Genedata and FRISYS Turn Over New Leaf in Systems Biology Collaboration
07 May 2008

The long standing collaboration between bioinformatics provider Genedata and the University of Freiburg, supported by the initiative of excellence of the German Federal Government and States, is being taken to the next level with the latest development at the Freiburg Initiative for Systems Biology (FRISYS). Within the FRISYS framework, Genedata`s established Phylosopher research data management and analysis system has been applied to seamlessly integrate public, experimental and in-licensed data, enabling systems biology for various model organisms like the moss Physcomitrella patens.

As systems biology projects rely on the completely reconstructed part list of molecular entities encoded in the genome, deciphering the genome and its capabilities is a prerequisite to reconstruct and model the living cell towards systems biology. Earlier in 2008, after 8 years of work, the International Moss Sequencing Consortium had reported the draft genome sequence of Physcomitrella patens, a moss with impressive survival qualities and important source to improve cultivated plants in biotech applications. “A milestone for systems biology and moss research,” said PD Dr. Stefan Rensing, Head of the Core Facility Data Management at FRISYS and first author of the genome sequence publication. “This genome is of high scientific relevance: Physcomitrella helps to understand the transition of photosynthetic organisms from the aquatic environment to land. The adaptation included e.g. enhanced osmoregulation and -protection, desiccation and freezing tolerance, heat resistance, and the development of protective ‘sunscreens’.”

Genedata Phylosopher’s GeneIndex and its pathway-centric analysis environment integrates public, in-licensed and proprietary experimental omics data and thus streamlines the iterative process of systems biology. “Beyond comparative genomics, the further reconstruction of the moss metabolism and its regulation requires, in addition to a comprehensive GeneIndex, new approaches for pathway analysis and de novo prediction of transcription factor binding sites. We are delighted that Genedata Phylosopher supports this comprehensive integrative workflow so efficiently,” explained Prof. Ralf Reski, Chair Plant Biotechnology at FRISYS. “We will complete the parts list for moss, identify missing pieces of the system and decipher P. patens’ fascinating way through evolution. This will help us to make plant biotechnology even safer and to extend its human benefit in various areas.”

“This outstanding FRISYS project builds a bridge from basic research to applied systems biology in industry for agro, biotech and biologics, or nutrition and cosmetics applications, to name just a few,” said Dr. Othmar Pfannes, CEO of Genedata. “P. patens adds to Genedata`s impressive track record of economically and socially highly relevant projects that rely on our proven software solutions and computational expertise.“

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