March 27,2007 — Joint ICM UW/LCB UU Seminar

The joint ICM LCB bioinformatics seminar will be held on March 28 at 10:15. Seminar will be transmitted by Marratech software. Due to technical problems in Uppsala only one way communication will be possible..
Professor Ron D. Appelds, a member of Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Computer Science Department at Geneva University and Geneva Bioinformatics (GeneBio) SA, Geneva, Switzerland, will deliver the lecture :
“Analytical bioinformatics: from data to knowledge”

Bioinformatics is the application of computer sciences to molecular biology, and in particular to the study of macromolecules such as proteins, nucleic acids and oligosaccharides. It encompasses many diverse aspects, such as the development and annotation of protein or DNA sequence databases, the development of programs to analyse the intrinsic properties of DNA or protein sequences, or three-dimensional structure visualisation and modelling tools. Analytical bioinformatics focuses on the computational analysis of experimental biological data, such as micro-array data, genome sequencing data or proteomics data. The proteome is the protein complement of the genome, i.e. the set of expressed genes (proteins) in a given organism, at a given point in time, in a given situation. Proteomics deals with the qualitative and quantitative analysis and comparison of proteomes under different conditions to further unravel biological processes. Proteomics experiments typically separate proteins in biological samples using techniques such as two-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), followed by high resolution mass spectrometry (MS) analysis. These experiments produce up to thousands of mass spectra per day that must be analysed on efficient informatics platforms in order to extract pertinent biological knowledge. Analytical bioinformatics provides imaging tools to analyse the results of the protein separation step (2-DE or LC), powerful identification and characterisation software from MS data, as well as databases containing annotated data resulting from the analysis of experimental data.

The Swiss Institute of Bioinformatics (SIB) coordinates the activities of currently eighteen bioinformatics groups throughout Switzerland in association with seven universities and research institutes, carrying out services, education and research in many areas of bioinformatics. At the Proteome Informatics Group (PIG) of SIB and its sister company Geneva Bioinformatics (GeneBio) SA, in collaboration with the Biomedical Proteomics Research Group (BPRG) at Geneva University, we have been developing several platforms for high-confidence analysis of proteomics data. Melanie is a software architecture for image analysis that served as the basis for two software packages. One is ImageMaster for 2-DE image analysis, the other one is MSight, a comprehensive package for the analysis of MS data obtained after protein or peptide separation, such as LC-MS or electrophoresis-MS. The software allows for differential analysis as well as for quality control of experimental design, data exploration and linking to identification results. Phenyx provides efficient identification of proteins from MS-MS data. A new platform, swissPIT, is designed for the analysis of MS-MS data using several identification engines (currently Phenyx and X!Tandem) and two characterization software (Popitam and InsPecT), giving access to automated protein identification and characterization through a unique Web portal. The platform runs on the SwissBioGrid environment for high-throughput usage. The various tools offer tight integration among themselves and with external data sources.

| March 23rd, 2007 | Posted in Uncategorized |

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