Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

SCI Publications

2007


 D. Reed, C.R. Johnson. “CRA-NIH Computing Research Challenges in Biomedicine Workshop Recommendations,” Note: Computing Research Association (CRA), 2007.


J. Van Rij, T. Harman, T. Ameel. “The effect of creep flow on two-dimensional isoflux microchannels,” In International Journal of Thermal Sciences, Vol. 46, No. 11, pp. 1095--1103. November, 2007.
DOI: 10.1016/j.ijthermalsci.2007.04.007

ABSTRACT

Microchannel convective heat transfer and friction loss characteristics are numerically evaluated for gaseous, two-dimensional, steady state, laminar, constant wall heat flux flows. The effects of Knudsen number, accommodation coefficients, second-order slip boundary conditions, creep flow, and hydrodynamically/thermally developing flow are considered. These effects are compared through the Poiseuille number and the Nusselt number. Numerical values for the Poiseuille and Nusselt numbers are obtained using a continuum based three-dimensional, unsteady, compressible computational fluid dynamics algorithm that has been modified with slip boundary conditions. To verify the numerical results, analytic solutions of the hydrodynamically and thermally fully developed momentum and energy equations have been derived subject to both first- and second-order slip velocity and temperature jump boundary conditions. The resulting velocity and temperature profiles are then utilized to obtain the microchannel Poiseuille and Nusselt numbers as a function of Knudsen number, first- and second-order velocity slip and temperature jump coefficients, Brinkman number, and the ratio of the thermal creep velocity to the mean velocity. Excellent agreement between the numerical and analytical data is demonstrated. Second-order slip terms and creep velocity are shown to have significant effects on microchannel Poiseuille and Nusselt numbers within the slip flow regime.

Keywords: Microchannel, Slip, Creep, Viscous dissipation, Nusselt number, Poiseuille number


 N. Sadeghi, T. Tasdizen, N.L. Foster, A.Y. Wang, S. Minoshima, A.P. Lieberman.. “Automatic Classification of Alzheimers Disease vs. Frontotemporal Dementia: A Decision Tree Approach with FDG-PET,” SCI Institute Technical Report, No. UUSCI-2007-016, University of Utah, 2007.


A. Santamaria, E.G. Eddings, F. Mondragon. “Effect of Ethanol on the Chemical Structure of the Soot Extractable Material of an Ethylene Inverse Diffusion Flame,” In Combustion and Flame, Vol. 151, No. 1-2, pp. 235--244. October, 2007.
DOI: 10.1016/j.combustflame.2007.06.004

ABSTRACT

The effect of fuel-side ethanol addition on the chemical structure of the soot extractable material generated in an ethylene inverse diffusion flame was evaluated by means of average structural parameters. The results indicate that the ethanol effect on the aromatic components was more pronounced, with an increase of about 40% in the average number of aromatic fused rings (R a) as compared to the results of a neat flame. This observation also helps explain the low percentage of chloroform-extractable material in the soot samples obtained from the flame with ethanol addition. In contrast, the aliphatic component of the extractable material did not demonstrate significant changes with ethanol addition.


 A. Santamaria, F. Mondragon, W. Quinones, E.G. Eddings, A.F. Sarofim. “Average Structural Analysis of the Extractable Material of Young Soot Gathered in an Ethylene Inverse Diffusion Flame,” In FUEL, Vol. 86, No. 12-13, pp. 1908--1917. August, 2007.
DOI: 10.1016/j.fuel.2006.12.002

ABSTRACT

Conventional analytical methods such as 1H NMR, vapor pressure osmometry (VPO) and elemental analysis were used to characterize the soot precursor material represented by the chloroform extractable fractions of the young soot gathered at different heights of an ethylene inverse diffusion flame in terms of average structural parameters. The results indicate that the soot soluble fraction obtained at a 6 mm height has a relatively large molecular weight and has long aliphatic chains which later disappear with an increase in height above the burner base, especially in the region where the temperature is high (1200 K). This behavior is also accompanied by an increase in the aromaticity (fa) of the samples.


 C.E. Scheidegger, H.T. Vo, D. Koop, J. Freire, C.T. Silva. “Querying and Creating Visualizations by Analogy,” In Proceeding of IEEE Visualization 2007, pp. 1560--1567. 2007.


J.F. Shepherd. “Topologic and Geometric Constraint-Based Hexahedral Mesh Generation,” School of Computing, University of Utah, May, 2007.


J.F. Shepherd, C.R. Johnson. “Hexahedral Mesh Generation for Biomedical Models in SCIRun,” SCI Institute Technical Report, No. UUSCI-2007-008, University of Utah, 2007.


S. Shome, R.L. Lux, B.B. Punske, R.S. MacLeod. “Ischemic Preconditioning Protects Against Arrhythmogenesis Through Maintenance of Both Active as well as Passive Electrical Properties in Ischemic Canine Hearts,” In Journal of Electrocardiology, Vol. 40, No. 6 supp, pp. S150--S159. Nov-Dec, 2007.


S. Shome, J.G. Stinstra, C Henriquez, R.S. Macleod. “Influence of Extracellular Potassium and Reduced Extracellular Space on Conduction Velocity During Acute Ischemia: A Simulation Study,” In Journal of Electrocardiology, Vol. 40, No. 4, pp. S5--S6. 2007.


C.T. Silva, J. Freire, S.P. Callahan. “Provenance for Visualizations: Reproducibility and Beyond,” In IEEE Computing in Science and Engineering, Vol. 9, No. 5, pp. 82--89. 2007.


J.G. Stinstra, M. Jolley, M. Callahan, D.M. Weinstein, M. Cole, D.H. Brooks, J. Triedman, R.S. MacLeod. “Evaluation of Different Meshing Algorithms in the Computation of Defibrillation Thresholds in Children,” In Proceedings of the 29th Annual International Conference of the IEEE EMBS, pp. 1422--1425. 2007.


M. Styner, S. Xu, M. El-Sayed, G. Gerig. “Correspondence Evaluation in Local Shape Analysis and Structural Subdivision,” In Proceedings of ISBI 2007, IEEE Press, pp. 1192--1195. 2007.


M. Styner, I. Oguz, S. Xu, D. Pantazis, G. Gerig. “Statistical Group Differences in Anatomical Shape Analysis using Hotelling T2 Metric,” In Proceedings of the 2007 SPIE Medical Imaging Conference, Vol. 6512, 2007.


W.D. Taylor, J.R. MacFall, G. Gerig, K.R. Krishnan. “Structural Integrity of the Uncinate Fasciculus in Geriatric Depression: Relationship with Age of Onset,” In Neuropsychiatric Disease and Treatment, Vol. 3, No. 5, pp. 669--674. 2007.


T.B. Terriberry, J.N. Damon, S.M. Pizer, S. Joshi, G. Gerig. “Population-Based Fitting of Medial Shape Models with Correspondence Optimization,” In Proceedings of Information Processing in Medical Imaging (IPMI '07), Lecture Notes in Computer Science, Vol. 20, pp. 700--712. July, 2007.


L.T. Tran, J. Kim, M. Berzins. “Solving Time-Dependent PDEs using the Material Point Method, A Case Study from Gas Dynamics,” SCI Institute Technical Report, No. UUSCI-2007-010, University of Utah, 2007.


J.K. Triedman, M. Jolley, R.S. MacLeod, J.G. Stinstra, D.H. Brooks, S. Pieper. “A System for Image Based Finite Element Modeling of Novel Defibrillation Strategies,” In Life Science Systems and Applications Workshop, 2007. LISA 2007, pp. 63--66. 2007.


J.K. Triedman, M. Jolley, R.S. MacLeod, J. Stinstra, D.H. Brooks, S. Pieper. “Finite Element Modeling of Novel Defibrillation Approaches in Children and Adults,” In Proc. LISSA Conf., Bethesda, MD, November, 2007.


S.X. Vasquez, A.N. Bahadur, J.T. Johnson III, D.R. Rodriguez, C. Keller. “Severe Runting of a Laboratory Mouse (Mus musculus),” In Lab Animal, Vol. 36, No. 1, pp. 19, 22--23. January, 2007.