Section: Other Grants and Activities
European Activities
Yeast Systems Biology Network (FP6)
Participants : David James Sherman, Macha Nikolski [ correspondant ] .
Our team is actively involved in the Yeast Systems Biology Network (YSBN) Coordinated Action, sponsored by the EU sixth framework programme. The allocated budget is 1.3 million Euros. The CA is coordinated by Prof. Jens Nielsen (Technical University of Denmark) and involves 17 European universities and 2 start-up biotech companies: InNetics AB and Fluxome Sciences A/S.
The activities of this CA aim at facilitating and improving research in yeast systems biology. The EU team creates standardised methods for research, reference databases, develops inter-laboratory benchmarking, and organizes a international conference, a number of PhD courses, and workshops.
The project involves most of the best EU academic centres in this field of science: Biozentrum University of Basel, Bogazici University Istanbul, Budapest University of Technology and Economics and Hungarian Academy of Sciences, CNSR/LaBRI University Bordeaux, ETH Zurich, Gothenburg University, Manchester University, Lund University, Max Plank Institute of Molecular Genetics, Medical University Vienna, Stuttgart University, Technical University of Denmark, Technical University Delft, University of Milano Bicocca, Virje University Amsterdam, VTT Technical Research Centre Finland.
ProteomeBinders (FP6)
Participants : David James Sherman [ correspondant ] , Julie Bourbeillon.
The ProteomeBinders Coordination Action, sponsored by the EU sixth framework programme, coordinates the establishment of a European resource infrastructure of binding molecules directed against the entire human proteome. The allocated budget is 1.8 million Euros. The CA is coordinated by Prof. Mike Taussig of the Babraham Institute in the UK.
A major objective of the “post-genome” era is to detect, quantify and characterise all relevant human proteins in tissues and fluids in health and disease. This effort requires a comprehensive, characterised and standardised collection of specific ligand binding reagents, including antibodies, the most widely used such reagents, as well as novel protein scaffolds and nucleic acid aptamers. Currently there is no pan-European platform to coordinate systematic development, resource management and quality control for these important reagents.
The ProteomeBinders Coordination Action (proteomebinders.org ) coordinates 26 European partners and two in the USA, several of which operate infrastructures or large scale projects in aspects including cDNA collections, protein production, polyclonal and monoclonal antibodies. They provide a critical mass of leading expertise in binder technology, protein expression, binder applications and bioinformatics. Many have tight links to SMEs in binder technology, as founders or advisors. The CA will organise the resource by integrating the existing infrastructures, reviewing technologies and high throughput production methods, standardising binder-based tools and applications, assembling the necessary bioinformatics and establishing a database schema to set up a central binders repository. A proteome binders resource will have huge benefits for basic and applied research, impacting on healthcare, diagnostics, discovery of targets for drug intervention and therapeutics. It will thus be of great advantage to the research and biotechnology communities.
Within ProteomeBinders, our team is responsible for formalizing an ontology of binder properties and a set of requirements for data representation and exchange, and for developing a database schema based on these specifications that could be used to set up a central repository of all known ligand binders against the human proteome. The adoption of the proposed standards by the scientific community will determine the success of this activity.
IntAct
Participants : David James Sherman [ correspondant ] , Julie Bourbeillon.
The IntAct project, led by the European Bioinformatics Institute (EBI) within the framework of the European project TEMBLOR (The European Molecular Biology Linked Original Resources), develops a federated European database of protein-protein interactions and their annotations. IntAct partners develop a normalized representation of annotated protein interaction data and the necessary ontologies, a protocol for data exchange between the nodes of the federated database, and a software infrastructure for the installation of these local nodes. In this infrastructure, a large number of software tools have been realized to aid biological user exploit these data reliably and efficiently. Our own tool Proviz is part of this set of tools. Curator annotation, optimization, and quality control tools have also been developed [6] . We also submit experimental data to the repository.
