Software Development for Genetics, Genetic Resources and Plant Breeding

The Software Development Group within Information and Computational Sciences at the James Hutton Institute are involved in the development of bespoke applications, database systems and tools to facilitate the analysis, quality control and visualization of genetic, genetic resources and plant breeding data. While predominantly working with barley, the group also has links to Lolium and Festuca (Germinate Grasses) in collaboration with the Institute of Experimental Botany in Oloumouc, Czech Republic and Wheat and Maize as part of the Seeds of Discovery programme run from CIMMYT in Mexico. The Germinate platform is also used to support the storage of data from other species including potato (Germinate CPC) with the James Hutton Institute Potato Group and pea (Germinate Pea) in collaboration with the University of Dundee and the John Innes Centre in Norwich.

The work carried out by the group is broken down into two main areas, database development and visualization software development. Germinate forms the core of the database development work by the group and is used to hold data from a number of diverse data types including genotypic, passport, phenotypic and pedigree data types. It provides both a web-based user interface and acts as a hub from which other analysis tools such as Helium and Flapjack can connect.

We also have a number of information visualization tools which we have developed including Helium (pedigree visualization), Flapjack (graphical genotyping), Tablet (NGS visualization), CurlyWhirly (3D scatter plot) and Strudel (comparative map viewer). For more information on these tools please visit our software pages on the Information and Computational Sciences website (http://ics.hutton.ac.uk).

More recently we have been looking at using mobile technology to allow us to help in the collection of experimental data as a means to reduce the overhead of handling this sort of data and to try and reduce data collection errors. Tools such as Germinate Scan allow users to connect external bar code readers to Android based devices to allow the quick and efficient collection of data.

PrintFor further information on this work please contact Paul Shaw (paul.shaw@hutton.ac.uk) from the James Hutton Institute.