Biological databases
The amount of information and datasets generated by the R&D activities within the Life Science industry is growing exponentially since the advent of the Omics breakthrough technologies such as micro-arrays , Next Gen Sequencing and Mass Spectrometry. These stacks of data are kept in different database dotted across the different industries , different universities and research institutes throughout the world. There is an increasing need for the creation of intelligent systems (database and connections) to query, collect, link, combine, analyse and give biological sense to these different data to tackle more and more intricate and challenging scientific problems. BioXpr has acquired a wide know-how in the field of database creation and especially in:· The actual design of the database,· The creation of data-mining , search engines and user-friendly interfaces,· The setting-up of data-warehousing solutions such as automatic updates,· The building of secured servers and database networksOur scientific team masters the different language industry standards such as Oracle, MySQL; PostgreSQL for any types of database development and deployment.. Case Study:Challenge:From 2006 onwards BioXpr is actively involved in a European Union-financed multinational FP6 project entitled ”Streptomics”. The project’s goal is to improve Streptomyces strains ability to produce high-value recombinant proteins (drugs, enzyme,...) and other chemical intermediates. The consortium gathered a balanced number of universities (Riga Institute from the Leuven university, B, Manchester University, UK, Greifswald university, D,...), small and medium size biotechs (Eurogentec, B, Matis, Is, bioXpr, B,...) and blue-chip pharma (Bayer-Schering & Direvo, D, GSK Pharma, UK). The project calls upon the new Life Siences Omics technologies to study the Streptomyces biosynthesis pathways at genomic, transcriptomic, proteomic and metabolomic levels.Actions:The different consortium members are studying various Streptomyces strains, growth conditions and target proteins under proteomics (mass.spec) , Metabolomics (mass.spec) and genomics’s (low and medium density micro-arrays & Next Gen Seq) perspectives.BioXpr has been developing the necessary bioinformatics infrastructure and tools to collect, safe-guard and analyse the different “omics” datasets generated by the different partners and combine the data in one global picture.Results and PerspectivesThe analysis and interpretation work is well underway and one hopes to produce soon a global picture helping the understanding of the production pathways. The next step will be for BioXpr to build a predictive model to anticipate the production level and quality of the compounds of interest depending of several key parameters such as type of strain, compound features,...(link to a PDF detailing the Case Study)
