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July 2015

Green light for CORBEL

Taking collaboration between biomedical sciences research infrastructures to the next level

The biomedical sciences Research Infrastructures will carry forward the successful collaboration they established with BioMedBridges into a new cluster project. CORBEL---Coordinated Research Infrastructures Building Enduring Life-science Services---has been funded with €14.5 million spread over four years. CORBEL will establish and support a new model for biological and medical research in Europe. It will harmonise user access to resources, unify data management and create common ethical and legal services. CORBEL will also build on BioMedBridges' efforts to develop the tools, services and data management capabilities required by cutting-edge European research projects, enabling users to deliver advanced, cross-disciplinary research.

Unlocking biomolecule volume data

Shape-matching service enables browsing of rich protein data resources based on 3D structure

Information on the structure of macromolecules is vital for biological and medical research because the function of many important biological processes is directly linked to macromolecular structure or changes therein.
For example, information on how a drug is bound to a target may yield vital clues on how to optimize its structure to promote more efficient binding. Structural biology is producing unprecedented amounts of structural data. However, it is not only the volume of data which is exploding but also its complexity and the range of resolutions in which it is available. While good bioinformatics tools are available for the analysis, validation and comparison of atomic structures, very few tools deal with low-resolution data (i.e. data on volume or shape).

To meet this need, BioMedBridges has developed a web-based shape-matching service that allows the wealth of low-resolution volume data in the EMDB and PDB resources to be searched based on their shape. This will provide entirely new perspectives on the relationships between structures. Shape matching will also enable automated segmentation (the identification of sub-regions) of low resolution structures and the annotation of the segmentations with biological identifiers and ontologies. This in turn will enable more effective meta-data searching of the structural data.
As a first step, the shape-matching software SMaSB was completed in December 2014 and is available as a compressed tarball from the downloads page of the CCP-EM project. The web-based shape-matching service was launched in June 2015.

Workshop on ethics review equivalency

Symposium: Open bridges for life science data, 17-18 November, Wellcome Genome Campus

The open life science data symposium will address data challenges and possibilities in the life sciences in plenary sessions and a wide range of workshops. Workshop topics include concrete technical solutions---for example relating to translational research with medical image data---to regulatory and policy issues, such as international ethics review equivalency.

Research ethics committees charged with reviewing biomedical proposals involving human participants use worryingly inconsistent standards. International, multi-site studies frequently lack effective coordination. The implications for global health research are serious. This workshop aims to develop alternative models that will harmonise ethics review as well as better balancing the claims of research participants, science and society.
Organised by the Global Alliance for Genomics and Health, this session will be led by Bartha M Knoppers and Edward Dove. The Global Alliance for Genomics and Health works to help accelerate the potential of genomic medicine to advance human health. It brings together over 300 institutions in healthcare, research, disease advocacy, life science and information technology.

BioMedBridges data integration pilots completed

European e-Infrastructure projects, including those in the life sciences, are increasingly turning to Semantic Web technologies to address data integration challenges. The BioMedBridges semantic web pilot spans several deliverables and follows a step-wise approach to leverage experience where it exists while minimising the risks inherent in novel technology projects. With the “Pilot integration of Web Services based simple object queries”, project partners have now recently completed the latest push on the technical development of these pilots.

Explore the interoperability layers here!

News in brief

Training resources available online

BioMedBridges has compiled a number of training resources that cover the scientific and technical aspects of the project, and introduce users to basic aspects of the tools and services.

BioMedBridges at ISMB/ECCB conference

Meet BioMedBridges representatives at the ISMB/ECCB conference in Dublin on 10-14 July in Dublin — come visit us at booth 10!

Licensing data and code: testing real-life scenarios

During a “Birds of a Feather” session at the EGI conference last May in Lisbon, BioMedBridges partners and subject experts discussed issues around licenses for data and code encountered in "real life" use cases, including:
  • developing a limitation of liability clause that is effective in European jurisdictions
  • the appropriate apportionment of liability among data user, data provider and database administrator
  • how the provision of e-infrastructure can change the opportunities for and risks of research misconduct
  • server side scripts: the tension between IT security and scientific transparency
  • licenses for web services
  • the relationship between choice of a license and choice of the business model for sustainability of a resource.
Contact Chris Morris for more details.

Upcoming events

SYMPOSIUM: Open bridges for life science data

17-18 November 2015, Wellcome Trust Genome Campus, Hinxton, UK

Register now

Join us to discuss the latest advances in the technical infrastructure behind large-scale data sharing in the life sciences, and the interoperability of data resources supporting biological, medical, translational and clinical research.

Announcements and news from the biomedical science research infrastructures

  • BBMRI Hands on Biobanks, 29-31 July, Milan, Italy. HOBB 2015 will discuss the growing relevance of clinical biobanks, essential infrastructure for the development of personalized medicine. The programme will include sessions on quality in all aspects of the biobanking process, pre-analytical conditions, international outreach, partnership between academia and industry. The scientific programme will cover the major topics with plenary and parallel sessions; keynote lectures; posters; ethics café discussions and interactive idea labs. 
  • ECBS & ICBS joint meeting 2015,  October 7-9, Berlin, Germany. EU-OPENSCREEN will host this meeting which brings together chemical biology researchers from screening and drug discovery, systems biology and therapeutic innovation.
Are we missing an event or do you want to share your events with the BioMedBridges community? Please contact the BioMedBridges inreach/outreach team.

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