Information & Computational Sciences

Helium Technologies and Development

Until now, pedigree visualization, with a few exceptions, has primarily been focussed on work carried out in the human genetics domain. Because plant breeding programmes involve phenomena not normally seen in human populations, such as routine inbreeding, there are additional visualization challenges that need to be overcome. There are often large numbers of plant lines involved in any pedigree, many more so than in an average human pedigree due to factors such as generation time/time to sexual maturity which is far lower in most plant species than that of mammalian counterparts, thus solutions addressing the requirements of human genetics are not a suitable alternative.

The Visual Metaphor

Helium models pedigree data as a DAG (Directed Acyclic Graph). Graphs can be used to visualize the relationship between objects, and, unlike trees, graphs allow for the precise modelling of the complexity of plant breeding programmes. We have used the concept of nodes to represent plant varieties and edges to show mating events (or crossing). In essence, lines going into a node (of which there should be no more than two) are a varieties parents and lines going out from a variety are progeny of the particular variety. In this way complex pedigrees can be atomised into definite units and due to the nature of graph in which they are structured calculations can be performed to check for issues such as inheritance problems which may be indicative of germplasm handling errors.

Helium Development

The initial Helium prototype system was developed in Perl and used the GraphViz dot libraries to generate static bitmap images using one of dots standard layered (Sugiyama) layout algorithms. This, while very effective was lacking in interactive features that would allow scientists to explore their data. To overcome these problems we started work on a Java based interactive desktop application what would take the functionality of our static prototype but allow us to offer additional features that would allow users to explore and interrogate their data.

We use the Germinate platform developed at The James Hutton Institute by Paul Shaw to store our pedigree and underlying genotypic, passport and phenotypic data.

The Java based application uses the yFiles library from yWorks.