The Cold Spring Harbor Laboratory conference on Genome Informatics will focus on large scale genome annotation and utilisation. The focus for this conference is large scale genome informatics. The explosion of biological data requires a concomitant increase in the scale and sophistication of information technology. This ranges from the storage of data and their associated data models, to the design of effective algorithms to uncover non-obvious aspects of these datasets, to ontologies to concisely describe biological information, and finally to software systems to support curation, visualisation, and exploration. The conference brings together some of the leading scientists in this growing field, and we strongly encourage researchers from other large scale information handling disciplines to attend.