Life Science Research and Drug Discovery at the Turn of the 21st Century: The Experience of SwissBioGrid

  • Matthijs den Besten Oxford e-Research Centre
  • Arthur J. Thomas Oxford Internet Institute
  • Ralph Schroeder Oxford Internet Institute

Abstract

Background It is often said that the life sciences are transforming into an information science. As laboratory experiments are starting to yield ever increasing amounts of data and the capacity to deal with those data is catching up, an increasing share of scientific activity is seen to be taking place outside the laboratories, sifting through the data and modelling “in silico” the processes observed “in vitro.” The transformation of the life sciences and similar developments in other disciplines have inspired a variety of initiatives around the world to create technical infrastructure to support the new scientific practices that are emerging. The e-Science programme in the United Kingdom and the NSF Office for Cyberinfrastructure are examples of these. In Switzerland there have been no such national initiatives. Yet, this has not prevented scientists from exploring the development of similar types of computing infrastructures. In 2004, a group of researchers in Switzerland established a project, SwissBioGrid, to explore whether Grid computing technologies could be successfully deployed within the life sciences. This paper presents their experiences as a case study of how the life sciences are currently operating as an information science and presents the lessons learned about how existing institutional and technical arrangements facilitate or impede this operation. Results SwissBioGrid gave rise to two pilot projects: one for proteomics data analysis and the other for high-throughput molecular docking (“virtual screening”) to find new drugs for neglected diseases (specifically, for dengue fever). The proteomics project was an example of a data management problem, applying many different analysis algorithms to Terabyte-sized datasets from mass spectrometry, involving comparisons with many different reference databases; the virtual screening project was more a purely computational problem, modelling the interactions of millions of small molecules with a limited number of protein targets on the coat of the dengue virus. Both present interesting lessons about how scientific practices are changing when they tackle the problems of large-scale data analysis and data management by means of creating a novel technical infrastructure. Conclusions In the experience of SwissBioGrid, data intensive discovery has a lot to gain from close collaboration with industry and harnessing distributed computing power. Yet the diversity in life science research implies only a limited role for generic infrastructure; and the transience of support means that researchers need to integrate their efforts with others if they want to sustain the benefits of their success, which are otherwise lost.

Author Biographies

Matthijs den Besten, Oxford e-Research Centre
Matthijs den Besten is James Martin research fellow at the Oxford e-Research Centre of the University of Oxford.
Arthur J. Thomas, Oxford Internet Institute
Research Associate with the Oxford Internet Institute
Ralph Schroeder, Oxford Internet Institute
Senior Research Fellow at the Oxford Internet Institute
Published
2009-04-21
How to Cite
den Besten, M., Thomas, A. J., & Schroeder, R. (2009). Life Science Research and Drug Discovery at the Turn of the 21st Century: The Experience of SwissBioGrid. DISCO: Journal of Biomedical Discovery and Collaboration, 4, 5. https://doi.org/10.5210/disco.v4i0.2452
Section
Articles