title: Helium: visualization of large scale plant pedigrees.
abstract: BACKGROUND
  Plant breeders use an increasingly diverse range of data types to identify lines with desirable characteristics suitable to be taken forward in plant breeding programmes. There are a number of key morphological and physiological traits, such as disease resistance and yield that need to be maintained and improved upon if a commercial variety is to be successful. Computational tools that provide the ability to integrate and visualize this data with pedigree structure, will enable breeders to make better decisions on the lines that are used in crossings to meet both the demands for increased yield/production and adaptation to climate change.
  
  
  RESULTS
  We have used a large and unique set of experimental barley (H. vulgare) data to develop a prototype pedigree visualization system. We then used this prototype to perform a subjective user evaluation with domain experts to guide and direct the development of an interactive pedigree visualization tool called Helium.
  
  
  CONCLUSIONS
  We show that Helium allows users to easily integrate a number of data types along with large plant pedigrees to offer an integrated environment in which they can explore pedigree data. We have also verified that users were happy with the abstract representation of pedigrees that we have used in our visualization tool.
authors.affiliation: Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK. paul.shaw@hutton.ac.uk.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Shaw
authors.forename: Martin
authors.initials: M
authors.lastname: Graham
authors.forename: Jessie
authors.initials: J
authors.lastname: Kennedy
authors.forename: Iain
authors.initials: I
authors.lastname: Milne
authors.forename: David F
authors.initials: DF
authors.lastname: Marshall
mesh_terms: D000483:Alleles; D001947:Breeding; D019295:Computational Biology / Q000379:methods*; D003299:Cooperative Behavior; D005838:Genotype; D001467:Hordeum / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny
references.citation: Bioinformatics. 2007 Jul 15;23(14):1854-6
references.pmid: 17488757
references.citation: IEEE Trans Vis Comput Graph. 2012 Dec;18(12):2431-40
references.pmid: 26357151
references.citation: Bioinformatics. 2005 Apr 15;21(8):1730-2
references.pmid: 15377505
references.citation: Bioinformatics. 2006 Apr 15;22(8):1013-4
references.pmid: 16488908
references.citation: Philos Trans R Soc Lond B Biol Sci. 2005 Nov 29;360(1463):2139-48
references.pmid: 16433099
references.citation: IEEE Trans Vis Comput Graph. 2009 Nov-Dec;15(6):921-8
references.pmid: 19834155
references.citation: IEEE Trans Vis Comput Graph. 2009 Nov-Dec;15(6):1121-8
references.pmid: 19834180
references.citation: IEEE Trans Vis Comput Graph. 2012 Sep;18(9):1520-36
references.pmid: 22144529
references.citation: Eur J Hum Genet. 2005 Aug;13(8):987-9
references.pmid: 15870825
references.citation: BMC Bioinformatics. 2012;13 Suppl 8:S5
references.pmid: 22607476
references.citation: Genome Inform Ser Workshop Genome Inform. 2000;11:63-72
references.pmid: 11700588
references.citation: IEEE Trans Vis Comput Graph. 2010 Nov-Dec;16(6):1063-72
references.pmid: 20975144
references.citation: J Hered. 2005 Jul-Aug;96(4):465-8
references.pmid: 15829728
references.citation: IEEE Trans Vis Comput Graph. 2010 Nov-Dec;16(6):1073-81
references.pmid: 20975145
references.citation: Bioinformatics. 2010 Dec 15;26(24):3133-4
references.pmid: 20956241
references.citation: Bioinformatics. 2005 Aug 15;21(16):3445-7
references.pmid: 15947021
references.citation: Am J Hum Genet. 1995 Mar;56(3):745-52
references.pmid: 7887430
references.citation: Bioinformatics. 2008 May 1;24(9):1210-1
references.pmid: 18346980
references.citation: J Hered. 2012 Nov-Dec;103(6):903-7
references.pmid: 23087384