In the "Applied bioinformatics: Transcriptomics" workshop, state-of-the art techniques will be presented that allow gene identification by expression profiling (Normalization pipelines, statistical analyses, expression profile clustering, mapping of expression profiles to metabolic pathways, data mining, webservices, MGED ontologies), using the EMMA software of the Bioinformatics Resource Facility (Center for Biotechnology, Bielefeld University) as an example to communicate general aspects related to the evaluation of expression profiles. Due to the multitude of microarray and GeneChip layouts that will be used in the frame of the SPP1212, these cannot all be integrated into the software, but training in general principles of transcriptome profiling can be useful to ease the usage of those software platforms being available to SPP1212 members in their home institutions. The EMMA software is currently extended to support the analysis of Affymetrix GeneChip data, and relevant aspects of data evaluation using such tools will be integrated once the software extension is available. As far as possible, transcriptomics aspects of the PhD theses carried out within the frame of the SPP will be addressed in the course. The duration of the course is 2 days.