistics of Shape and Pose," Proceedings of the 2007 SPIE Conference, 2007.

J. Shepherd and C.R. Johnson. "Hexahedral Mesh Generation Constraints," Journal of Engineering with Computers, 2007.

J.K. Triedman and M. Jolley and R.S. MacLeod and J. Stinstra and D.H. Brooks and S. Pieper. "Finite Element Modeling of Novel Defibrillation Approaches in Children and Adults," Proceedings of the LISSA Conference, 2007.

Bernardon, FF; Callahan, SP; Comba, JLD; Silva, CT. "An adaptive framework for visualizing unstructured grids with time-varying scalar fields," PARALLEL COMPUTING, v.33, 2007, p. 391. 

Berzins, M. "Is there still more to science than simulation?," COMPUTING IN SCIENCE & ENGINEERING, v.9, 2007, p. 98. 

L. Butler and A. Stephens. "Bullet Ray Vision," Proceedings of the IEEE Symposium on Interactive Ray Tracing, 2007.

C. Dietrich, J. Comba, L. Nedel, C. Scheidegger, C.T. Silva. "Edge Groups: A New Approach to Understanding the Mesh Quality of Marching Methods," Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2008), 2008.

Lujan, TJ; Dalton, MS; Thompson, BM; Ellis, BJ; Weiss, JA. "Effect of ACL deficiency on MCL strains and joint kinematics," JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME, v.129, 2007, p. 386. 

Ionescu, I; Guilkey, JE; Berzins, M; Kirby, RM; Weiss, JA. "Simulation of soft tissue failure using the material point method," JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME, v.128, 2006, p. 917. 

E.W. Bethel and C.R. Johnson and C. Aragon and Prabhat and O. R{\'u}bel and G. Weber and V. Pascucci and H. Childs and P.-T. Bremer. "SciDAC Visualization and Analytics Center for Enabling Technology," CTWatch Quarterly, v.3 (4), 2007.

F. Zhang and C. Goodlett and E. Hancock and G. Gerig. "Probabilistic White Matter Fiber Tracking using Particle Filtering," Proceedings of The 10th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2007), 2007.

A.R. Sanderson, M.R. Meyer, R.M. Kirby, C.R. Johnson.. "â??A Framework for Exploring Numerical Solutions of Advection Reaction Diffusion Equations using a GPU Based Approach,â??," Journal of Computing and Visualization in Science,, v.12, 2009, p. 155.

J. Anderson, B. Jones, J. Yang, M. Shaw, C. Watt, P. Koshevoy, J. Spaltenstein, E. Jurrus, Kannan U.V., R.T. Whitaker, D. Mastronarde, T. Tasdizen, R. Marc.. "Ultra Structural Mapping of Neural Circuitry: A Computational Framework," IEEE International Symposium on Biomedical Engineering (ISBI 2009)., 2009.

Scheidegger, CE; Vo, HT; Koop, D; Freire, J; Silva, CT. "Querying and creating visualizations by analogy," IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, v.13, 2007, p. 1560. 

T.J. Lujan and C.J. Underwood and H.B. Henninger and B.M. Thompson and J.A. Weiss. "Effect of Dermatan Sulfate Glycosaminoglycans on the Quasi-Static Material Properties of the Human Medial Collateral Ligament," Journal of Orthopaedic Research, v.25 (7), 2007, p. 894.

R. Palmer and G. Gopalakrishnan and R.M. Kirby. "Semantics Driven Dynamic Partial-Order Reduction of MPI-based Parallel Programs," Proceedings of Parallel and Distributed Systems: Testing and Debugging (PADTAD), 2007.

L. Bavoil, S. Callahan, and C. Silva. "Robust Soft Shadow Mapping with Depth Peeling," Journal of Graphics Tools, v.13-1, 2008, p. 19.

.R. Anderson, B.W. Jones, J.-H. Yang, M.V. Shaw, C.B. Watt, P. Koshevoy, J. Spaltenstein, E. Jurrus, Kannan U.V., R.T. Whitaker, D. Mastronarde, T. Tasdizen, R.E. Marc.. "â??A Computational Framework for Ultrastructural Mapping of Neural Circuitry,â??," PLoS Biology, v.7(3), 2009, p. 74.

T.J. Badger, R.S. Oakes, M. Daccarett, N.S. Burgon, N. Akoum, E.N. Fish, J.J. Blauer, S.N. Rao, Y. Adjei-Poku, E.G. Kholmovski, S. Vijayakumar, E.V. Di Bella, R.S. MacLeod, N.F. Marrouche.. "â??Temporal Left Atrial Lesion Formation After Ablation of Atrial Fibrillation,â??," Heart Rhythm,, 2009.

M. Schott, V. Pegoraro, C.D. Hansen, K. Boulanger, K. Bouatouch.. "â??A Directional Occlusion Shading Model for Interactive Direct Volume Rendering,â??," Computer Graphics Forum, v.28(3), 2009, p. 855.

Gilmore, JH; Lin, W; Corouge, I; Vetsa, YSK; Smith, JK; Kang, C; Gu, H; Hamer, RM; Lieberman, JA; Gerig, G. "Early postnatal development of corpus callosurn and corticospinal white matter assessed with quantitative tractography," AMERICAN JOURNAL OF NEURORADIOLOGY, v.28, 2007, p. 1789. 

Gilmore, JH; Lin, W; Prastawa, MW; Looney, CB; Vetsa, YSK; Knickmeyer, RC; Evans, DD; Smith, JK; Hamer, RM; Lieberman, JA; Gerig, G. "Regional gray matter growth, sexual dimorphism, and cerebral asymmetry in the neonatal brain," JOURNAL OF NEUROSCIENCE, v.27, 2007, p. 1255. 

Yilmaz, B; MacLeod, RS. "Generalized training subset selection for statistical estimation of epicardial activation maps from intravenous catheter measurements," COMPUTERS IN BIOLOGY AND MEDICINE, v.37, 2007, p. 328. 

K. Gorczowski and M. Styner and J.Y. Jeong and J.S. Marron and J. Piven and H.C. Hazlett and S.M. Pizer and G. Gerig. "Statistical Shape Analysis of Multi-Object Complexes," Proceedings of the 2007 IEEE Conference on Computer Vision and Pattern Recognition, 2007.

S. Klasky, M. Vouk, M. Parashar, A. Khan, N. Podhorszki, R. Barreto, D. Silver, S.G. Parker. "Collaborative Visualization Spaces for Petascale Simulations," Proceedings of 2008 International Symposium on Collaborative Technologies and Systems (CTS 2008),, 2008.

T. Ellkvist, D. Koop, J. Freire, C.T. Silva, L. Stromback.. "Using Mediation to Achieve Provenance Interoperability," Proceedings of the IEEE International Workshop on Scientific Workflows,, 2009.

Yong Wan, Charles Hansen. "Fast Volumetric Data Exploration with Importance-Based Accumulated Transparency Modulation," IEEE/EG Symposium on Volume Graphics 2010, 2010, p. 61.

Kindlmann, G; Ennis, DB; Whitaker, RT; Westin, CF. "Diffusion tensor analysis with invariant gradients and rotation tangents," IEEE TRANSACTIONS ON MEDICAL IMAGING, v.26, 2007, p. 1483. 

Ateshian, GA; Ellis, BJ; Weiss, JA. "Equivalence between short-time biphasic and incompressible elastic material responses," JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME, v.129, 2007, p. 405. 

Wald, I; Boulos, S; Shirley, P. "Ray tracing deformable scenes using dynamic bounding volume hierarchies," ACM TRANSACTIONS ON GRAPHICS, v.26, 2007. 

T. Ize and I. Wald and S.G. Parker. "Asynchronous BVH Construction for Ray Tracing Dynamic Scenes on Parallel Multi-Core Architectures," Proceedings of the 2007 Eurographics Symposium on Parallel Graphics and Visualization, 2007.

C.T. Silva and J. Freire and S.P. Callahan. "Provenance for Visualizations: Reproducibility and Beyond," IEEE Computing in Science and Engineering, 2007.

H.G. Martinez, S.I. Prajapati, C.A. Estrada, F. Jimenez, M.P. Quinones, I. Wu, A. Bahadur, A. Sanderson, C.R. Johnson, M. Shim, C. Keller, S.S. Ahuja.. "â??Images in Cardiovascular Medicine: Microscopic Computed Tomography Based Virtual Histology for Visualization and Morphometry of Atherosclerosis in Diabetic Apolipoprotein E Mutant Mice,â??," Circulation: Journal of the American Heart Association,, v.120(9), 2009, p. 821.

H.G. Martinez, S.I. Prajapati, C.A. Estrada, F. Jimenez, M.P. Quinones, I. Wu, A. Bahadur, A. Sanderson, C.R. Johnson, M. Shim, C. Keller, S.S. Ahuja.. "Images in Cardiovascular Medicine: Microscopic Computed Tomography Based Virtual Histology for Visualization and Morphometry of Atherosclerosis in Diabetic Apolipoprotein E Mutant Mice," Circulation: Journal of the American Heart Association,, v.120(9), 2009, p. 821.

G.A. Ateshian and B.J. Ellis and J.A. Weiss. "Equivalence Between Short-Time Biphasic and Incompressible Elastic Material Response," Journal of Biomechanical Engineering, v.129 (3), 2007, p. 205.

C.W. Hamman and R.M. Kirby and M. Berzins. "Parallelization and Scalability of a Spectral Element Channel Flow Solver for Incompressible Navier-Stokes Equations," Concurrency and Computation: Practice and Experience, v.14 (10), 2007, p. 1403.

B.W. Jones and R.E. Marc and C.B. Watt and K. Kinardi and D. DeMill and J.H. Yang and T. Tasdizen and P. Koshevoy and E. Jurrus and R.T. Whitaker. "Structure and Function of Microneuromas in Retinal Remodeling," The Association for Research in Vision and Ophthalmology (ARVO) Conference, 2007.

M. Styner and I. Oguz and S. Xu and D. Pantazis and G. Gerig. "Statistical Group Differences in Anatomical Shape Analysis using Hotelling T2 Metric," Proceedings of the 2007 SPIE Medical Imaging Conference, 2007.

S.P. Callahan, J.H. Callahan, C.E. Scheidegger, C. Silva. "Volume Rendering: A 3D Plotting Technique for Scientific Data," Computing in Science and Engineering, v.10-1, 2008, p. 88.

Aaron Knoll, Sebastian Thelen, Michael Papka, Ingo Wald, Hans Hagen, Charles Hansen. "Full-Resolution Interactive CPU Volume Rendering with Coherent BVH Traversal," IEEE Pacific Vis 2011, 2011, p. 3.

Parker, SG; Guilkey, J; Harman, T. "A component-based parallel infrastructure for the simulation of fluid-structure interaction," ENGINEERING WITH COMPUTERS, v.22, 2006, p. 277. 

C.P. Gribble and S.G. Parker. "Interactive Visualization with Advanced Shading Models using Lazy Evaluation," Proceedings of the 2007 Eurographics Symposium on Parallel Graphics and Visualization, 2007, p. 37.

B. Davis, P.T. Fletcher, E. Bullitt, S. Joshi. "Population Shape Regression from Random Design Data," International Journal of Computer Vision, 2008.

Aaron Knoll, Younis Hijazi, Rolf Westerteiger, Mathias Schott, Charles Hansen, Hans Hagen.. "â??Volume Ray Casting with Peak Finding and Differential Sampling,â??," IEEE Transactions on Visualization and Computer Graphics,, v.15(6), 2009, p. 1571.

A.N.M. Imroz Choudhury, S.G. Parker.. "â??Ray Tracing NPR-Style Feature Lines,â??," Proceedings of the 7th International Symposium on Non-Photorealistic Animation and Rendering (NPAR), 2009.

F. Shepherd, C.R. Johnson.. "Hexahedral Mesh Generation for Biomedical Models in SCIRun," Engineering with Computers,, v.25(1), 2009, p. 97.

M. Datar, J. Cates, P.T. Fletcher, S. Gouttard, G. Gerig, R.T. Whitaker.. "Particle Based Shape Regression of Open Surfaces with Applications to Developmental Neuroimaging," Medical Image Computing and Computer-Assisted Intervention â?? MICCAI 2009, Lecture Notes in Computer Science LNCS,, v.5762, 2009.

G.-S. Li, X. Tricoche, C.D. Hansen. "Physically-based Dye Advection for Flow Visualization," Computer Graphics Forum Journal, v.27-3, 2008.

T. Ellkvist, L. Stromback, L. Lins, J. Freire.. "A First Study on Strategies for Generating Workflow Snippets," Proceedings of the ACM SIGMOD Intenational Workshop on Keyword Search on Structured Data (KEYS),, 2009.

T. Ize, C.D. Hansen. "RTSAH Traversal Order for Occlusion Rays," Computer Graphics Forum (Proceedings of Eurographics 2011), v.30(2), 2011, p. 297.

Meyer, M; Kirby, RM; Whitaker, R. "Topology, accuracy, and quality of isosurface meshes using dynamic particles," IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, v.13, 2007, p. 1704. 

E.W. Bethel and C.R. Johnson and K. Joy and S. Ahern and V. Pascucci and H. Childs and J. Cohen and M. Duchaineau and B. Hamann and C. Hansen and D. Laney and P. Lindstrom and J. Meredith and G. Ostrouchov and S.G. Parker and C.T. Silva and A. Sanderson a. "SciDAC Visualization and Analytics Center for Enabling Technology," Journal of Physics, 2007.

T. Ellkvist, L. Stromback, L. Lins, J. Freire.. "â??A First Study on Strategies for Generating Workflow Snippets,â??," Proceedings of the ACM SIGMOD Intenational Workshop on Keyword Search on Structured Data (KEYS),, 2009.

T.J. Badger, R.S. Oakes, M. Daccarett, N.S. Burgon, N. Akoum, E.N. Fish, J.J. Blauer, S.N. Rao, Y. Adjei-Poku, E.G. Kholmovski, S. Vijayakumar, E.V. Di Bella, R.S. MacLeod, N.F. Marrouche.. "Temporal Left Atrial Lesion Formation After Ablation of Atrial Fibrillation," Heart Rhythm,, 2009.

Silva, CT; Freire, J; Callahan, SP. "Provenance for visualizations - Reproducibility and beyond," COMPUTING IN SCIENCE & ENGINEERING, v.9, 2007, p. 82. 

Goodyer, CE; Berzins, M. "Parallelization and scalability issues of a multilevel ellastohydrodynamic lubrication solver," CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, v.19, 2007, p. 369. 

Wiebel, A; Tricoche, X; Schneider, D; Jaenicke, H; Scheuermann, G. "Generalized streak lines: Analysis and visualization of boundary induced vortices," IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, v.13, 2007, p. 1735. 

J.H. Gilmore and L. Smith and C. Kang and R. Hamer and H. Wolfe and B. Hertzberg and J.K. Smith and N. Chescheir and W. Lin and G. Gerig. "Neonatal Brain Structure in Children with Prenatal Isolated Mild Ventriculomegaly," Proceedings American Conference of Neuropharmacology (ACNP) 2007, 2007.

.N.M. Imroz Choudhury, K.C. Potter, S.G. Parker. "Interactive Visualization for Memory Reference Traces," Proceedings of EuroVis 2008, 2008.

V. Pegoraro, C. Brownlee, P.S. Shirley, S.G. Parker. "Towards Interactive Global Illumination Effects via Sequential Monte Carlo Adaptation," Proceedings of the 3rd IEEE Symposium on Interactive Ray Tracing, 2008.

D.F. Wang, R.M. Kirby, C.R. Johnson. "Resolution Strategies for the Finite-Element-Based Solution of the ECG Inverse Problem," IEEE Transactions on Biomedical Engineering, v.57(2), 2010, p. 220.


BOOKS/ONE TIME PROCEEDING

S.G. Parker and K. Damevski and A. Khan and A. Swaminathan and C.R. Johnson. "The SCIJump Framework for Parallel and Distributed Scientific Computing", 03/01/2007-02/28/2008, , Parashar, M., X. Li, and S. Chandra"Advanced Computational Infrastructures for Parallel/Distributed Adaptive Applications",  2007, "Wiley Publishing".

A. Wiebel and X. Tricoche and G. Scheuerman. "Extraction of Separation Surfaces Using Topological Structures in Flow Cross Sections", 03/01/2007-02/28/2008, "Topology-based Methods in Visualization, Mathematics and Visualization",  2007, "Springer Verlag".

S.G. Parker and K. Damevski and A. Khan and A. Swaminathan and C.R. Johnson. "The SCIJump Framework for Parallel and Distributed Scientific Computing", 03/01/2008-02/28/2009, , Parashar, M., X. Li, and S. Chandra"Advanced Computational Infrastructures for Parallel/Distributed Adaptive Applications",  2007, "Wiley Publishing".

A. Wiebel and X. Tricoche and G. Scheuerman. "Extraction of Separation Surfaces Using Topological Structures in Flow Cross Sections", 03/01/2008-02/28/2009, "Topology-based Methods in Visualization, Mathematics and Visualization",  2007, "Springer Verlag".

M. Callahan, M.J. Cole, J.F. Shepherd, J.G. Stinstra, C.R. Johnson. "A Meshing Pipeline for Biomedical Computing,?", 03/01/2008-02/28/2009,  2008, "Engineering with Computers, Note: DOI:10.1007/s00366-008-0106-1, SpringerLink, pp. (published online). 2008.".

Y. Livnat, S.G. Parker, C.R. Johnson. "Fast Isosurface Extraction Methods for Large Image Data Sets", 03/01/2008-02/28/2009, , Isaac N. Bankman 2008, "Handbook of Medical Image Processing and Analysis, 2nd edition, Ch. 47, Note: (to appear), Edited by Isaac N. Bankman, Elsevier, pp. 801--816. 2008.".

X. Tricoche, R. MacLeod, C.R. Johnson. "Visual Analysis of Bioelectric Fields", 03/01/2008-02/28/2009,  2008, "Visualization in Medicine and Life Sciences, Mathematics and Visualization, Springer-Verlag, pp. 205--220. 2008.".

S.G. Parker and K. Damevski and A. Khan and A. Swaminathan and C.R. Johnson. "The SCIJump Framework for Parallel and Distributed Scientific Computing", 03/01/2009-02/28/2010, , Parashar, M., X. Li, and S. Chandra"Advanced Computational Infrastructures for Parallel/Distributed Adaptive Applications",  2007, "Wiley Publishing".

A. Wiebel and X. Tricoche and G. Scheuerman. "Extraction of Separation Surfaces Using Topological Structures in Flow Cross Sections", 03/01/2009-02/28/2010, "Topology-based Methods in Visualization, Mathematics and Visualization",  2007, "Springer Verlag".

M. Callahan, M.J. Cole, J.F. Shepherd, J.G. Stinstra, C.R. Johnson. "A Meshing Pipeline for Biomedical Computing,?", 03/01/2009-02/28/2010,  2008, "Engineering with Computers, Note: DOI:10.1007/s00366-008-0106-1, SpringerLink, pp. (published online). 2008.".

Y. Livnat, S.G. Parker, C.R. Johnson. "Fast Isosurface Extraction Methods for Large Image Data Sets", 03/01/2009-02/28/2010, , Isaac N. Bankman 2008, "Handbook of Medical Image Processing and Analysis, 2nd edition, Ch. 47, Note: (to appear), Edited by Isaac N. Bankman, Elsevier, pp. 801--816. 2008.".

X. Tricoche, R. MacLeod, C.R. Johnson. "Visual Analysis of Bioelectric Fields", 03/01/2009-02/28/2010,  2008, "Visualization in Medicine and Life Sciences, Mathematics and Visualization, Springer-Verlag, pp. 205--220. 2008.".

C.D. Hansen, C.R. Johnson, V. Pascucci, C.T. Silva.. "?Visualization for Data-Intensive Science,?", 03/01/2009-02/28/2010, , Edited by Dan Fay, Kristin Tolle and Tony Hey,"The Fourth Paradigm of Scientific Discovery",  2009, "The Fourth Paradigm: Data-Intensive Scientific Discovery, Microsoft Research,
Edited by Tony Hey, Stewart Tansley, and Kristin Tolle, ISBN: 978-0-9825442-0-4, pages 153-164,
2009".

S.G. Parker and K. Damevski and A. Khan and A. Swaminathan and C.R. Johnson. "The SCIJump Framework for Parallel and Distributed Scientific Computing", 03/01/2010-02/28/2011, , Parashar, M., X. Li, and S. Chandra"Advanced Computational Infrastructures for Parallel/Distributed Adaptive Applications",  2007, "Wiley Publishing".

A. Wiebel and X. Tricoche and G. Scheuerman. "Extraction of Separation Surfaces Using Topological Structures in Flow Cross Sections", 03/01/2010-02/28/2011, "Topology-based Methods in Visualization, Mathematics and Visualization",  2007, "Springer Verlag".

M. Callahan, M.J. Cole, J.F. Shepherd, J.G. Stinstra, C.R. Johnson. "A Meshing Pipeline for Biomedical Computing,?", 03/01/2010-02/28/2011,  2008, "Engineering with Computers, Note: DOI:10.1007/s00366-008-0106-1, SpringerLink, pp. (published online). 2008.".

Y. Livnat, S.G. Parker, C.R. Johnson. "Fast Isosurface Extraction Methods for Large Image Data Sets", 03/01/2010-02/28/2011, , Isaac N. Bankman 2008, "Handbook of Medical Image Processing and Analysis, 2nd edition, Ch. 47, Note: (to appear), Edited by Isaac N. Bankman, Elsevier, pp. 801--816. 2008.".

X. Tricoche, R. MacLeod, C.R. Johnson. "Visual Analysis of Bioelectric Fields", 03/01/2010-02/28/2011,  2008, "Visualization in Medicine and Life Sciences, Mathematics and Visualization, Springer-Verlag, pp. 205--220. 2008.".

C.D. Hansen, C.R. Johnson, V. Pascucci, C.T. Silva.. "?Visualization for Data-Intensive Science,?", 03/01/2010-02/28/2011, , Edited by Dan Fay, Kristin Tolle and Tony Hey,"The Fourth Paradigm of Scientific Discovery",  2009, "The Fourth Paradigm: Data-Intensive Scientific Discovery, Microsoft Research,
Edited by Tony Hey, Stewart Tansley, and Kristin Tolle, ISBN: 978-0-9825442-0-4, pages 153-164, 2009".