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inPHAP

inPHAP is an interactive visualization tool for genotype and phased haplotype data. inPHAP features a variety of interaction possibilities such as zooming, sorting, filtering and aggregation of rows in order to explore patterns hidden in large genetic data sets. As a proof of concept, we apply inPHAP to the phased haplotype data set of Phase 1 of the 1000 Genomes Project. Thereby, inPHAP's ability to show genetic variations on the population as well as on the individuals level is demonstrated for several disease related loci.

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Institution: University of Tübingen

Deutsche Forschungsgemeinschaft and Open Access Publishing Fund of Tübingen University supported this project.

VIPER

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. 

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Institution: The Roslin Institute University of Edinburgh, School of Computing Edinburgh Napier University

LayerCake

LayerCake is a tool designed to assist in the exploration of the genetic variability of the population of viruses at multiple time points and in multiple individuals, a task that necessitates considering large amounts of sequence data and the quality issues inherent in obtaining such data in a practical manner. This design affords the examination of the amount of variability and mutation at each position in the genome for many populations of viruses. This design contains novel visualization techniques that support this specific class of analysis while addressing the issues of data aggregation, confidence visualization, and interaction support that arise when making use of large amounts of sequence data with variable uncertainty. These techniques generalize to a wide class of visualization problems where confidence is not known a priori, and aggregation in multiple directions is necessary.

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Institution: University of Wisconsin, Madison

This work was supported by NSF awards IIS-0946598 and CMMI-0941013. Related virology research was supported by NIH R01 AI084787.

iHAT

The iHAT prototype tool supports the visualization of multiple sequence alignments, associated metadata, and hierarchical clusterings. Moreover, data-type dependent colormaps and aggregation strategies as well as different filtering options support the user in finding correlations between sequences and metadata. Similar to other visualizations such as parallel coordinates or heatmaps, iHAT is aimed at exploiting the human pattern-recognition ability for spotting patterns that might indicate correlation or anticorrelation. Together with its interactive features and a database backend for fast data retrieval, iHAT is a prototype for a visual analytics system for genome-wide association studies.

See the project page for further details.

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Institution: VISUS – Visualization Research Center, University of Stuttgart, Germany; University of Tuebingen, Germany

Vesper

VESpeR is a suite of web-based visualisation components that enable biologists to investigate the taxonomic, temporal and geographic coverage of DWCA species-referenced data that can be placed directly into the workflow of biologists who use such data. VESpeR allows biologists to perform tasks such as sanity checking of data, view patterns in geographical, taxonomic or temporal aspects in an interrelated context, and accurately view data even when it spans conflicting taxonomic classifications. This can make a significant contribution to the efficiency and usability of online catalogues for both the providers and end-users of the data they hold. Co-ordinated components The components are co-ordinated such that selections and actions in one component will be reflected in the data shown in other components. VESpeR multiple views VESpeR includes

  • a novel cross-taxonomy viewer that allows users to crosswalk different classifications, allowing them to accurately match specimens between data from different sources
  • interactive map to investigate specimen geographic coverage
  • interactive timeline to investigate specimen temporal coverage
  • sanity checker to view data completeness and vocabulary size

Bio-visualisation Visualisation techniques have been recognised as one of the major directions in future research when handling and querying biological data, offering the ability to find patterns and outliers in data which traditional query interfaces cannot match. A case in point is the multitude of species-referenced databases covering data from genomic to biodiversity data linked by taxonomic classifications that hold geographic and temporal-faceted data alongside other data. Many online databases hold collections of such data, often in archive format, but visual querying tools are invariably limited to a map interface of spatial distribution, neglecting the fact that biologists may wish to query or explore other facets of the data such as the classification or temporal distribution. Add onto this the problem of many complementary databases using different taxonomic classifications to reference their specimens and we have a situation where much of the potential utility of this data remains unused. VESpeR is designed to help address this.

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Institution: IIDI

VESpeR is a project at the Institute for Informatics and Digital Innovation. The Institute is part of Edinburgh Napier University based in Scotland, United Kingdom. At the Institute for Informatics & Digital Innovation we are dedicated to helping you and your organisation deal with new digital challenges and opportunities as they arise. We can help you to look ahead and shape our digital future. We work across every field of computer technology from sensors and mobile networks to data intensive applications requiring intelligent processing and filtering. We can help you explore not just the technology but how people interact with the technology and how it impacts on society. www.iidi.napier.ac.uk Tel: +44 (0)131 455 2651 Email: iidi@napier.ac.uk

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