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MAD & IBU

I am heading the microarray technology and bioinformatics expertise centre of the FNWI named “The MicroArray Department (MAD)” and the bioinformatics research group “Integrative Bioinformatics Unit (IBU)” .  The group consists of about 11 multidiciplinary experts in the fields of microarray and bioinformatics. For detailed information see our website: www.micro-array.nl

Service: The MAD is a fully licensed microarray technology centre with NimbleGen, Affymetrix Genechip®, and Agilent platforms. We operate as platform for R&D, as well as service center. As a licensed Affymetrix  and Agilent Service Provider, we offer tailor-made services in the field of gene expression, DNA analysis and related bioinformatics. Our expertise includes:

1. consultancy about experiment design;
2. fully licensed use of Genechips® as official Dutch Affymetrix, Agilent and NimbleGen Service Provider;
3. high quality microarray experiments;
4. comprehensive transcriptomics data analysis by expert bioinformaticians.

The MAD comprises a wet-lab and a dry-lab. The wet-lab takes care of all microarray technology services. The dry-lab acts as a bioinformatics support group for all microarray data analyses.  

Research: The MAD acts not only as a service provider but also as a partner in scientific projects. These projects range from toxicogenomics (genomic analysis and in vivo imaging of stress in aging-related disease funded by IOP -EMC, LUMC, LACDR, RIVM), food safety (Unilever) and mechanistic studies (e.g. Biofilm -ACTA-) and biomarkers (RIVM). The MAD is always in for collaboration or participation in projects concerning microarray technology or analysis. If you need an expert microarray or bioinformatics partner for your project, please contact Dr Timo Breit (t.m.breit@uva.nl) or Dr Floyd Wittink (r.a.wittink@uva.nl).

Both wet-lab and dry-lab have their own research program. While the wet-lab focuses on technology research (e.g. design of new arrays) and implementation of high and up-to-date QC standards, the dry-lab concentrates on the evaluation and implementation of tools for microarray data analysis.

The Integrative Bioinformatics Unit (IBU) emerged in 2003 from the MAD. IBU's main research effort is aimed at evaluating the possibilities for computer-assisted experimental biology research by building an e-BioScience problem solving environment (eBioPSE). The focus is on development of a comprhenesive a microarray data analysis eBioPSE for biological problem-solving and phenomenon discovery by means of data integration and computational experimentation. In 2007 we opened a e-BioLab. This is a lab formultidisciplinary discussions supported by various visualisation tools, such as a 20 screen tiled display.

The most important IBU long-term goals:

1. Develop a problem solving environment for microarray data analysis;
2. Experiment with the prototype e-BioLab where biologist can perform truly multidisciplinary, collaborative research;
3. Research on in-silico experimentation approach with genomics data and knowledge models.

There are numerous methods and tools to analyze microarray experiments and many more are being developed continuously. Each method and tool has its own use and merits. We are trying to keep track of what has been and is being developed worldwide. We aim to create a comprehensive suite of microarray data analysis tools by drawing up an inventory, evaluation, and selection of valuable methods and tools. The total microarray data analysis environment will be built by introducing methods and tools to it, embedded in workflows. This will enhance the re-usability of data, methods, and tools dramatically.

We participate in three large integrated national projects: "BioRange", "BioAssist", BiG Grid, and "Virtual Lab for e-Science (VL-e)". BioRange is a nation-wide NBIC bioinformatics research project; BioAssist is a nation-wide NBIC bioinformatics support program; BiGGrid is a nation-wide e-science infrastructure program;  and VL-e is the Dutch e-science project concerned with ICT infrastructure and methods, meant to support applications from a wide range of scientific disciplines.

MAD-IBU website