Open-source lab launches in Australia
On June 11, 2013, Queensland University of Technology (QUT) launched the Open Source Software Group and Virtual Lab at the university’s new Science and Engineering Center in the heart of Brisbane. This exciting venture will enable students to create software solutions for real-world problems—through emerging projects, such as Glycogen (a learning environment built for the One Laptop per Child initiative); through hackathons built around the D3.js visualization libraries, making open data in biology and healthcare visible to all; and through global competitions such as QUT’s Change the World series and Microsoft Imagine Cup.
The new Science and Engineering Centre (left) on the QUT campus
The launch represents the culmination of hard work by QUT, along with support from Microsoft Research, the Microsoft Australian subsidiary, Red Hat Asia Pacific, and Technology One, a Brisbane-based enterprise software company. Each of these partners sees value in working cooperatively on open-source projects, understanding the model of community driven projects operating hand-in-hand with commercial services and products. The launch activities included a keynote address by Pia Waugh, a veteran of the Australian open-source community and now a leading figure in such open-government initiatives as GovHack.
The Open Source Software Group and Virtual Lab will take a leading role in the .NET Bio project, an open-source library of common bioinformatics functions that simplifies the creation of life-science applications for the Windows platform. In fact, QUT students are already authoring extensions to the library’s core algorithms and developing new pattern-matching components that will allow complex, structured searches across genomes. Other students are working to link .NET Bio parsing and search capabilities to open-visualization tools, allowing better understanding of the structure of genomes and their regulatory systems.
The Open Source Software Group and Virtual Lab is located in QUT’s state-of-the-art Science and Engineering Center.
In one key project under development, QUT students are building a new toolset on top of .NET Bio to simplify population studies in human disease. The new tools will support the analysis of samples from multiple individuals by using next-generation sequencing techniques. These approaches, a variant of restriction-site associated DNA sequencing (better known as RADseq), allow identification of subtle genomic differences that are important markers of diseases. The .NET Bio library will provide an integrated platform for these analyses, with the important additional benefit of allowing direct interaction with tools such as Microsoft Excel, enabling researchers to capture and further analyze results in a familiar environment.
Microsoft Research is pleased to support QUT’s exciting open-source venture, and we will be looking for great things to emerge from Down Under!
—Simon Mercer, Director, Health and Wellbeing, Microsoft Research Connections