The capture, storage, handling, and analysis of large data sets will present a specific challenge for future systems genetics projects. Ritsert Jansen and Pjotr Prins presented their approaches to integrate data from various phenotypic studies, encompassing gene expression, metabolome, and classical traits, and to develop new tools for advanced and improved mapping of QTLs (Jansen et al. 2009; Li et al. 2008; Swertz and Jansen 2007) . These tools will be provided to the scientific community. Andreas Beyer gave a report on how to integrate data obtained at the post-transcriptional level with RNA expression data. Several loci that influence the post-transcriptional regulation of gene products could be identified in yeast. Steffen Möller presented his suite for the analysis of expression QTL (http://eqtl.berlios.de), which is being applied to the analysis of experimental autoimmune encephalomyelitis in mouse and rat. Anastasios Bezerianos presented a platform and developments for the identification of gene regulatory networks integrating protein-protein interactions and microarray data (Bezerianos and Maraziotis 2008). They started with yeast data and will soon expand to mouse, concentrating on time-varying gene regulatory networks. Morris Swertz presented XGAP, a software platform developed for data management and integration of large data sets from phenotyping and genotyping studies (Swertz et al. 2010) . Grant Morahan described the development of an extended tool for WebQTL that allows a genome-centric analysis of QTL interactions (unpublished).