Collaborations
	VIB microarray facility The cooperation with the VIB microarray facility is mainly focused on data representation and the integration of the dataflow in a lab environment. We developed a Laboratory Information Data model as well as a Gene Expression Data model. The latter one was in cooperation with the international users forum, MGED. The goal of this group is to facilitate the adoption of standards for DNA-array experiment annotation and data representation, as well as the introduction of standard experimental controls and data normalisation methods. The underlying goal is to facilitate the establishing of gene expression data repositories, comparability of gene expression data from different sources and interoperability of different gene expression databases and data analysis software. We had the privilege to be part of the steering committee directing these efforts. Several reasons motivate a standardization. First, gene expression data are more complicated than sequence data, it has meaning only in the context of detailed annotations. Currently microarrays do not measure gene expression levels in any objective units, in fact most measurements report only relative gene expression level changes. Different microarray platforms and experimental designs produce data in different formats and normalized in different ways, which makes comparison and integration of these data difficult. In order to comply with this required information specification in practice, a meticulous recording of every step in the laboratory process is needed. Due to the scale of the problems tackled, the traditional labworkers' notebook is replaced by a electronic repository, preferably driven by a flexible user interface. We developed a prototype interface meant to steer a data-driven environment such as the VIB MicroArray Facility. To some extent, tracking the history of biological material (such as clones in cDNA microarrays) provides insight in what kind of noise levels there are present in the data one wishes to produce. This understanding helps us in developing a more accurate insight in the nature of this data. Ghent Bioinformatics Group Center for microbial and plant genetics
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