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Victor Renault (CEPH Fondation Jean Dausset, Paris, France)
The Operon system is a non-relational database management system build with the overall purpose to maintain biomedical information. The system consists of databases and a software framework that permits scientist and engineers develop their own applications to store and retrieve data with the Oracle Berkeley DB . The software is open-source, and the applications provide access to data by standard command-line tools and web applications. One of these databases named "STypes," stores the genotyping data of a set of patients affected by cancer. Each patient was sequenced twice from tumor cells and peripheral cells. We created a command-line java tool and a java server for scanning the "STypes" database. The program draws custom histograms along a genomic region using the Scalable Vector Graphics ( SVG ) format; it takes as input an XML file where the user defines a filter by applying a simple javascript code. Each used defined function returns an integer that will be used as a value to draw the histogram. The definition of each histogram is highly customizable, and there is no need to create a complex HTML form or implement a specific query language.