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共 101 条记录，以下是31-40 订阅

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Analysis of large-scale scalar data using hixels

Analysis of large-scale scalar data using hixels

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1st IEEE symposium on Large-Scale Data Analysis and visualization 2011, LDAV 2011

作者： Thompson, David Levine, Joshua A. Bennett, Janine C. Bremer, Peer-Timo Gyulassy, Attila Pascucci, Valerio Pébay, Philippe P. Sandia National Laboratories United States SCI Institute University of Utah United States Lawrence Livermore National Laboratory United States

ISBN: (纸本)9781467301541

One of the greatest challenges for today's visualization and analysis communities is the massive amounts of data generated from state of the art simulations. Traditionally, the increase in spatial resolution has driven most of the data explosion, but more recently ensembles of simulations with multiple results per data point and stochastic simulations storing individual probability distributions are increasingly common. This paper introduces a new data representation for scalar data, called hixels, that stores a histogram of values for each sample point of a domain. The histograms may be created by spatial down-sampling, binning ensemble values, or polling values from a given distribution. In this manner, hixels form a compact yet information rich approximation of large scale data. In essence, hixels trade off data size and complexity for scalar-value "uncertainty". Based on this new representation we propose new feature detection algorithms using a combination of topological and statistical methods. In particular, we show how to approximate topological structures from hixel data, extract structures from multi-modal distributions, and render uncertain isosurfaces. In all three cases we demonstrate how using hixels compares to traditional techniques and provide new capabilities to recover prominent features that would otherwise be either infeasible to compute or ambiguous to infer. We use a collection of computer tomography data and large scale combustion simulations to illustrate our techniques. © 2011 IEEE.

关键词： visualization

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A visual analysis system for metabolomics data

A visual analysis system for metabolomics data

引用

1st IEEE symposium on Biological Data visualization, BioVis 2011

作者： Livengood, Philip MacIejewski, Ross Chen, Wei Ebert, David S. Purdue University Visualization and Analytics Cente United States Arizona State University United States State Key Lab of CADandCG Zhejiang University China

ISBN: (纸本)9781467300025

When analyzing metabolomics data, cancer care researchers are searching for differences between known healthy samples and unhealthy samples. By analyzing and understanding these differences, researchers hope to identify cancer biomarkers. In this work we present a novel system that enables interactive comparative visualization and analysis of metabolomics data obtained by two-dimensional gas chromatography-mass spectrome-try (GCxGC-MS). Our system allows the user to produce, and interactively explore, visualizations of multiple GCxGC-MS data sets, thereby allowing a user to discover differences and features in real time. Our system provides statistical support in the form of mean and standard deviation calculations to aid users in identifying meaningful differences between sample groups. We combine these with multiform, linked visualizations in order to provide researchers with a powerful new tool for GCxGC-MS exploration and bio-marker discovery. © 2011 IEEE.

关键词： visualization

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Modeling and visualization of receptor clustering on the cellular membrane

Modeling and visualization of receptor clustering on the cel...

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1st IEEE symposium on Biological Data visualization, BioVis 2011

作者： Falk, Martin Daub, Markus Schneider, Guido Ertl, Thomas VISUS - Visualization Research Center University of Stuttgart Germany Institute of Analysis Dynamics and Modeling University of Stuttgart Germany

ISBN: (纸本)9781467300025

In cell biology, apopotosis is a very important cellular process. Apopotosis, or programmed cell death, allows an organism to remove damaged or unneeded cells in a structured manner in contrast to necrosis. Ligands bind to the death receptors located on the cellular membrane forming ligand-receptor clusters. In this paper, we develop a novel mathematical model describing the stochastic process of the ligand-receptor clustering. To study the structure and the size of the ligand-receptor clusters, a stochastic particle simulation is employed. Besides the translation of the particles on the cellular membrane, we also take the particle rotation into account as we model binding sites explicitly. Glyph-based visualization techniques are used to validate and analyze the results of our in-silico model. Information on the individual clusters as well as particle-specific data can be selected by the user and is mapped to colors to highlight certain properties of the data. The results of our model look very promising. The visualization supports the process of model development by visual data analysis including the identification of cluster components as well as the illustration of particle trajectories. © 2011 IEEE.

关键词： visualization

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RuleBender: Integrated visualization for biochemical rule-based modeling

RuleBender: Integrated visualization for biochemical rule-ba...

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1st IEEE symposium on Biological Data visualization, BioVis 2011

作者： Smith, Adam M. Xu, Wen Sun, Yao Faeder, James R. Marai, G. Elisabeta Computer Science University of Pittsburgh United States Systems and Computational Biology University of Pittsburgh United States

ISBN: (纸本)9781467300025

We introduce RuleBender, a novel visualization system for the integrated visualization, modeling and simulation of rule-based intra-cellular biochemistry. Rule-based modeling (RBM) is a powerful and increasingly popular approach to modeling cell signaling networks. However, novel visual tools are needed in order to make RBM accessible to a broad range of users, to make specification of models less error prone, and to improve workflows. We present the user requirements, visual paradigms, algorithms and design decisions behind RuleBender, with emphasis on visual global/local model exploration and integrated execution of simulations. The support of RBM creation, debugging, and interactive visualization expedites the RBM learning process and reduces model construction time;while built-in model simulation and results with multiple linked views streamline the execution and analysis of newly created models and generated networks. A development cycle that includes close interaction with expert users allows RuleBender to better serve the needs of the systems biology community. © 2011 IEEE.

关键词： visualization

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The Galaxy Track Browser: Transforming the genome browser from visualization tool to analysis tool

The Galaxy Track Browser: Transforming the genome browser fr...

引用

1st IEEE symposium on Biological Data visualization, BioVis 2011

作者： Goecks, Jeremy Li, Kanwei Clements, Dave Taylor, James Galaxy Project Emory University United States

ISBN: (纸本)9781467300025

The proliferation of next-generation sequencing (NGS) technologies and analysis tools present new challenges to genome browsers. These challenges include supporting very large datasets, integrating analysis tools with data visualization to help reason about and improve analyses, and sharing or publishing fully interactive visualizations. The Galaxy Track Browser (GTB) is a Web-based genome browser integrated into the Galaxy platform that addresses these challenges. GTB is the first Web-based genome browser to provide a full multi-resolution data model;this model supports efficient data retrieval from very large datasets. GTB leverages the Galaxy platform to combine data visualization and data analysis;users can specify parameter values and run tools to produce new data, all within GTB. GTB also provides interactive filters that dynamically show and hide data and can be used to identify data for further investigation. GTB is available on every Galaxy server, and visualizations can be created for both standard and custom genome builds. Fully interactive GTB visualizations can be shared with colleagues and published on the Web using a simple graphical user interface. © 2011 IEEE.

关键词： Genome

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Visual exploration of microbial populations

Visual exploration of microbial populations

引用

1st IEEE symposium on Biological Data visualization, BioVis 2011

作者： Fernstad, Sara Johansson Johansson, Jimmy Adams, Suzi Shaw, Jane Taylor, David C-Research Linkõping University Sweden Unilever Discover Port Sunlight United Kingdom

ISBN: (纸本)9781467300025

studies of the ecology of microbial populations are increasingly common within many research areas as the field of microbiomics develops rapidly. The study of the ecology in sampled microbial populations generates high dimensional data sets. Although many analysis methods are available for examination of such data, a tailored tool was required to fulfill the need of interactivity and flexibility for microbiologists. In this paper, MicrobiVis is presented. It is a tool for visual exploration and interactive analysis of micro-biomic populations. MicrobiVis has been designed in close collaboration with end users. It extends previous interactive systems for explorative dimensionality reduction by including a range of domain relevant features. It contributes a flexible and explorative dimensionality reduction as well as a visual and interactive environment for examination of data subsets. By combining information visualization and methods based on analytic tasks common in microbiology as a means for gaining new and relevant insights. The utility of MicrobiVis is demonstrated through a use case describing how a microbiologist may use the system for a visual analysis of a microbial data set. Its usability and potential is indicated through positive feedback from the current end users. © 2011 IEEE.

关键词： visualization

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visualization of anisotropic contact potentials within protein structures

Visualization of anisotropic contact potentials within prote...

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1st IEEE symposium on Biological Data visualization, BioVis 2011

作者： Vehlow, Corinna Preim, Bernhard Lappe, Michael VISUS University of Stuttgart Germany ISG University of Magdeburg Germany Max Planck Institute for Molecular Genetics Berlin Germany

ISBN: (纸本)9781467300025

The use of local covalent geometry for quality assessment and refinement of protein structure models is a well-established methodology. The question arises whether information on non-covalent geometry contained within resolved structures can be harnessed to improve structure prediction. Moreover, incorporation of different combinations of priors would pave the way towards multi-body potentials. Existing empirical force-fields do not facilitate an interactive exploration of the parameter space and an assignment of spatial propensities to contacts. Hence, we investigate the possibility of making such propensities available for synergistic modeling. We present an approach that facilitates the extraction and analysis of anisotropic contact potentials for a multitude of parameters describing an amino acid and the conditions within its microenvi-ronment. For this purpose, two novel visualization principles will be introduced. The first visualization illustrates anisotropic residue-dependent contact density potentials in the form of a map projection. A second visualization is overlaid onto this, showing similar local neighborhoods as abstract traces of residues contained within each individual neighborhood. The Contact Geometry Analysis Plugin (CGAP) (for CMView) we developed allows incorporation of geometric orientation propensities into the process of interactive protein modeling and can be used for the generation of improved energy functions. It further supports the analysis of model quality, as it directly illustrates model consistency with known spatial propensities which, in turn, enables users to detect possible structural errors. © 2011 IEEE.

关键词： visualization

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Evaluating the VIPER pedigree visualisation: Detecting inheritance inconsistencies in genotyped pedigrees

Evaluating the VIPER pedigree visualisation: Detecting inher...

引用

1st IEEE symposium on Biological Data visualization, BioVis 2011

作者： Paterson, Trevor Graham, Martin Kennedy, Jessie Law, Andy Roslin Institute University of Edinburgh United Kingdom School of Computing Edinburgh Napier University United Kingdom

ISBN: (纸本)9781467300025

VIPER (Visual Pedigree Explorer) is a tool for exploring large complex animal pedigrees and their associated genotype data. The tool combines a novel, space-efficient visualisation of the pedigree structure with an inheritance-checking algorithm. This allows users to explore the apparent errors within the genotype data in the full context of the family and pedigree structure. Ultimately, the aim is to develop an interactive software application that will allow users to identify, confirm and then remove errors from the pedigree structure and scored genotypes. This paper describes an evaluation of how VIPER displays the different scales and types of data set that can occur, along with a description of the further interface functionality necessary to meet the challenges such data presents. This is followed by an examination of a range of possible pedigree genotype errors by replicating these errors in controlled simulated data sets and showing how they are manifested in the VIPER interface and observed by a domain expert. The data sets used include both real and artificially generated data, the advantage of the latter being that they produce known effects in the visualization which the domain expert can then interpret as being useful or unhelpful as they see fit. © 2011 IEEE.

关键词： visualization

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GenAMap: visualization strategies for structured association mapping

GenAMap: Visualization strategies for structured association...

引用

1st IEEE symposium on Biological Data visualization, BioVis 2011

作者： Curtis, Ross E. Kinnaird, Peter Xing, Eric P. Joint Carnegie Mellon-University of Pittsburgh Program for Computational Biology United States Human Computer Interaction Institute Carnegie Mellon University United States Machine Learning Department Carnegie Mellon University United States

ISBN: (纸本)9781467300025

Association mapping studies promise to link DNA mutations to gene expression data, possibly leading to innovative treatments for diseases. One challenge in large-scale association mapping studies is exploring the results of the computational analysis to find relevant and interesting associations. Although many association mapping studies find associations from a genome-wide collection of genomic data to hundreds or thousands of traits, current visualization software only allow these associations to be explored one trait at a time. The inability to explore the association of a genomic location to multiple traits hides the inherent interaction between traits in the analysis. Additionally, researchers must rely on collections of in-house scripts and multiple tools to perform an analysis, adding time and effort to find interesting associations. In this paper, we present a novel visual analytics system called GenAMap. GenAMap replaces the time-consuming analysis of large-scale association mapping studies with exploratory visualization tools that give geneticists an overview of the data and lead them to relevant information. We present the results of a preliminary evaluation that validated our basic approach. © 2011 IEEE.

关键词： visualization

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visualization and interaction system for surgical planning

Visualization and interaction system for surgical planning

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1st International Workshop on Engineering Interactive Computing Systems for Medicine and Health Care, EICS4Med 2011 - Co-located with the ACM SIGCHI symposium on Engineering Interactive Computing Systems, EICS 2011

作者： De Paolis, Lucio T. Aloisio, Giovanni Dept. of Innovation Engineering Salento University Lecce Italy

Modern technologies give a great support to the minimally invasive surgical procedures through medical image processing and visualization, 3D organ's reconstruction and intra-operative surgical guidance. The practice of Minimally Invasive Surgery is becoming more and more widespread and is being adopted as an alternative to the classical procedure. This technique presents some limitations for surgeons. In particular, the lack of depth in perception and the difficulty in estimating the distance of the specific structures in laparoscopic surgery can impose limits to delicate dissection or suturing. The presence of new systems for the pre-operative planning can be very useful to the surgeon. In this paper we present a visualization and interaction system that allows surgeon to visualize the 3D model of the patient's organs built from the CT images. Different visualization modalities are available according to the surgeon needs in laparoscopy and an Augmented Reality application permits the choice of the best insertion points of the trocars on the 3D virtual model and the visualization of these points on the real patient's body. Two case studies have been considered. The system can be used as support for the diagnosis, for the surgical preoperative planning and also as visual support during the surgical procedure. Copyright © 2011 for the individual papers by the papers' authors.

关键词： Augmented reality

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