CSC

	Tehdyt toimenpiteet Turku Centre for Biotechnology Bioinformatics core facility Group leader: Stephen Rudd Home page: http://www.btk.fi/TCB_Personnel/ID_Cards/id_cards_140.html The bioinformatics core facility at the Centre for Biotechnology is acting as a support infrastructure for scientists within the BioCity Turku initiative. The bulk of our time and energy is currently utilised in a fruitful cooperation with the Finnish DNA microarray centre that is also located at the Centre for Biotechnology. We are providing critical systems within production, quality and analysis of expression data experiments. These systems may be summarized as: Laboratory information management systems (LIMS). This production software is used to track the features that are arrayed on in-house cDNA and oligonucleotide microarrays, The database is used in the process of quality control, production and in the generation of GAL files for the end users of a physical array Array reannotation services. Typical annotation associated with a commercial array, or even the features on in-house arrays tend to be minimal and do not form a suitable substrate for meaningful hypothesis based data analysis. Typical GAL files are reannotated to add additional nuance of function, structure and metabolic pathway. Using the openSputnik genome database that has been developed in house we add additional layers of user-specified annotation to our datasets. Microarray database. We are developing a MIAME-MAGE compliant microarray database. This is planned as a central repository for all in-house data. The resource will also be scaled up to include large sets of relevant public expression data - this will include all array experimental data from human, mouse and other species that are being actively used within our research sphere. Microarray data analysis. We are using the Inforsense Knowledge Discovery Edition to perform in depth analysis and annotation within and across large microarray datasets. We have additionally developed various other in-house statistical modules that we would like to make available to other Finnish researchers. This will require some commitment from CSC to provide access to the required development kit. We provide microarray data analysis as a service to all researchers in Finland. Research and development. We are actively trying, testing and evaluating other software packages that might provide quantitative or qualitative improvements to user experiences within the field of microarray analysis. In additon to our roles within microarray analysis the Bioinformatics group has an active research function. We have developed the openSputnik platform for comparative and functional genomics for trait discovery and characterisation. We provide the largest and most comprehensive plant EST database worldwide and perform bioinformatics and genomics research into genome evolution and adaptation. We concentrate on the lower plant clades of hornworts, lycophytes and ferns. In promoting a holistic view of the contemporary edges of the biological sciences were are developing a database for integrated and holistic access to high-throughput biology. We are developing an automated pipeline for the user-world handling of all data that stem from sequencing machines, real-time PCR machines, microarray scanners, mass-spectrometers and advanced microscopes, cell-sorters and other expensive machinery. We have already developed computational solutions for the handling of sequence data, proteomics and cell imaging data integration will be completed over the summer. Back to the group list