CSC

	Tehdyt toimenpiteet Medicel Ltd. Bioinformatics contact person: Christophe Roos Home page: http://www.medicel.com Medicel is a privately owned company founded 2001 in Helsinki. Medicel has two departments: A molecular biology laboratory and a software development laboratory. Each of them occupies about 25 persons including medical doctors, molecular biologists, biochemists, bioinformaticians, statisticians, mathematicians, engineers, and software-engineers. In the wet lab, operating at Biomedicum, new methodology is developed and applied to drug target discovery and validation projects related to inflammatory diseases and also to protein production in yeast. A special emphasis is put on development of high-throughput measurement technologies using among other highly automated fermentors and sample collection, mass spectroscopy, microarray technology and related wet-lab methods and microscopy. The software development effort aims at creating an integrated data warehouse platform suitable typically for systems biology research and drug target discovery, but more generally for mostly any molecular biomedical research project. For this purpose we have created Silvermine, a data management and analysis platform accessible through a set of product suites: Project editor (LIMS) , Workflow editor, Pathway editor (any network/map), Quantitative data workbench (visualisation of high-dimensional data), Microscopy workbench, Text mining workbench, General search and Annotators workbench. The Medicel integration framework is built to allow the plugging in of any tool, from simple perl scripts to complex software modules. On a low level, we have designed tools for importing data from external databases or published results such as Uniprot, PDB, EMBL, Ensembl, Bind, Kegg (pathways, ligand, glycans), Refseq, SGD, Interpro, GO-Database, Pubmed, GEO, transcription factor binding data, GFP-localisation data etc. ntegrating any ontology in standard format like GO, ChEBI, Human development, tissue, cell, phenotype, IntAct etc. analysing and calculating sugar structures based on MS-data, for statistical analysis of e.g. microarray measurements or for sequence analysis using a.o. hidden Markov models. We have also integrated external tools such as the Emboss suite tools, Clustalw, Meme and Blast. Altogether, the use of Silvermine offers an integrated environment where very disparate measurements and data types can be used together in a flexible environment allowing high automatisation and auditing. Back to the group list