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XCluSim

  A visual analytics tool for interactively comparing multiple clustering results of bioinformatics data based on the Visual Information Seeking Mantra. We build a taxonomy for categorizing existing techniques of clustering results visualization in terms of the Gestalt principles of grouping. Using the taxonomy, we choose the most appropriate interactive visualizations for presenting individual clustering results from different types of clustering algorithms.

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Institution: Seoul National University

This work and publication was partly supported by the National Research Foundation of Korea (NRF) grants funded by the Korea government of MSIP (No. NRF-2014R1A2A2A03006998) and by the Korea government of MEST (No. 2011-0030813). BK (Kim) was supported by the Seoul National University Bundang Hospital Research Fund (No. 12-2013-017).

Cell-o-pane: a cell lineage visualisation tool

Cell-o-pane was developed to assist scientists in understanding fundamental cellular processes captured by cell lineage data sets. This includes the study of cell differentiation and the pharmacodynamic action of anticancer agents. To achieve this, Cell-o-pane was designed to emphasise three important properties:

  • Multimodality: cell lineages combine spatial, temporal, and other properties;
  • Symmetry: which characterises the lineage branching structure; and
  • Synchrony: which is related to temporal alignment of cellular events.

Our approach has been valuable for determining the cytotoxic action of anticancer drugs.

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Institution: University of Leeds

FoldSynth

Abstract: FoldSynth is an interactive multimedia platform designed to help understand the characteristics and commonly used visual abstractions of molecular strands with an emphasis on proteins. It uses a simple model of molecular forces to give real time interactive animations of the folding and docking processes. The shape of a molecular strand is shown as a 3D visualisation floating above a 2D triangular matrix representing distance constraints, contact maps or other features of residue pairs. As well as more conventional raster plots, contact maps can be shown with vectors representing the grouping of contacts as secondary structures. The 2D visualisation is also interactive and can be used to manipulate a molecule, define constraints, control and view the folding dynamically, or even design new molecules.


Keywords: Interaction, multimedia, proteins, folding, 2D/3D, scientific visualisation, molecular design, physically based modelling.

Video (version 0.5): http://www.youtube.com/watch?v=B1wksNB0zvk

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Institution: Goldsmiths, University of London

Pipit

Pipit is a gene-centric interactive visualization tool designed to study structural genomic variations. Through focusing on individual genes as the functional unit, researchers are able to study and generate hypotheses on the biological impact of different structural variations, for instance, the deletion of dosage-sensitive genes or the formation of fusion genes. Pipit is a cross-platform Java application that visualizes structural variation data from Genome Variation Format files.

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Institution: KU Leuven

Gremlin

Gremlin is a novel, interactive visualization model for comparative analysis of structural variants and rearrangements in human and cancer genomes, with emphasis on data integration and uncertainty visualization. Gremli is a genomic rearrangement explorer with multi-scale, linked interactions, which we apply to four human cancer genome data sets for evaluation. Using an insight-based evaluation methodology, we compare Gremlin to Circos, the state-of-the-art in genomic rearrangement visualization, through a small user study with computational biologists working in rearrangement analysis. Results from user study evaluations demonstrate that this visualization model enables more total insights, more insights per minute, and more complex insights than the current state-of-the-art for visual analysis and exploration of genome rearrangements.

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Institution: Brown University

TiBi-Scatter

TiBi-Scatter is a tool enabling correlation analysis in 2D. This approach allows for analyzing multidimensional data while keeping the use of resources such as memory small. Thus, it is in particular applicable to large data sets. Conclusions: TiBi-Scatter is a resource-friendly and easy to use tool that allows for the hypothesis-free analysis of large multidimensional biological data sets.

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Institution: Leipzig University

Gene-RiViT

The Genomic Ring Visualization Tool (Gene-RiViT) is a high speed, intuitive visualization tool for investigating sequence environments of conserved genes among related genomes. Gene-RiViT allows the user to interact with interconnected global and local visualizations of gene neighborhoods and gene order, through a web-based interface that is easily accessible in any browser. The primary visualization is a wheel of nested rotating circles, each of which represents a single genome. This visualization is similar to common circular genome alignment views, except that the rings can be realigned with each other dynamically based on user selections within the ring view or one of the coordinated views. By allowing the user to dynamically realign genomes and focus on a locally conserved region of interest, and using or-thology connections to highlight corresponding structures among genomes, this view provides insight into gene context and preservation of neighbor relationships as genomes evolve. Visualizations are linked into a coordinated multiple view interface to provide multiple selection methods and entry points into the data. These approaches make Gene-RiViT a flexible, unique tool for examining gene neighborhoods that improves on existing methods.

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Institution: University of North Carolina at Charlotte

This work was supported in part by the National Science Foundation, award number 1047896.

Electron Microscopy Visualisation

Serial electron microscopy (EM) has the ability to improve three-dimensional imaging dramatically by providing nanometer-scale resolution. Serial EM data sets of brain tissue can potentially be used to reconstruct the complex structure of biological neural networks. These data sets consist of gigabytes of volumetric data densely packed with anatomical information. This makes three-dimensional EM data sets difficult to visualize.These are new methods for visualizing EM data sets using a novel transfer function based on the local variance of volumetric features.

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Institution: Beckman Institute for Advanced Science and Technology, Department of Computer Science, University of Illinois at Urbana-Champaign

We would like to thank Hans-Jörg Schulz for his input. This work is supported by the following grants: Caleydoplex (P22902, FWF), Tumorheterogeneity (GZ:A3–22.M-5/2012–21, state of Styria), IMGuS (Austria Wirtschaftsservice), and inGeneious (385567, FFG).

INCIDE

This is a software solution for processing recordings of honeybee brain activity in real time. It employs an adaptive algorithm for image processing, along with a fast implementation for the graphics processing unit that enables semantic segmentation in real time. Semantics is based on the temporal dimension, relying on the fact that time series of pixels within a glomerulus are correlated.

 

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Institution: Interdisciplinary Center for Interactive Data Analysis, Modelling and Visual Exploration (INCIDE) and Neurobiology, University of Konstanz, Germany

This work has been carried out within the PhysioIllustration research project (# 218023), which is funded by the Norwegian Research Council.

CAB Visualization

These visual-analytic tools delineate specific structures involving F-actin in cells. Concave actin bundles (CABs) often occur in hybrid cell-seeded fibrillar scaffolds and seem to envelope the fibers, as a possible mechanism of stable attachment. There is much uncertainty that accompanies the detection and the identification of fibers. These tools rely on well-known algorithms of image analysis.

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Institution: The Ohio State University

This work was supported in part by the NIH Grants RC2 AG-036559 and R01 HL-096524 (to NM).

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