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Visual analysis of gel-free Proteome data

IEEE TRANSACTIONS ON visualization AND COMPUTER GRAPHICS 2006年第4期12卷 497-508页

作者： Linsen, L Löcherbach, J Berth, M Becher, D Bernhardt, J Ernst Moritz Arndt Univ Greifswald Dept Math & Comp Sci Greifswald Germany Ernst Moritz Arndt Univ Greifswald Dept Microbiol Greifswald Germany

We present a visual exploration system supporting protein analysis when using gel-free data acquisition methods. The data to be analyzed is obtained by coupling liquid chromatography (LC) with mass spectrometry ( MS). LC-MS data have the properties of being nonequidistantly distributed in the time dimension ( measured by LC) and being scattered in the mass-to-charge ratio dimension ( measured by MS). We describe a hierarchical data representation and visualization method for large LC-MS data. Based on this visualization, we have developed a tool that supports various data analysis steps. Our visual tool provides a global understanding of the data, intuitive detection and classification of experimental errors, and extensions to LC-MS/MS, LC/LC-MS, and LC/LC-MS/MS data analysis. Due to the presence of randomly occurring rare isotopes within the same protein molecule, several intensity peaks may be detected that all refer to the same peptide. We have developed methods to unite such intensity peaks. This deisotoping step is visually documented by our system, such that misclassification can be detected intuitively. For differential protein expression analysis, we compute and visualize the differences in protein amounts between experiments. In order to compute the differential expression, the experimental data need to be registered. For registration, we perform a nonrigid warping step based on landmarks. The landmarks can be assigned automatically using protein identification methods. We evaluate our methods by comparing protein analysis with and without our interactive visualization-based exploration tool.

关键词： interactive visual exploration hierarchical data representation visualization in bioinformatics proteomics

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analysis of Japanese information systems co-authorship data

Analysis of Japanese information systems co-authorship data

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11th International conference on Information visualization (IV 2007)

作者： LaRowe, Gavin Ichise, Ryutaro Boerner, Katy Indiana Univ Cyberinfrastruct Network Sci Ctr Bloomington IN 47405 USA Natl Inst Informat Tokyo Japan

ISBN: (纸本)9780769529004

This paper reports a bibliometric analysis of evolving co-author networks. Using 5,009 articles covering the years 1993 to 2005 from Transactions D. (Information Systems) of the Institute of Electronics Information and Communication. Engineers (IEICE), we attempt to compare the network characteristics for each year the co-author network characteristics for the entire time span, and the four major components of the entire data set. Finally, we analyze each of these in contrast to extant co-authorship network data and find that the pattern of co-authorship within Information Systems does not change significantly over this time period.

关键词： Information systems

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Geoscience visualization with GPU programming

Geoscience visualization with GPU programming

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conference on visualization and data analysis 2005

作者： Lin, JCR Landmark Graph Houston TX 77042 USA

ISBN: (纸本)081945642X

In recent years, off-the-shelf graphics cards have provided the ability to program the a aphics processing unit (GPU) as an alternative to using fixed function pipelines. We believe that this capability can enable a new paradigm in geoscience data visualization. In the past, the geoscience data preparation, interpretation, and simulation were all done by the central processing unit (CPU), and then the generated graphics primitives were fed into a GPU for visualization. This approach was dictated by the constraints imposed by the general-purpose graphics application programming interfaces (APIs). With GPU programming, this front-end processing can be done in the GPU and visualized immediately. After passing the geometry data into the GPU, parameters can be used to control these processes inside the GPU. The different algorithms associated with these processes can be applied at run time by loading a new shading program. To prove this concept, we designed and implemented Java-based shader classes, which operate on top of Cg, a high-level language for graphics programming. These shader classes load Cg shaders to provide a new method for visualizing and interacting with geoscience data. The results from this approach show better visual quality for seismic data display and dramatically improved performance for large 3D seismic data sets. For editing geological surfaces, tests demonstrate performance levels 10 times faster than the typical approach. This paper describes the use of these shaders and presents the results of shader application to geoscience data visualization.

关键词： geoscience visualization shader GPU programming data visualization volume visualization

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DEX: Increasing the capability of scientific data analysis pipelines by using efficient bitmap indices to accelerate scientific visualization

DEX: Increasing the capability of scientific data analysis p...

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17th International conference Scientific and Statistical database Management, SSDBM 2005

作者： Stockinger, Kurt Shalf, John Bethel, Wes Wu, Kesheng Lawrence Berkeley National Laboratory University of California 1 Cyclotron Road Berkeley CA 94720 United States

We describe a new approach to scalable data analysis that enables scientists to manage the explosion in size and complexity of scientific data produced by experiments and simulations. Our approach uses a novel combination of efficient query technology and visualization infrastructure. The combination of bitmap indexing, which is a data management technology that accelerates queries on large scientific datasets, with a visualization pipeline for generating images of abstract data results in a tool suitable for use by scientists in fields where data size and complexity poses a barrier to efficient analysis. Our architecture and implementation, which we call DEX (short for dexterous data explorer), directly addresses the problem of "too much data" by focusing analysis on data deemed to be "scientifically interesting" via a user-specified selection criteria. The architectural concepts and implementation are applicable to wide variety of scientific data analysis and visualization applications. This paper presents an architectural overview of the system along with an analysis showing substantial performance over traditional visualization pipelines. While performance gains are a significant result, even more important is the new functionality not present in any visualization analysis software - namely the ability to perform interactive, multi-dimensional queries to refine regions of interest that are later used as input to analysis or visualization.

关键词： visualization

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Knowledge precepts for design and evaluation of information visualizations

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IEEE TRANSACTIONS ON visualization AND COMPUTER GRAPHICS 2005年第4期11卷 432-442页

作者： Amar, RA Stasko, JT Georgia Inst Technol Coll Comp GVU Ctr Atlanta GA 30332 USA

The design and evaluation of most current information visualization systems descend from an emphasis on a user's ability to "unpack" the representations of data of interest and operate on them independently. Too often, successful decision-making and analysis are more a matter of serendipity and user experience than of intentional design and specific support for such tasks;although humans have considerable abilities in analyzing relationships from data, the utility of visualizations remains relatively variable across users, data sets, and domains. In this paper, we discuss the notion of analytic gaps, which represent obstacles faced by visualizations in facilitating higher-level analytic tasks, such as decision-making and learning. We discuss support for bridging these gaps, propose a framework for the design and evaluation of information visualization systems, and demonstrate its use.

关键词： information visualization visualization techniques and methodologies theory and methods

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On optimal mapping of visualization pipeline onto linear arrangement of network nodes

On optimal mapping of visualization pipeline onto linear arr...

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conference on visualization and data analysis 2005

作者： Zhu, MX Wu, QS Rao, NSV Yengar, S Louisiana State Univ Dept Comp Sci Baton Rouge LA 70803 USA

ISBN: (纸本)081945642X

This paper discusses algorithmic and implementation aspects of optimally mapping a visualization pipeline onto a linear arrangement of wide-area network nodes to minimize the total delay. The first network node typically is a data source, the last node could be a display device ranging from a personal computer to a powerwall, and each intermediate node could be a workstation or computational cluster. This mapping scheme appropriately distributes the filtering, geometry generation, rendering, and display modules of the visualization pipeline onto the linear arrangement of network nodes to make an efficient use of the computing resources at end nodes and network bandwidths between them. Regression-based network daemons are developed to measure the available bandwidth between the network nodes. We present an analytical formulation of this problem by taking into account the computational power of nodes, bandwidths between them, and sizes of messages exchanged between visualization modules. We propose a polynomial-time optimal algorithm that uses the dynamic programming method to compute the mapping with a minimum total delay. An OpenGL-based remote visualization system is implemented and deployed at three geographically distributed nodes for preliminary experiments.

关键词： remote visualization visualization pipeline bandwidth measurement network mapping

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Effective registration and visualization of fluorescent neural images

Effective registration and visualization of fluorescent neur...

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conference on visualization and data analysis 2005

作者： Vaidhyanathan, N Sun, YL Duerstock, B Koob, AA Purdue Univ Dept Civil Engn W Lafayette IN 47907 USA

ISBN: (纸本)081945642X

Neuroimaging using fluorescent markers is an effective technique to study specific structures and functions in the brain. However, it is very challenging to register the fluorescent image series. This is because the problem involves complex factors such significant noise, non-uniform slice thickness, and inhomogeneous deformation. hi this paper, we propose a method to register such fluorescent images. Based on the edges in images, we propose a multi-level clustering approach to isolate individual features. This approach can effectively produce control points on edge features. Then we apply an elastic registration using the thin plate spline algorithm. Finally, we apply the elliptic weighted average (EWA) splatting technique for 3D volume visualization.

关键词： image registration clustering thin-plate splines visualization neuroimaging

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Interactive visual analysis and exploration of injection systems simulations

Interactive visual analysis and exploration of injection sys...

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IEEE visualization 2005 conference

作者： Matkovic, K Jelovic, M Juric, J Konyha, Z Gracanin, D VRVis Res Ctr Vienna Austria

ISBN: (纸本)0780394623

Simulations often generate large amounts of data that require use of SciVis techniques for effective exploration of simulation results. In some cases, like ID theory of fluid dynamics, conventional SciVis techniques are not very useful. One such example is a simulation of injection systems that is becoming more and more important due to an increasingly restrictive emission regulations. There are many parameters and correlations among them that influence the simulation results. We describe how basic information visualization techniques can help in visualizing, understanding and analyzing this kind of data. The ComVis tool is developed and used to analyze and explore the data. ComVis supports multiple linked views and common information visualization displays such as 2D and 3D scatter-plot, histogram, parallel coordinates, pie-chart, etc. A Diesel Common Rail Injector with 2/2 Way Valve is used for a case study. data sets were generated using a commercially available AVL HYDSIM simulation tool for dynamic analysis of hydraulic and hydro-mechanical systems, with the main application area in the simulation of fuel injection systems.

关键词： information visualization visual exploration simulation injection system

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visualization techniques for analyzing patterns in system performance data

Visualization techniques for analyzing patterns in system pe...

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31st International conference on Computer Measurement Group

作者： Holtman, James Convergys Corp. Cincinnati OH United States

This paper will describe some of the analysis and visualization techniques that the author has used in analyzing performance data from a variety of systems. Usage patterns provide information on what activities are being performed on the system, thus providing insight into what components of the system might be candidates for optimization. These techniques can also show what activities correlate to resource consumption, and this provides data for constructing performance models. The analysis and graphics were done using the R freeware package. © Convergys Corporation 2005.

关键词： data visualization

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visualization tools facilitate geological investigations of Mars exploration rover landing sites

Visualization tools facilitate geological investigations of ...

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conference on visualization and data analysis 2005

作者： Schwehr, KD Nishimura, C Johnson, CL Kilb, D Nayak, A Univ Calif San Diego Inst Geophys & Planetary Phys Scripps Inst Oceanog San Diego CA 92103 USA

ISBN: (纸本)081945642X

The current rate of Mars exploration data acquisition demands that geoscientists and computer scientists coordinate central storage, processing and visualization strategies to anticipate future technological advancements. We investigate how existing 3-D visualization tools can be used to study a part of the Mars orbiter and lander data (about 4 terabytes of data). Our tools assist in juxtaposition of different datum and in viewing data that spans multiple orders of magnitude, specifically for current scientific research pertaining to Mars' geophysics and geology. These tools also permit effective data fidelity and resolution assessment, allowing quick identification of problems related to the use of differing spatial coordinate systems, a continued problem. Knowledge gained from the small dataset we test, helps us identify key tools needed to accommodate the technology required to process and analyze approximately 64 terabytes of Mars data expected by 2008. We use the current planetary data archives, and identify key visualization techniques and tools that distill multiple data types into manageable end products. Our goal is to broaden the user base, using readily available platform-independent freeware packages, while simultaneously including sufficient modularity to be compatible with future technologies.

关键词： earth space and environmental sciences visualization

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