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Issue 18: Summer 2016        
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Informed: ELIXIR Newsletter

With ELXIR-EXCELERATE in full swing, there are many activities currently taking place in ELIXIR. In this issue we present an overview of recent activities in our Training and Interoperability Platforms. You can also read reports from the launch of the ELIXIR Data Nodes Network and from our latest Innovation and SME Forum in Oslo, Norway.

The ELIXIR Board held its fifth meeting in Prague in April and approved the application of three more countries to join ELIXIR: Germany, Ireland and Luxembourg will become ELIXIR members once they ratify the ELIXIR Consortium Agreement.

Finally, we have launched a Call for ELIXIR Posters at ECCB 2016 in the Hague, this September. Alongside the ELIXIR Applications track, the ELIXIR Poster session will present the full scope of ELIXIR technical and scientific activities.

I wish you a relaxing summer break and hope to see you in September in the Hague at the ECCB.


Dr Niklas Blomberg
ELIXIR Director
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In this issue:

Demonstrating impact of bioinformatics resources
 

Researchers from ELIXIR published a new paper to examine citations of biological databases in research articles and patent applications. They found that life scientists in industry and academia extensively reuse data from bioinformatics resources - in 2014 there were more than 8,000 patents referring to ten different bioinformatics repositories.
Research topics in patents applications with the most extensive use of bioinformatics resources.

The article Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources, investigated the citations of molecular data in the European Nucleotide Archive (ENA), the Protein Data Bank in Europe (PDBe) and other repositories. It was published in ELIXIR Reports, the ELIXIR Channel on F1000Research platform.

Read more »

ELIXIR Innovation and SME Forum: Data-driven innovation in the aquaculture and marine industries

ELIXIR organised its fourth Innovation and SME Forum on 12-13 May 2016 in Oslo, Norway. The event introduced some of the public tools, data resources and services for aquaculture and marine industries available through ELIXIR and highlighted examples of research-intensive companies making use of big data in marine sciences (ArcticZymes, XELECT, Marine Harvest, AquaGen). The participants also learnt about the Malaspina expedition data, resources for salmon farming, the AquaGenome project and others.

ELIXIR Poster session at ECCB 2016

The poster session at the ECCB 2016 conference in The Hague, the Netherlands, will include a dedicated ELIXIR track. The track will bring together submissions from researchers, developers and infrastructure service providers across ELIXIR Nodes and present the full scope of ELIXIR services and activities.

The Call for posters is open until 22 July.

Towards user centric services for the Marine community

ELIXIR Norway and EMBL-EBI successfully concluded an ELIXIR Pilot action towards harmonising their existing metagenomics pipelines: EMBL-EBI’s metagenomics portal and ELIXIR Norway's META-pipe. The main goal of the pilot was to ensure interoperability between the two platforms and explore the potential of EMBL-EBI Embassy Cloud technology in marine metagenomics.

The results of the pilot have been presented at the ELIXIR All Hands meeting and will soon be published in the ELIXIR Reports, the ELIXIR F1000Research publication channel.

Updates from ELIXIR Training

The ELIXIR Training Platform has recently organised three workshops. The joint ELIXIR-GOBLET workshop in April in Hinxton, UK, focused on the re-use of metagenomics training materials, the Train the Trainer workshop at Cambridge University in May, brought together trainers from ELIXIR Nodes to improve their teaching skills. Finally, ELIXIR Finland held an ELIXIR-EXCELERATE training course on using VMs and clouds in bioinformatics.

The Training Platform also continued collaboration with the US BD2K's (Big Data to Knowledge) Training Coordinating Centre (TCC, www.bigdatau.org), defining the following areas in which they will continue to work: Training portals; Competences; summer schools; collaboration with GOBLET; and bioinformatics training standards.

ELIXIR launches its Data Nodes network

A workshop in April 2016 marked the launch of ELIXIR’s Data Nodes Network. The goal is to bring together Nodes with large data collections and databases to work together to facilitate collection and linking of data to international deposition archives run by ELIXIR Nodes (e.g. EMBL-EBI). Hosted in Prague by ELIXIR Czech Republic, the workshop included presentations from several ELIXIR Nodes on their experience in data storage, and discussion on the objectives for the Data Nodes Network. The priority for 2016 will be Local EGA and Data Management Plans.

ELIXIR Interoperability Platform expands community involvement

The ELIXIR Interoperability Platform has continued to develop its interoperability product portfolio through collaboration with partners. In March, the platform organised a Samples Club BYOD (Bring Your Own Data) workshop in Manchester, UK, to discuss a common framework for samples and samples metadata and modelling with partners from ELIXIR Nodes, BBMRI, ISBE, FAIRDOM, BD2K and others. Discussions are also continuing apace with Google about extending schema.org to describe life science datasets through interactions with the Bioschemas.org initiative. Efforts such as these help data producers to create consistent structured information. They improve data interoperability by making it much easier for data aggregators and search engines (Google and others) to discover, collate and analyse distributed data.

Many ELIXIR Interoperability experts are also involved in the CHARME initiative, which brings together various projects in standardisation of life science data. The initiative organises its first conference in Warsaw, Poland on 21-22 June, which  feature several ELIXIR-related talks, including two keynotes by Barend Mons, Head of ELIXIR Netherlands, and Chris Evelo, the new co-leader of the ELIXIR Interoperability platform.

ELIXIR Board spring meeting - new countries, new Implementation studies

In its 2016 Spring meeting in Prague, Czech Republic on 11-12 April 2016, the ELIXIR Board approved the applications of Germany, Ireland and Luxembourg to join ELIXIR. The three countries will now become members once they ratify the ELIXIR Consortium Agreement, which is expected shortly. With these three countries, ELIXIR membership will round to 20.

The Board has also approved a portfolio of Implementation Studies for 2016. They will focus on collaboration with the Global Alliance of Genomics and Health (GA4GH), and support the integration of resources from ELIXIR Nodes into ELIXIR platforms.

Read more about the conclusions from ELIXIR Board meeting»

Forthcoming meetings

 
GA4GH-ELIXIR Beacon Security workshop
Hinxton, UK, 30 June 2016

Second Annual Danish Bioinformatics Conference
Odense, Denmark, 25-26 August 2016

ECCB 2016
The Hague, The Netherlands, 3-7 September 2016
Contact ELIXIR

For further information on ELIXIR please contact the team at:

ELIXIR Hub
Wellcome Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom

Tel: +44 (0)1223 492-670
Email: info@elixir-europe.org

www.elixir-europe.org