EMMA

As a high throughput technique, microarray experiments produce large data sets, consisting of measured data, laboratory protocols, and experimental settings. We have implemented the open source platform EMMA to store and analyze these data. EMMA gives access to all the transcriptomics data sets stored in the ArrayLIMS and provides automated pipelines for data processing, allowing an automated or manual analysis of expression profiles. Its modular architecture that can be easily extended. EMMA features detailed reports about spots and their corresponding measurements. In addition to routine data analysis algorithms, the system can be integrated with other components that contain additional data sources (e.g., genome annotation systems). In the design of the microarray experiments, special care must be taken in projects within the same network, to ensure comparability of these data and compliance to new and arising international standards. This system will also provide automated tools to perform data normalizations, tests for the identification of statistically significant up or down-regulated genes, clustering algorithms and, in the long run, support for time-course analyses.

ArrayLIMS

ArrayLIMS is a Microarray Laboratory Information Management system developed in close cooperation with biologists that are carrying out microarray experiments for many years. The LIMS has been designed in order to streamline their data acquisition and reporting processes. It provides a permanent and consistent storage of the microarray experiment data as well as a fast information retrieval, making the data rapidly available. The stored data is standardized, consisting of the hybridization steps (e.g. RNA production), production of the hybridization targets or the hybridization itself. It is also possible to store images of the hybridized and scanned slides as well as the corresponding data files. Overall, the LIMS will not only contain the raw experimental data, but also all relevant biological and technical information, (the experimental setup, the experimental and technical conditions used and the relevant parameters of the biological material analyzed).