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Conference on visualization and Data Analysis 2011

作者： Pellegrino, Donald Chen, Chaomei Drexel Univ Coll Informat Sci & Technol Philadelphia PA 19104 USA

ISBN: (纸本)9780819484055

This paper introduces a new method for creating an interactive sequence similarity map of all known influenza virus protein sequences and integrating the map with existing general purpose analytical tools. The NCBI data model was designed to provide a high degree of interconnectedness amongst data objects. Substantial and continuous increase in data volume has led to a large and highly connected information space. Researchers seeking to explore this space are challenged to identify a starting point. They often choose data that is popular in the literature. Reference in the literature follow a power law distribution and popular data points may bias explorers toward paths that lead only to a dead-end of what is already known. To help discover the unexpected we developed an interactive visual analytics system to map the information space of influenza protein sequence data. The design is motivated by the needs of eScience researchers.

关键词： Visual Knowledge Discovery bioinformatics visualization Data Fusion and Integration Data Aggregation

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Multiscale dynamic visualization of signal transduction processes with detailing of target-genes activation in three-dimensional genome structure 6th

Multiscale dynamic visualization of signal transduction proc...

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6th Annual International Young Scientists Conference on HPC and Computational Science (YSC)

作者： Bureiko, Kseniia Semashko, Maria Mukhina, Ksenia D. Karsakov, Andrey ITMO Univ St Petersburg Russia

Given the complexity of modem biological data it is essentially crucial to accord a consistent expounding. Interpreting such data into complex networks and visualizing them can reveal understanding of various processes in a cell. A consequence mapping of signal transduction processes to the spatial genome structure can benefit new insights in interaction detection in the spatial arrangement of genes. We present an approach for multiscale dynamic visualization of signal transduction processes with detailing of target-genes activation in spatial genome structure. The usage of this approach is demonstrated for the WNT signaling pathway in a human cell. We conclude with suggesting future research questions to improve our approach by considering new available data. (C) 2018 The Authors. Published by Elsevier B.V.

关键词： bioinformatics visualization signaling pathways spatial genome structure

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GeneShelf: A Web-based Visual Interface for Large Gene Expression Time-Series Data Repositories

GeneShelf: A Web-based Visual Interface for Large Gene Expre...

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IEEE Information visualization Conference/IEEE visualization Conference

作者： Kim, Bohyoung Lee, Bongshin Knoblach, Susan Hoffman, Eric Seo, Jinwook Seoul Natl Univ Seoul 151 South Korea

A widespread use of high-throughput gene expression analysis techniques enabled the biomedical research community to share a huge body of gene expression datasets in many public databases on the web. However, current gene expression data repositories provide static representations of the data and support limited interactions. This hinders biologists from effectively exploring shared gene expression datasets. Responding to the growing need for better interfaces to improve the utility of the public datasets, we have designed and developed a new web-based visual interface entitled GeneShelf (hftp://***/GeneShelf). It builds upon a zoomable grid display to represent two categorical dimensions. It also incorporates an augmented timeline with expandable time points that better shows multiple data values for the focused time point by embedding bar charts. We applied GeneShelf to one of the largest microarray datasets generated to study the progression and recovery process of injuries at the spinal cord of mice and rats. We present a case study and a preliminary qualitative user study with biologists to show the utility and usability of GeneShelf.

关键词： bioinformatics visualization augmented timeline animation zoomable grid gene expression profiling

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Implicit Representation of Molecular Surfaces

Implicit Representation of Molecular Surfaces

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5th IEEE Pacific visualization Symposium

作者： Parulek, Julius Viola, Ivan Univ Bergen Dept Informat N-5020 Bergen Norway

ISBN: (纸本)9781467308649

Molecular surfaces are an established tool to analyze and to study the evolution and interaction of molecules. One of the most advanced representations of molecular surfaces is called the solvent excluded surface. We present a novel and a simple method for representing the solvent excluded surfaces (SES). Our method requires no precomputation and therefore allows us to vary SES parameters outright. We utilize the theory of implicit surfaces and their CSG operations to compose the implicit function representing the molecular surface locally. This function returns a minimal distance to the SES representation. Additionally, negative values of the implicit function determine that the point lies outside SES whereas positive ones that the point lies inside. We describe how to build this implicit function composed of three types of patches constituting the SES representation. Finally, we propose a method to visualize the iso-surface of the implicit function by means of ray-casting and the set of rendering parameters affecting the overall performance.

关键词： visualization of Molecular Surfaces Geometrical Modeling Implicit Surfaces bioinformatics visualization

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Boundary Labeling Methods for Dynamic Focus Regions

Boundary Labeling Methods for Dynamic Focus Regions

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IEEE Pacific visualization Symposium (PacificVis)

作者： Heinsohn, Niklas Gerasch, Andreas Kaufmann, Michael Univ Tubingen Dept Comp Sci Tubingen Germany

ISBN: (纸本)9781479928736

The display of data related to graphical objects on a map is a well studied problem in cartography and several approaches have been published. Adapting the idea of boundary labeling using a focus region, we face the problem of emphasizing additional information and labels for objects within a focus region even when the region might be moving. We propose four different approaches that support effective solutions in various ways, and discuss advantages and drawbacks. Our algorithms regard the dynamic nature of the focus region to place the labels and preserve the mental map of the analyzed drawing. We demonstrate our methods by applying them to biological networks.

关键词： biology computing biological networks boundary labeling methods cartography dynamic focus regions graphical objects mental map Biology Data visualization Force Gaussian distribution Heuristic algorithms Labeling visualization bioinformatics visualization Focus + Context Techniques Visual Knowledge Discovery

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iDotter - an interactive dot plot viewer 25

iDotter - an interactive dot plot viewer

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25th International Conference on Central Europe on Computer Graphics, visualization and Computer Vision (WSCG)

作者： Gerighausen, Daniel Hausdorf, Alrik Zaenker, Sebastian Zeckzer, Dirk Univ Leipzig Image & Signal Proc Grp Leipzig Germany Univ Leipzig Bioinformat Leipzig Germany

ISBN: (纸本)9788086943497

Bioinformaticians judge the likelihood of the overall RNA secondary structure based on comparing its base pair probabilities. These probabilities can be calculated by various tools and are frequently displayed using dot plots for further analysis. However, most tools produce only static dot plot images which restricts possible interactions to the capabilities of the respective viewers (mostly PostScript-viewers). Moreover, this approach does not scale well with larger RNAs since most PostScript viewers are not designed to show a huge number of elements and have only legacy support for PostScript. Therefore, we developed iDotter, an interactive tool for analyzing RNA secondary structures. iDotter overcomes the previously described limitations providing multiple interaction mechanisms facilitating the interactive analysis of the displayed data. According to the biologists and bioinformaticians that regularly use out interactive dot plot viewer, iDotter is superior to all previous approaches with respect to facilitating dot plot based analysis of RNA secondary structures.

关键词： bioinformatics visualization Tabular Data User Interfaces Dot Plots

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ABySS-Explorer: Visualizing Genome Sequence Assemblies

ABySS-Explorer: Visualizing Genome Sequence Assemblies

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IEEE Information visualization Conference/IEEE visualization Conference

作者： Nielsen, Cydney B. Jackman, Shaun D. Birol, Inanc Jones, Steven J. M. BC Cancer Agency Genome Sciences Centre Canada

One bottleneck in large-scale genome sequencing projects is reconstructing the full genome sequence from the short sub-sequences produced by current technologies. The final stages of the genome assembly process inevitably require manual inspection of data inconsistencies and could be greatly aided by visualization. This paper presents our design decisions in translating key data features identified through discussions with analysts into a concise visual encoding. Current visualization tools in this domain focus on local sequence errors making high-level inspection of the assembly difficult if not impossible. We present a novel interactive graph display, ABySS-Explorer, that emphasizes the global assembly structure while also integrating salient data features such as sequence length. Our tool replaces manual and in some cases pen-and-paper based analysis tasks, and we discuss how user feedback was incorporated into iterative design refinements. Finally, we touch on applications of this representation not initially considered in our design phase, suggesting the generality of this encoding for DNA sequence data.

关键词： bioinformatics visualization design study DNA sequence genome assembly

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Color Illusions on Liquid Crystal Displays and Design Guidelines for Information visualization

Color Illusions on Liquid Crystal Displays and Design Guidel...

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作者： Yoo, Hyun Seung Virginia Tech | University

The influence of color on size and depth perception has been explored for a century, but there is very limited research on interventions that can reduce the color illusions. This study was motivated to identify interv... 详细信息

This study replicated the color size illusion and color depth illusion on an LCD monitor and it was found that yellow is the smallest and farthest color among red, yellow, green, and blue on a white background. Three types of interventions (background brightness, border color, and background grid brightness) were tested to identify the conditions that reduce the color illusions, but all of them were not statistically significant.

Based on the experiment results and literature survey, design guidelines were proposed. To extend the guidelines to the bioinformatics field, design recommendations were proposed and implementation examples were illustrated. Evaluations on design implementations were evaluated by interviewing domain experts.

Additionally, the relationship between the color size illusion and the color depth illusion was explored.

关键词： Design Guideline Apparent Depth Apparent Size Color Depth Illusion Color Size Illusion bioinformatics visualization Thesis

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Generalized box-plot for root growth ensembles

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BMC bioinformatics 2017年第Sup2期18卷 65-65页

作者： Vad, Viktor Cedrim, Douglas Busch, Wolfgang Filzmoser, Peter Viola, Ivan TU WIEN Karlspl 13 A-1040 Vienna Austria Univ Sao Paulo ICMC BR-15260 Sao Carlos SP Brazil Gregor Mendel Inst Mol Plant Biol GmbH Dr Bohr Gasse 3 A-1030 Vienna Austria

Background: In the field of root biology there has been a remarkable progress in root phenotyping, which is the efficient acquisition and quantitative description of root morphology. What is currently missing are means to efficiently explore, exchange and present the massive amount of acquired, and often time dependent root phenotypes. Results: In this work, we present visual summaries of root ensembles by aggregating root images with identical genetic characteristics. We use the generalized box plot concept with a new formulation of data depth. In addition to spatial distributions, we created a visual representation to encode temporal distributions associated with the development of root individuals. Conclusions: The new formulation of data depth allows for much faster implementation close to interactive frame rates. This allows us to present the statistics from bootstrapping that characterize the root sample set quality. As a positive side effect of the new data-depth formulation we are able to define the geometric median for the curve ensemble, which was well received by the domain experts.

关键词： Uncertainty visualization bioinformatics visualization Curve ensembles

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Dynamic visualization of coexpression in systems genetics data

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IEEE TRANSACTIONS ON visualization AND COMPUTER GRAPHICS 2008年第5期14卷 1081-1094页

作者： New, Joshua Kendall, Wesley Huang, Jian Chesler, Elissa Univ Tennessee Dept Elect Engn & Comp Sci Knoxville TN 37996 USA Oak Ridge Natl Lab Mammalian Genet & Genom Biosci Div Oak Ridge TN 37831 USA

Biologists hope to address grand scientific challenges by exploring the abundance of data made available through microarray analysis and other high-throughput techniques. However, the impact of this large volume of data is limited unless researchers can effectively assimilate the entirety of this complex information and integrate it into their daily research;interactive visualization tools are called for to support the effort. Specifically, typical studies of gene coexpression can make use of novel visualization tools that enable the dynamic formulation and fine-tuning of hypotheses to aid the process of evaluating sensitivity of key parameters and achieving data reduction. These tools should allow biologists to develop an intuitive understanding of the structure of biological networks and discover genes that reside in critical positions in networks and pathways. By using a graph as a universal data representation of correlation in gene expression data, our novel visualization tool employs several techniques that when used in an integrated manner provide innovative analytical capabilities. Our tool for interacting with gene coexpression data integrates techniques such as graph layout, qualitative subgraph extraction through a novel 2D user interface, quantitative subgraph extraction using graph-theoretic algorithms or by querying an optimized B-tree, dynamic level-of-detail graph abstraction, and template-based fuzzy classification using neural networks. We demonstrate our system using a real-world workflow from a large-scale systems genetics study of mammalian gene coexpression.

关键词： visualization in physical sciences life sciences and engineering graph and network visualization bioinformatics visualization focus plus context techniques

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