Requirements: JVM 1.5 or above A folder with the following structure is strictly required: - "GoldBinchII.jar" that is the algorithm runnable file. It must be in the same place that "Data" - "Data" folder which contains "IN" subfolder and where an "OUT" subfolder is generated - "IN" subfolder that contains the processed input datasets. The algorithm can be run with the following syntax: java -jar GoldBinch.jar numBi measureOption matrix.txt geneNames.txt annotationFile.goa annotationFile.obo M1 M2 M3 where: numBi: number of biclusters to obtain measureOption: simGIC or simUI or Corr matrix.txt: gene expression data matrix geneNames.txt: gene names file annotationFile.goa: annotation file downloaded from GO annotationFile.obo: GO structure file downloaded from GO M1: parameter for volume control M2: parameter for average correlation control M3: parameter for GO measure control (It's important to note that in the text of the paper M1 control the GO measure and M3 the volume) Examples: 1 simGIC GDS2415_Micro.txt GDS2415_GenesCorr.csv gene_association.goa_ref_human gene_ontology_ext.obo 1 1 2 1 simUI GDS2415_Micro.txt GDS2415_GenesCorr.csv gene_association.goa_ref_human gene_ontology_ext.obo 1 1 2 1 Corr GDS2415_Micro.txt GDS2415_GenesCorr.csv gene_association.goa_ref_human gene_ontology_ext.obo 1 1 2 The output file is saved inside "Data" folder in the "OUT" folder Contact (questions, help, etc): janepo@us.es