VIPER

01/08/2010 - 31/01/2012

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The implementation of a software tool for analysing large and complex pedigree genotype datasets (thousands of individuals genotyped for thousands of markers). The tool will combine genetic inference algorithms that report inheritance inconsistencies for marker genotypes across the pedigree with an information visualisation interface that allows the user to explore inheritance patterns in the context of the pedigree structure. This interface will assist the user in identifying the likely root data point errors that generate the reported inheritance inconsistencies, allow the user to explore the consequences of masking and editing problematic genotypes and hence facilitate data cleansing of bad data points.
VIPER is a Research Councils project funded by BBSRC. Carried out in collaboration with and others. For further information please refer to http://www.viper-project.org.uk/.
 
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Collaborators link icon

  • Roslin Institute
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Areas of Expertise link icon

  • Information Visualisation
    Information visualisation is the use of enhanced Graphical User Interfaces (GUIs) to communicate and interact with complex data sets such as social networks, multiattribute tables, and financial data. Pages of text and numbers are not the most effective way to communicate or understand information.
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Project Team

Dr Martin Graham
(not currently an institute member)
Jessie Kennedy
Dean of Research and Innovation
j.kennedy@napier.ac.uk
+44 131 455 2772

Associated Publications

Kennedy, J., Graham, M., Paterson, T., Law, A. (2013). Visual Cleaning of Genotype Data. In: (Ed.) Proceedings of BioVis 2013, , () ( ed.). (pp. 105-112). : . IEEE Computer Society Press.

Graham, M., Kennedy, J., Paterson, T., Law, A. (2012). Redeeming Pedigree Data with an Interactive Error Cleaning Visualisation. In: Tortora, G., Levialdi, S., Tucci, M. (Eds.) Proceedings of Advanced Visual Interfaces 2012, , () ( ed.). (pp. 741-744). : . ACM New York, NY, USA.

Paterson, T., Graham, M., Kennedy, J., Law, A. (2012). VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees. BMC Bioinformatics, 13 (Suppl 8), (S5), .

Graham, M., Kennedy, J., Paterson, T., Law, A. (2011). Visualising Errors in Animal Pedigree Genotype Data. Computer Graphics Forum, 30, (3), 1011-1020.

Kandel, S., Heer, J., Plaisant, C., Kennedy, J., Ham, F., Riche, N., Weaver, C., Lee, B., Brodbeck, D., Buono, P. (2011). Research directions in data wrangling: Visualizations and transformations for usable and credible data. Information Visualization, October 2011, (10), 271-288.

Paterson, T., Graham, M., Kennedy, J., Law, A. (2011). Evaluating the VIPER pedigree visualisation: detecting inheritance inconsistencies in genotyped pedigrees. In: (Ed.) Proc. of IEEE BioVis 2011, , () ( ed.). (pp. 119-126). Providence, RI, USA: . IEEE Computer Society Press.

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