This is the Java implementation of a research project on modelling and analysis of complex systems. Release contains Local implementation of the BiMax algorithm, refactored code of BiCat toolbox, Bayesian post-analysis which uses NCI Curated Pathways database, possibilities of calling R script from Java code, Parser that maps illumina names to HGNC Symbols and usage cases of all the above mentioned. Also, a class that can read and process bigger datasets with which BiCat GUI had a trouble. Also, Mean Squared Residue Score implementation is included in the bicluster class to have a numeric metric for assessment as well. Please visit http://www.tik.ethz.ch/sop/bicat/?page=licensingAgree.php in order to obtain the native libraries used for the project