Hi there, I updated the bingo class again, with some fresh code from Steven: - bingo parameters are read directly from the jar file, - some bingo param. are then overridden by values specified in the lemone property file (species, annotation file name, etc..) - output is now one (big) file for each module set, written in the bingo_results directory (created in the current directory). Be sure to link to the latest bingo jar file which is in: /group/biocomp/projects/segal/java/lib/BiNGO_11-2007/BiNGO.jar Bingo parameters example: #BiNGO parameters BiNGO=true signif_def=0.05 annotation_file_def=A_thaliana_default ontology_file_def=GO_Biological_Process annotation_default=true ontology_default=true -- Eric