List of OpenBiomind commands:

• EnhanceDataset: adds "synthetic" or "enhanced" features to datasets based on the match of the genes in the dataset to existing gene and protein ontologies. In other words, it is a way to enrich the dataset using systematized domain knowledge.
• DatasetTransformer: used for dividing a given dataset into validation folds and selection of features more relevant to the classification problem at hand.
• MetaTask: executes a large number of non-deterministic classification experiments (or tasks) over the same dataset.
• UtilityComputer: computes the utility of genes (as well as enhanced features) based on they frequency across a large number of classification models (generated by a metatask).
• ClusteringTransformer: generates clustering datasets using as inputs either categorial datasets or large numbers of classification models (again, those generated by a metatask).
• Clusterize: clustering using Omniclust, OpenBiomind's simple clustering algorithm.
• ViewClusters: clustering visualization in classic raster image view.
• GraphFeatures: portrays relations (of co-expression, co-occurrence in models) among genes (and enhanced features) in a graph visualization, displaying also several other kinds of related information.
• CompletePipeline: runs all the processes above over a categorial dataset, in a coordinated way, channeling outputs of some commands as inputs of others.
• FoldSelectSNPs: converts a SNP dataset into a float-coded version divided in folds and feature-selected - that is, ready for metatasks.
• SNPUtilityComputer: similar to UtilityComputer and operating under the same principles, but dealing with conceptual particularities of SNP experiments.

Note: in all commands above, the openbiomind-bin_x.xx.jar executable (often called simply openbiomind.jar for sake of simplicity and version-independence), as well as the pipeline.properites file and the datafiles directory present at the extras package, are assumed to be in the classpath. Indeed often openbiomind.jar is evoked explicitly in the command line for sake of emphasis.