Researchers studying Pacific migration patterns and viruses such as HIV are benefiting from a new generation of locally-developed grid computing software.
Biomatters and New Zealand’s Bioinformatics Institute at the University of Auckland have released version 2 of its Geneious bioinformatics software for grid computing on BeSTGRID (the Broadband enabled Science and Technology Grid) running on KAREN, the Kiwi Advanced Research and Education Network.
The cross-platform bioinformatics software suite can be used for manipulating, finding, sharing and exploring biological data, such as DNA sequences or proteins, phylogenies, 3D structure information and publications, says Allen Rodrigo, director of the Bioinformatics Institute.
The Geneious grid plug-in allows researchers to seamlessly connect their desktop to BeSTGRID and run the applications from Geneious, says Rodrigo. The plug-in is free to researchers in New Zealand, he says.
The Geneious platform enables users to easily track, manage and analyse their data, says Rodrigo. The plug-ins initially delivered a basic analysis application, but version 2 has some new additions, says Rodrigo. Many of the programs that researchers were using previously were clunky and command-driven, he says, but the new plug-in allows users to generate an XML description of a command-line program and its options.
“Geneious then uses this [XML] script to construct a dialogue box that looks exactly like any other Geneious program,” he says. Users can run the program within the Geneious graphical user interface.
Workflow has been enhanced by automating common processes such as matching and analysing sequences.
The types of software available on BeSTGRID are for example related to looking at genetic information — such as tracing the history of people and animals, and genetic profiles of populations, says Rodrigo.
One of the projects the Bioinfor-matics Institute is currently involved in is looking at the colonisation of the Pacific. “But we are doing it by looking at the animals that would have accompanied the colonists, for example rats,” he says.
Tracking the animals that follow populations is an alternative way of investigating how populations migrate, he adds. Another area of research is virus populations. Rodrigo’s team does research on for example HIV, hepatitis B and the cat equivalent of HIV, feline immunodeficiency virus (FIV), he says.
Biomatters and the Bioinformatics Institute have focused on making the software easy to use for biologists, Rodrigo says.
All applications developed under the project will be open source and freely available to researchers in New Zealand. The applications will work with Biomatters’ free basic version of Geneious desktop software, as well as the expanded version Geneious Pro.
The project is funded by REANNZ and TelstraClear.