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Freiburg Initiative for Systems Biology (FRISYS)

Education & Training

     PD Dr. S. Rensing

Core facility Data Management

    

With the rapid advancements in high-throughput technologies such as genomics, transcriptomics and proteomics, it becomes challenging to manage as well as analyze the data generated, as these data are not only of huge amount, but also in diverse and complex structure. The first step to this end is to collect, store and normalize the different kinds of experimental data in an organized way so that further analysis is possible, and this is our main task at the Core facility Data Management of the Freiburg Initiative for Systems Biology (FRISYS).

We maintain a number of bioinformatics software to fulfill the data management and analysis needs of researchers in different FRISYS groups. These include Expressionist®, an 'omics' data integration, processing and analysis tool; Phylosopher®, a gene-centered environment for information management and integration; Pathway Studio®, a tool to interpret the various 'omics' data in the context of pathways and networks. Also we have installed Transfac® database, which is a comprehensive knowledgebase of transcription factor binding sites.

These bioinformatics software run on a dedicated Linux server and the performances are generally good, even if the number of users has been continuously increasing. However, several tasks of Phylosopher® are computational expensive, e.g. microarray probe mapping, protein domain prediction and protein family calculation. Furthermore, these tasks have to be done for each genome studied by the FRISYS groups. Running these tasks on our server would have compromised the normal usage of other available software. We realized that the idea of sharing computing resources at the Black Forest Grid (BFG) is excellent, and therefore decided to run these computational expensive tasks on the BFG cluster. Up to now the experiences with the BFG cluster are very satisfactory.

Freiburg Initiative for Systems Biology (FRISYS)

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