Genedata and the University of Freiburg have applied the bioinformatics company’s Phylosopher research data management and analysis system to seamlessly integrate public, experimental and in-licensed data.
Within the Freiburg Initiative for Systems Biology (FRISYS framework), Genedata's Phylosopher has enabled 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 eight 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.
Dr Stefan Rensing, head of the Core Facility Data Management at FRISYS and first author of the genome sequence publication, said: ‘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 Professor Ralf Reski, chair of 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.’
