Drs. Han Rauwerda,
Swammerdam Institute for Life Sciences,
University of Amsterdam
From seed breeding to research into DNA damage: the results of the University of Amsterdam’s Microarray Department/Integrative Bioinformatics Unit (MAD/IBU) have broad applications. In its research on gene transcription across the entire genome, the MAD/IBU makes intensive use of SURFsara's HPC Cloud. “Whenever we need computing power, we can start up and run the HPC Cloud straight away. It works very nicely,” says MAD/IBU bioinformatician Han Rauwerda.
“We conduct research into how genes are used under different circumstances,” says Rauwerda. “For example: what happens to a person who is sick? Or to a healthy person? What is amazing is that nowadays, we can measure more than a million different transcriptions per sample simultaneously, representing a huge step forward. But it also means that the need for computing power is constantly growing.”
Until now, MAD/IBU research as part of numerous different partnerships has led to many new insights and publications, information that researchers and companies can ultimately use to develop practical applications. “In 2010 we completed over 60 projects for researchers in biology, for which we provided the expertise in the field of gene-transcription analysis. For example: together with the Utrecht UMC, we conduct research into the virulence of various forms of hospital bacteria; another example is research into ageing. We are no experts on ageing, but we do supply the data and analyze it together with the biological experts.”
Rauwerda and his colleagues do their calculations on the SURFsara HPC Cloud, which forms part of the BiG Grid infrastructure. Rauwerda is very happy with it: “The workflow in life sciences is variable and includes a range of elements, something that the HPC Cloud is very suited to. Large calculations can be split up and run parallel. HPC Cloud also allows us to work on demand and install our software easily.”
Rauwerda believes that the Cloud not only has lots to offer in the field of research: “We could also use the Cloud for educational purposes, such as during a practical class. You just turn on the virtual machines at the start of the class, and turn them off again at the end. Teachers would no longer need to prepare twenty computers; just make one image, and clone that. We could also use the Cloud to enable companies to share software, allowing them to collaborate on software development without having to share their data.”
Rauwerda has been working with SURFsara for nearly a decade: “We work together on various projects, including the e-BioGrid project. The partnership is excellent, not least because the project management includes both life scientists and HPC experts. They complement each other, and it works very well.”
Analyzing gene-transcription experiments together with biologists in a space specially designed for the purpose: the e-BioLab.