1 Extending the BioArray Software Environment through PrognoChip-BASE

information system for the management of spotted DNA microarray experiments and the massive amounts of generated data. In particular, it is a MIAME-compliant1 database server and analysis platform, designed to be installed in any microarray laboratory and serve many users simultaneously via the web. BASE v1.2 has been developed by Lund University and is a free software release under the GNU General Public License. It runs on a Linux Server using a MySQL database backend, and it has been developed using PHP, Java, JavaScript, and C++ programming languages. In short, BASE v1.2 manages biomaterials (samples, extracts, labeled extracts), reporters (i.e., the oligonucleotides spotted on a microarray slide), and related annotations. Additionally, it manages the details of array production. When all related information is available, raw hybridization data sets (also, called measured bioassay data in MAGE-OM: MicroArray and Gene Expression-Object Model2) can be stored. Several scanners and image processors are supported. Each step of a microarray experiment is associated with a protocol description. Raw (hybridization) data sets can be organized in Experiments and normalized. Normalization plug-ins are already installed, but it is also possible to develop and install your own plug-ins. Normalization is performed in