Helium: visualization of large scale plant pedigrees

Paul D Shaw*, Martin Graham, Jessie Kennedy, Iain Milne, David F Marshall

*Corresponding author for this work

Research output: Contribution to journalArticle

15 Citations (Scopus)

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.

Original languageEnglish
Article number259
JournalBMC Bioinformatics
Volume15
DOIs
Publication statusPrint publication - 1 Aug 2014
Externally publishedYes

Fingerprint

Pedigree
Helium
Visualization
Climate change
Integrate
Prototype
User Evaluation
Subjective Evaluation
Disease Resistance
Barley
Line
Climate Change
Hordeum
Range of data

Keywords

  • Alleles
  • Breeding
  • Computational Biology/methods
  • Cooperative Behavior
  • Genotype
  • Hordeum/genetics
  • Phenotype
  • Phylogeny

Cite this

Shaw, Paul D ; Graham, Martin ; Kennedy, Jessie ; Milne, Iain ; Marshall, David F. / Helium : visualization of large scale plant pedigrees. In: BMC Bioinformatics. 2014 ; Vol. 15.
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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.",
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Helium : visualization of large scale plant pedigrees. / Shaw, Paul D; Graham, Martin; Kennedy, Jessie; Milne, Iain; Marshall, David F.

In: BMC Bioinformatics, Vol. 15, 259, 01.08.2014.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Helium

T2 - visualization of large scale plant pedigrees

AU - Shaw, Paul D

AU - Graham, Martin

AU - Kennedy, Jessie

AU - Milne, Iain

AU - Marshall, David F

PY - 2014/8/1

Y1 - 2014/8/1

N2 - 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.

AB - 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.

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KW - Computational Biology/methods

KW - Cooperative Behavior

KW - Genotype

KW - Hordeum/genetics

KW - Phenotype

KW - Phylogeny

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DO - 10.1186/1471-2105-15-259

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