EBI to Lead $7M Project to Create Sustainable European Bioinformatics Infrastructure
The European Commission has awarded €4.5 million ($7 million) to a consortium led by the European Bioinformatics Institute that will integrate Europe’s biological data resources into a “sustainable, integrative bioinformatics network for the life sciences,” EBI said this week.
The project, called the European Life-science Infrastructure for Biological Information, or ELIXIR, involves 32 partners from 13 countries and aims to create a long-term infrastructure for biological information in Europe.
Biological databases currently depend on “insecure or short-term funding, meaning that the valuable data they contain and provide access to, are jeopardized when funding ends,” EBI said in a statement.
EBI said that ELIXIR aims to address this issue by creating an infrastructure for storing, accessing, and integrating biological data that will be supported by a “secure funding mechanism.”
The project, funded under the EU’s 7th Framework Program, stems from a roadmap published in 2005 by the European Strategic Forum for Research Infrastructures that identified 35 large-scale European infrastructure projects, including the creation of a “shared platform for data resources in the life sciences.”
EBI submitted the proposal for ELIXIR in response to a restricted call to coordinators of these 35 projects.
The activities of ELIXIR are separated into two phases over three years: a preparatory phase, in which EBI will consult with the “stewards and users of Europe’s current biological resources to define the requirements, attributes and structure of the network;” and the implementation phase, in which EBI will report its findings from the preparatory phase and will seek “sustainable financial support” from national funding bodies.
According to the EBI, “key issues” that it seeks to define in the community consultation phase include:
- how best to integrate “core and specialist” data resources, including the development of standards for emerging fields;
- how the network can effectively connect with other interdisciplinary research areas;
- how to meet the needs of related European industries; and
- how to train life science researchers so that they can effectively use the information made available through the infrastructure.
EBI officials were not able to comment further on the project before deadline.
Further information on ELIXIR is available here.
Johnson & Johnson PRD Licenses Simcyp Simulator
The drug development arm of Johnson & Johnson, J&JPRD, has joined the Simcyp Consortium, which provides access to Simcyp’s Population-based ADME Simulator for pharmacokinetics modeling.
The simulator is a software platform to model drug absorption and disposition in virtual populations to help assess potential drug-drug interactions and to identify individuals potentially at extreme risk for adverse reactions from a given drug, the company said.
Sheffield, UK-based Simcyp also announced that it will be providing its consortium members access to Simulator’s population-based ADME Simulator and Paediatric module, geared toward pharmacokinetic modeling in infants, neonates, and children.
According to Simcyp, prior to signing the deal for three server licenses, 11 J&JPRD ADME scientists from multiple sites evaluated the simulation software, including the pediatric module. The contract between Simcyp and J&JPRD, a division of Janssen Pharmaceutica, will run for three years.
Financial terms of the agreement were not provided.
GeneBio to Distribute Protagen’s Modiro
Geneva Bioinformatics, GeneBio, said this week that it will distribute Protagen AG’s software tool Modiro for the rapid and automated detection of post-translational modifications in MS/MS datasets.
GeneBio and Protagen plan to “collaborate closely” to link Modiro’s functionalities to GeneBio’s Phenyx software platform for MS data analysis, GeneBio said.
GeneBio will have a global distribution range for the package.
CTSA Award for Albert Einstein College of Medicine of Yeshiva University and Montefiore Medical Center
The National Institutes of Health has awarded Albert Einstein College of Medicine of Yeshiva University and Montefiore Medical Center a Clinical and Translational Science Award totaling $22 million over five years.
The award is one of 14 CTSA grants totaling $533 million that the NIH awarded this week.
The grant will support the new Einstein-Montefiore Institute for Clinical and Translational Research.
Among other goals, the award will support development of a centralized infrastructure that will integrate the information systems and research databases at the two institutions, Brian Currie, co-director of the institute, vice president and medical director for research at Montefiore, and assistant dean for clinical research at Einstein, said in a statement.
Researchers Propose ISBN-like Identifiers for Biobanks
Writing on behalf of a collection of European research networks, a pair of scientists proposed in last week’s Journal of the American Medical Association that the international research community develop an identification scheme for biobanks that would be similar to the International Standard Book Number, or ISBN, code used in book publishing.
The authors note that biorepositories are “key tools in biological research, especially in genetics, genomics, and postgenomics research,” and particularly genome-wide association studies. Since these studies require large numbers of samples to ensure statistical rigor, researchers would benefit from data residing in other biobanks around the world. Currently, however, tracing these resources is “difficult because there are no standardized operational tools,” according to the JAMA commentary.
Francine Kauffmann and Anne Cambon-Thomsen, both of France’s Inserm, explain in the article that “the easiest way to trace the various uses of a given collection could be a common identifier attributed at the early stages of the collection,” but note that “no such structured identifier seems to exist for biobanks, whereas it is of common use in other domains.”
Kauffmann and Cambon-Thomsen propose that each biobank be assigned a unique, structured numerical code, similar to the ISBN, which comprises multi-digit “elements” that identify the language or geographical region, the publisher, and the specific edition of the publication.
In the case of biobanks, the elements of the code could identify the host of the biobank, its home country, and the individual collection, the authors write.
“Identification through ISBN for books is quite sophisticated and allows, for example, easy identification of a book, various volumes of a book, a book with several volumes, and the translation of a book, all of which represent various publication elements of one book,” Kauffmann and Cambon-Thomsen write. Using a similar approach for biobanks, “it would be easy to identify a biological collection, the various surveys in a longitudinal study, or an international program made of collections built up in various countries.”
In practice, they add, a unique identifier for biorepositories “would allow individuals to trace uses and results for various research partners or other interested parties; would provide a way to trace what is done with the information and the samples that individuals have provided for science; and would allow genetic data to be put in context with other dimensions of research to be considered for potential secondary users.”
The authors acknowledge that there are a number of practical issues associated with adopting an ISBN-like system that have yet to be addressed, including “who would maintain the system, who would provide funding for the system, and how uptake would be ensured.”
Several large-scale European research projects support the proposal and helped prepare the JAMA manuscript, including GA2LEN (Global Allergy and Asthma European Network) and PHOEBE (Promoting the Harmonization of Epidemiological Biobanks in Europe), which are funded under the European Union’s Sixth Framework Program; and GEN2PHEN (Genotype to Phenotype Databases: a Holistic Solution) and BBMRI (Biobanking and Biomolecular Resources Research Infrastructure'), which are funded through the EU’s Seventh Framework Program.