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Information Management


The amount of biological information produced each year is growing exponentially. This increases the need for tools that can organize and analyze this wealth of information as well as tools that can "learn" from well-studied areas of biology and predict features of areas where little or nothing is known.


I'm involved in various research projects that roughly can be broken down into three areas; first, information management and analysis, second, method development, and thirdly application, and I prototype most of the code in the DDB software suite. Large-scale computational studies require sophisticated strategies and increasingly rely on heterogeneous infrastructure. Prototyping and testing are generally performed in house on Beowulf-type clusters. In contrast, large scale production-level calculations increasingly are performed in clouds or grids. In 2007, I designed and built Apollo, an 800-core cluster in David Goodlett's lab in collaboration with Greg Taylor. Most of the production work is carried out on the world community grid.


Nr. Reference
7. Kunszt, Peter; Blum, Lorenz; Hullar, Bela; Schmid, Emanuel; Srebniak, Adam; Wolski, Witold; Rinn, Bernd; Elmer, Franz-Josef; Ramakrishnan, Chandrasekhar; Quandt, Andreas; Malmstrom, Lars; Improving the Swiss Grid Proteomics Portal: Requirements and new Features based on Experience and Usability Considerations. conf proc. of the 5th International Workshop on Science Gateways (IWSG 2013), Zurich, 3-5 June 2013, in CEUR Workshop Proceedings Vol 993 (2013), 993: -.
6. Malmstrom, Lars; Nordenfelt, Pontus; Malmstrom, Johan; Business intelligence strategies enables rapid analysis of quantitative proteomics data. Journal of Proteome Science and Computational Biology (2012), 1 (1): -.
5. Bauch, Angela; Adamczyk, Izabela; Buczek, Piotr; Elmer, Franz-Josef; Enimanev, Kaloyan; Glyzewski, Pawel; Kohler, Manuel; Pylak, Tomasz; Quandt, Andreas; Ramakrishnan, Chandrasekhar; Beisel, Christian; Malmstrom, Lars; Aebersold, Ruedi; Rinn, Bernd; openBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinformatics (2011), 12: 468.
4. Kunszt, Peter; Espona Pernas, Lucia; Quandt, Andreas; Schmid, Emanuel; Hunt, Ela; Malmstrom, Lars; The Swiss Grid Proteomics Portal. Proceedings of the Second International Conference on Parallel, Distributed, Grid and Cloud Computing for Engineering (2011), -: 81.
3. Malmstrom, Lars; Marko-Varga, Gyorgy; Westergren-Thorsson, Gunilla; Laurell, Thomas; Malmstrom, Johan; 2DDB - a bioinformatics solution for analysis of quantitative proteomics data. BMC Bioinformatics (2006), 7: 158.
2. Riffle, Michael; Malmstrom, Lars; Davis, Trisha; The yeast resource center public data repository. Nucleic Acids Res (2005), 33: D378-82.
1. Malmstrom, Lars; Malmstrom, Johan; Marko-Varga, Gyorgy; Westergren-Thorsson, Gunilla; Proteomic 2DE database for spot selection, automated annotation, and data analysis. J Proteome Res (2002), 1: 135-8.