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IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)

作者： Min-Yu Huang Gunther H. Weber Xiao-Yong Li Mark D. Biggin Bernd Hamann Institute for Data Analysis and Visualization (IDAV) Department of Computer Science University of California슠Davis Davis CA USA Visualization Group Lawrence Berkeley National Laboratory Berkeley CA USA Genomics Divisions Lawrence Berkeley National Laboratory Berkeley CA USA Institute for Data Analysis and Visualization (IDAV) Department of Computer Science University of California Davis Davis CA USA

Most analyses of ChIP-chip in vivo DNA binding have focused on qualitative descriptions of whether genomic regions are bound or not. There is increasing evidence, however, that factors bind in a highly overlapping manner to the same genomic regions and that it is quantitative differences in occupancy on these commonly bound regions that are the critical determinants of the different biological specificity of factors. As a result, it is critical to have a tool to facilitate the quantitative visualization of differences between transcription factors and the genomic regions they bind to understand each factor's unique roles in the network. We have developed a framework which combines several visualizations via brushing-and-linking to allow the user to interactively analyze and explore in vivo DNA binding data of multiple transcription factors. We describe these visualization types and also provide a discussion of biological examples in this paper.

关键词： Correlation Bioinformatics data visualization Genomics Image color analysis Browsers

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Crystal fingerprint space - A novel paradigm for studying crystal-structure sets

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Acta Crystallographica Section A: Foundations of Crystallography 2010年第5期66卷 507-517页

作者： Valle, Mario Oganov, Artem R. Data Analysis and Visualization Group Swiss National Supercomputing Centre (CSCS) 6928 Manno via Cantonale Galleria 2 Switzerland Department of Geosciences New York Center for Computational Sciences State University of New York Stony Brook NY 11794-2100 United States Geology Department Moscow State University 119992 Moscow Russian Federation

The initial aim of the crystal fingerprint project was to solve a very specific problem: to classify and remove duplicate crystal structures from the results generated by the evolutionary crystal-structure predictor USPEX. These duplications decrease the genetic diversity of the population used by the evolutionary algorithm, potentially leading to stagnation and, after a certain time, reducing the likelihood of predicting essentially new structures. After solving the initial problem, the approach led to unexpected discoveries: unforeseen correlations, useful derived quantities and insight into the structure of the overall set of results. All of these were facilitated by the projects underlying idea: to transform the structure sets from the physical configuration space to an abstract, high-dimensional space called the fingerprint space. Here every structure is represented as a point whose coordinates (fingerprint) are computed from the crystal structure. Then the spaces distance measure, interpreted as structure closeness, enables grouping of structures into similarity classes. This model provides much flexibility and facilitates access to knowledge and algorithms from fields outside crystallography, e.g. pattern recognition and data mining. The current usage of the fingerprint-space model is revealing interesting properties that relate to chemical and crystallographic attributes of a structure set. For this reason, the mapping of structure sets to fingerprint space could become a new paradigm for studying crystal-structure ensembles and global chemical features of the energy landscape. © 2010 International Union of Crystallography Printed in Singapore - all rights reserved.

关键词： crystal fingerprints fingerprint space structure classification USPEX

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Fast ultrasound beam prediction for linear and regular two-dimensional arrays

Fast ultrasound beam prediction for linear and regular two-d...

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作者： Hlawitschka, Mario McGough, Robert J. Ferrara, Katherine W. Kruse, Dustin E. Institute for Data Analysis and Visualization University of California Davis CA 95616 United States Department of Electrical and Computer Engineering Michigan State University East Lansing MI 48824 United States Department of Biomedical Engineering University of California Davis CA 95616 United States

ISBN: (纸本)9781457703829

Real-time beam predictions are desirable for ultrasound therapy guidance, as treatment planning requires individualized computations. To address the long-standing issue of the computational burden associated with calculating the acoustic field in large volumes, we use modern graphics processing units to accelerate the calculation of near-field pressure fields for therapeutic ultrasound arrays. First, we accelerate field computations for single rectangular pistons by employing the Fast Near-field Method (FNM) to accurately and efficiently estimate the complex near-field wave patterns in homogeneous media, and results are compared to the Rayleigh-Sommerfeld method. We then compute beam patterns of 1D and 2D piston arrays using pre-calculated beam patterns from a single piston. Our results show that these algorithms can benefit greatly from GPU computing hardware, exceeding a modern CPU by a factor of over 100. For a single rectangular piston, the FNM is able to calculate a 0.01% accurate field within 30 ns per field point. Furthermore, we demonstrate calculation speeds for arrays of up to 11.5 109 field points per second. Beam volumes containing 2563 field points are calculated within one second for arrays containing up to 512 pistons, thus, facilitating future real-time thermal dose predictions. © 2010 IEEE.

关键词： Pistons

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ParaText: Scalable text modeling and analysis 10

ParaText: Scalable text modeling and analysis

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Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing

作者： Dunlavy, Daniel M. Shead, Timothy M. Stanton, Eric T. Comp. Sci. and Informatics Sandia National Laboratories M/S 1318 P.O. Box 5800 Albuquerque NM 87185-1318 United States Data Analysis and Visualization Sandia National Laboratories M/S 1323 P.O. Box 5800 Albuquerque NM 87185-1323 United States

ISBN: (纸本)9781605589428

Automated analysis of unstructured text documents (e.g., web pages, newswire articles, research publications, business reports) is a key capability for solving important problems in areas including decision making, risk assessment, social net- work analysis, intelligence analysis, scholarly research and others. However, as data sizes continue to grow in these ar- eas, scalable processing, modeling, and semantic analysis of text collections becomes essential. In this paper, we present the ParaText text analysis engine, a distributed memory software framework for processing, modeling, and analyzing collections of unstructured text documents. Results on sev- eral document collections using hundreds of processors are presented to illustrate the exibility, extensibility, and scal- ability of the the entire process of text modeling from raw data ingestion to application analysis. © Copyright 2010 ACM.

关键词： Risk assessment

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visualization as a bridge between chemical and nuclear engineering simulations

Visualization as a bridge between chemical and nuclear engin...

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作者： Fogal, Thomas Xiao, Shanjie Yang, Xue Krüger, Jens Jevremovic, Tatjana Scientific Computing and Imaging Institute University of Utah United States Radiation Protection SLAC National Accelerator Laboratory United States Utah Nuclear Engineering Program University of Utah United States Interactive Visualization and Data Analysis Group DFKI Saarbrücken Germany Civil and Environmental Engineering University of Utah United States

ISBN: (纸本)9780816910656

Collaborating across disciplines can be a difficult task for a variety of reasons. One of which is the lack of common methodologies and tools for visualization and analysis. Tools developed in one group can rarely be applied directly to data from another group, due to differences in data formats, analysis methodologies, and learning curves associated with the advanced visualization systems necessary for modern scientific data. Despite these difficulties, multi-physics collaboration is key to developing and understanding the next generation of computational models, which couple the dynamic processes and scales of multiple disciplines. As a step towards integrative models, we propose a visualization and analysis system to serve as a common interconnect between chemical and nuclear engineering. This choice allows multiple organizations to fruitfully exchange data and example visualizations in a reproducible manner, providing a foundation for productive discussion. In this work, we demonstrate the utility of a visualization system as it applies to bridging simulation domains and providing for multidisciplinary research in nuclear and chemical engineering.

关键词： visualization

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Initial-state dependence of coupled electronic and nuclear fluxes in molecules

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Physical Review A 2010年第5期81卷 052502-052502页

作者： A. Kenfack F. Marquardt G. K. Paramonov I. Barth C. Lasser B. Paulus Physikalische und Theoretische Chemie Institut für Chemie und Biochemie Freie Universität Berlin D-14195 Berlin Germany Visualization and Data Analysis Zuse Institute Berlin D-14195 Berlin Germany Fachbereich Mathematik Freie Universität Berlin D-14195 Berlin Germany

We demonstrate that coupled electronic and nuclear fluxes in molecules can strongly depend on the initial state preparation. Starting the dynamics of an aligned D2+ molecule at two different initial conditions, the inner and the outer turning points, we observe qualitatively different oscillation patterns of the nuclear fluxes developing after 30 fs. This corresponds to different orders of magnitude bridged by the time evolution of the nuclear dispersion. Moreover, there are attosecond time intervals within which the electronic fluxes do not adapt to the nuclei motion depending on the initial state. These results are inferred from two different approaches for the numerical flux simulation, which are both in good agreement.

关键词： Molecules

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Large data visualization on Distributed Memory Multi-GPU Clusters 10

Large Data Visualization on Distributed Memory Multi-GPU Clu...

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Conference on High-performance Graphics

作者： Thomas Fogal Hank Childs Siddharth Shankar Jens Kriiger R. Daniel Bergeron Philip Hatcher Scientific Computing & Imaging Institute University of UtahDepartment of Computer Science University of New Hampshire Lawrence Berkeley National Laboratory Scientific Computing & Imaging Institute University of Utah Interactive Visualization and Data Analysis Group DFKI Germany Department of Computer Science University of New Hampshire

ISBN: (纸本)9781617827242

data sets of immense size are regularly generated on large scale computing resources. Even among more traditional methods for acquisition of volume data, such as MRI and CT scanners, data which is too large to be effectively visualized on standard workstations is now commonplace. One solution to this problem is to employ a 'visualization cluster,' a small to medium scale cluster dedicated to performing visualization and analysis of massive data sets generated on larger scale supercomputers. These clusters are designed to fit a different need than traditional supercomputers, and therefore their design mandates different hardware choices, such as increased memory, and more recently, graphics processing units (GPUs). While there has been much previous work on distributed memory visualization as well as GPU visualization, there is a relative dearth of algorithms which effectively use GPUs at a large scale in a distributed memory environment. In this work, we study a common visualization technique in a GPU-accelerated, distributed memory setting, and present performance characteristics when scaling to extremely large data sets.

关键词： distributed memory data visualisation visualization dataset supercomputer Representation of data performance characteristics

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Massive data visualization: A survey

Massive data visualization: A survey

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Workshop on Mathematical Foundations of Scientific visualization, Computer Graphics, and Massive data Exploration, 2004

作者： Joy, Kenneth I. Institute for Data Analysis and Visualization University of California Davis United States

ISBN: (纸本)9783642543005

Today’s scientific and engineering problems require a different approach to address the massive data problems in organization, storage, transmission, visualization, exploration, and analysis. Visual techniques for data exploration are now common in many scientific, engineering, and business applications. However, the massive amount of data collected through simulation, collection and logging is inhibiting the use of conventional visualization methods. We need to discover new visualization methods that allow us to explore the massive multidimensional time-varying information streams and turn overwhelming tasks into opportunities for discovery and analysis. © 2009 Springer-Verlag Berlin Heidelberg.

关键词： data visualization

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Ecological research can augment restoration practice in urban areas degraded by invasive species-examples from Chicago Wilderness

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Urban Ecosystems 2009年第1期12卷 63-77页

作者： Heneghan, Liam Umek, Lauren Bernau, Brad Grady, Kevin Iatropulos, Jamie Jabon, David Workman, Margaret Environmental Science Program DePaul University Chicago IL 60614 2325 North Clifton Avenue United States Scientific Data Analysis and Visualization Program DePaul University Chicago United States

Urban biodiversity conservation needs a firm scientific foundation, one that draws upon active and regionally calibrated research programs. Until recently this foundation has not existed. In this paper we examine the way in which the emerging discipline of restoration ecology in an urban context can learn from the experiences of ongoing restoration projects and in turn how novel insights from research of urban soils can help these projects define and reach their goals. Limitations on collaboration between academic researchers and practitioners continues be problematic. We discuss a model whereby this impediment may be removed. A case study of Rhamnus cathartica, an invader of Midwestern woodlands which modifies some important soil ecosystem properties will be used to illustrate the potential for engagement between research and practice. © 2008 Springer Science+Business Media, LLC.

关键词： Buckthorn Ecology and management Interdisciplinary research Invasive species Restoration Rhamnus cathartica Soil restoration Urban ecology

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Out-of-core data management for path tracing on hybrid resources

Out-of-core data management for path tracing on hybrid resou...

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30th Annual Conference on European Association for Computer Graphics, EUROGRAPHICS 2009

作者： Budge, Brian Bernardin, Tony Stuart, Jeff A. Sengupta, Shubhabrata Joy, Kenneth I. Owens, John D. Institute for Data Analysis and Visualization Department of Computer Science Davis United States Department of Electrical and Computer Engineering University of California Davis United States

We present a software system that enables path-traced rendering of complex scenes. The system consists of two primary components: an application layer that implements the basic rendering algorithm, and an out-of-core scheduling and data-management layer designed to assist the application layer in exploiting hybrid computational resources (e.g., CPUs and GPUs) simultaneously. We describe the basic system architecture, discuss design decisions of the system's data-management layer, and outline an efficient implementation of a path tracer application, where GPUs perform functions such as ray tracing, shadow tracing, importance-driven light sampling, and surface shading. The use of GPUs speeds up the runtime of these components by factors ranging from two to twenty, resulting in a substantial overall increase in rendering speed. The path tracer scales well with respect to CPUs, GPUs and memory per node as well as scaling with the number of nodes. The result is a system that can render large complex scenes with strong performance and scalability. © 2008 The Author(s).

关键词： Information management

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