- ELIXIR Europe

Transcript

- ELIXIR Europe

ELIXIR
Annual Report 2015
ELIXIR Scientific Programme 2014
2
With special thanks to all of those who contributed to the development of ELIXIR
infrastructure in 2015, most notably heads of Nodes, platform and use case leads,
Technical and Training coordinators and members of the various working groups.
1
ELIXIR Annual Report 2015
Table of Contents
Opening remarks by Robert-Jan Smits, Director-General,
DG Research and Innovation, European Commission
3
Foreword by Niklas Blomberg, Director of ELIXIR
4
ELIXIR Technical Platforms: Our framework for service delivery
5
Data6
7
Interoperability
Tools8
9
Compute
Training
10
ELIXIR Use Cases
11
Human data
12
Rare diseases
13
Marine metagenomics
14
Plant sciences
15
Highlights from ELIXIR Nodes
16
ELIXIR Members and Observers
17
ELIXIR Member updates
19
ELIXIR Observer updates
21
Accelerating implementation: ELIXIR-EXCELERATE
22
Highlights from Technical Coordinators
23
Industry engagement: ELIXIR Innovation and SME programme
24
Timeline: 2015 highlights
25
Scientific Advisory Board
27
International collaboration
28
Capacity building
29
Scientific collaborations - EU grants
30
Collaborations with biomedical research infrastructures
31
Activities at the ELIXIR Hub
33
ELIXIR Committees
35
Financial data
39
2
Opening remarks
I have been delighted to watch how
successfully ELIXIR has progressed
throughout 2015. From the start of two
major Horizon 2020-funded projects–ELIXIREXCELERATE and CORBEL–to recognition
by the G7 Group of Senior Officials (GSO),
2015 marked the year that ELIXIR moved full
swing into its operational phase and earned
recognition on the global stage.
What has been as equally pleasing to note is how ELIXIR’s
progress matches so closely the priorities of the new
Research Commissioner: Open Science, Open Innovation
and Open to the World.
To be able to realise the benefits of Open Science, it is
crucial for Europe to have a sustainable, interconnected
infrastructure for life-science data so that the data created
from national and EU research projects can be stored safely
and made available for re-use. The progress ELIXIR has
made with its Member States and the creation of national
centres for excellence (ELIXIR Nodes) demonstrates that in
the life sciences, this is well on track.
For Europe to transition to a knowledge-based economy, we
need a strong industrial sector and maximum commercial
use of our research infrastructures. In the life sciences,
companies are already major users of bioinformatics
services, and the progress ELIXIR has made through its
Innovation and SME programme has shown how it is
possible to engage companies as service users effectively.
Internationally, ELIXIR has been recognised by the G7’s
Group of Senior Officials as a research infrastructure of
global potential, and I am confident that as ELIXIR rolls
out its international strategy it will be at the forefront of
defining and implementing international standards for data
exchange, interoperability and training.
Robert-Jan Smits, Director-General,
DG Research and Innovation,
European Commission
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Robert-Jan Smits
Foreword
Boosting the implementation of ELIXIR
services, strengthening our infrastructure
capacities in ELIXIR Nodes and building the
foundations for sustainable life-science data
resources–those were ELIXIR’s main goals for
2015. This report shows our progress towards
achieving these goals: what we achieved over
the past year and what lies ahead.
Boosting service delivery
In 2015 ELIXIR entered a new phase, expanding its technical
and service delivery and preparing for future growth. I
would like to thank the Technical Platform and Use Case
leaders, and indeed the whole ELIXIR community, for
their enthusiasm and hard work in bringing to fruition five
technical platforms (Tools, Data, Compute, Interoperability
and Training) and four use cases (Plant sciences, Marine
metagenomics, Rare diseases and Human data). The
platforms and use cases are now fully operational and form a
solid foundation for our service delivery.
The Horizon 2020 ELIXIR-EXCELERATE grant, which started
in September 2015, is fully embedded into ELIXIR technical
platforms and use cases. The project will accelerate the
implementation of the ELIXIR scientific programme and
integrate ELIXIR bioinformatics resources into a coherent
portfolio of infrastructure services.
In 2015 the Training Platform rolled out its ELIXIR Software
and Data Carpentry Pilot Programme, which trained over
200 researchers. The Human data Use Case team started the
Beacon project, a collaboration with the Global Alliance for
Genomics and Health (GA4GH). The Marine metagenomics
Use Case successfully completed a pilot project to harmonise
ELIXIR’s metagenomics pipeline, which is run jointly by the
European Bioinformatics Institute (EMBL-EBI) and
ELIXIR Norway.
Welcome, new members
At the beginning of 2015 ELIXIR had 12 Members and six
Observers. We welcomed three new members during the
year: France, Spain and Belgium, which completed the
ratification process and became fully integrated into ELIXIR
activities. Italy and Slovenia completed their preparatory
work in 2015 to become Members in early 2016. Ireland
joined ELIXIR as an Observer and began the process of
establishing its national Node. ELIXIR also developed a
collaboration with the German Network for Bioinformatics
Infrastructure (de.NBI), which will pave the way for
Germany’s full membership in ELIXIR.
Niklas Blomberg
I believe that the collaboration among the growing number
of ELIXIR Members will strengthen both our national Nodes
and ELIXIR as a whole, and will bring real benefits to the lifescience community.
A global infrastructure
Science is international, and ELIXIR’s reach extends beyond
Europe. We started the first collaborations with our US
counterpart, the Big Data to Knowledge (BD2K) initiative
in 2015. We strengthened our ties with bioinformatics
communities in Australia and Canada, and I visited both
countries to discuss closer collaboration.
ELIXIR’s global reach was recognised by the “Group of
Seven” (G7). The Progress Report published by the G7
Group of Senior Officials categorised ELIXIR as a global
infrastructure with a potential for collaboration with
countries across the globe.
Looking ahead
Our progress in 2015 laid the groundwork for expanding
ELIXIR's portfolio of services, which will bring real benefits
to the research community. Our priorities for 2016 are to
provide effective services to life-science researchers in
Europe and globally, to build bioinformatics expertise and
capacities in our national Nodes, and to bring these together
in a coherent, joined-up infrastructure.
I am impressed and pleased to see what we have all achieved
in such a short time. With such a strong start, I eagerly await
many new developments as our implementation progresses.
Niklas Blomberg, Director of ELIXIR
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Technical Platforms: Our framework for
service delivery
The ELIXIR Platforms comprise Data, Tools,
Interoperability, Compute and Training,
forming the basic operational units within
ELIXIR. They bring together resources
and expertise from the ELIXIR Nodes and
provide a framework for the delivery of our
infrastructure services.
range of mechanisms, from Hub-funded activities, such as
implementation studies, to European grants, such as ELIXIREXCELERATE and CORBEL.
The platforms, formally set up in June 2015 by the ELIXIR
Heads of Nodes Committee, established their structure
and leadership and developed roadmaps for their activities.
These were reviewed by the ELIXIR Scientific Advisory
Board (SAB) in December 2015. With its platforms now
fully operational, ELIXIR is equipped to expand its
technical delivery.
The overall scope and objectives of the platforms are
defined in the ELIXIR Scientific Programme 2014-2018. The
activities carried out by platforms are funded through a
Structure of ELIXIR activities in 2015: Technical platforms for compute, data, tools and interoperability complemented by use cases for marine
metagenomics, rare diseases, human data and plants sciences.
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Data: Sustaining Europe’s life science
data infrastructure
The ELIXIR Data Platform brings together
Europe’s life science data resources and
drives their integration and sustainability.
The main goals of the ELIXIR Data Platform are to:
• F
ormalise the indicators and quality criteria for ELIXIR
Core Data resources across Europe;
• P
romote excellence in resource development and
operation through spreading best practice;
• I nform life-cycle management of resources, so that
they can continue to form a reliable foundation for lifescience research projects;
• I ncrease the sustainability of curated resources through
literature–data integration and resource cross-linking.
ELIXIR Core Data Resources are defined as a set of European
data resources that are of fundamental importance to
the broad life science community and the long-term
preservation of biological data. They provide complete
collections of generic value to the life sciences and tend
to be well known in their field, with high levels of scientific
quality and service. The objectives of this platform are to
develop indicators for these key bioinformatics resources
and contribute to their long-term sustainability.
Jo McEntyre, EMBL-EBI and
Christine Durinx, SIB Swiss Institute of
Bioinformatics
2015 highlights:
• I nitiated discussions about the process of identifying
ELIXIR Core Data Resources and delivered a first draft
to the ELIXIR SAB (December 2015), with the final
report scheduled for 2016;
• D
rafted a set of indicators that reflect the multiple
facets of data resources, and submitted it for review by
the ELIXIR SAB (December 2015), with the report on
qualitative and quantitative indicators to be published
in 2016;
• W
rapped up the pilot project for integrating
repositories for mass-spectrometry proteomics data
from ELIXIR Sweden (BILS) with the ProteomeXchange
consortium (EMBL-EBI), demonstrating the potential
of distributed data storage and replication. This project
explored the possibilities of connecting national datastorage services with international repositories through
the EUDAT infrastructure. It also showed the potential
of collaboration among research infrastructures and
e-infrastructures for optimising large-scale data
management, and helped improve the evaluation of
technical requirements for such federated systems.
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Interoperability : Integration of data
and services
The ELIXIR Interoperability Platform is
developing a framework to support people
and machines in the discovery, access,
integration and analysis of biological data.
This platform implements the guiding principles for
‘Findable, Accessible, Interoperable, and Reusable’ (FAIR)
data, working in partnership with a range of international
initiatives, from community grassroots endeavours to
governmental programmes such as BD2K.
The interoperability domain is large, complex and
fragmented. To make meaningful progress, the platform
focuses on specific issues and use cases to improve services
where gaps are identified. In contrast to the other ELIXIR
technical platforms, users of the Interoperability Platform
are almost exclusively those who build infrastructure
and tools.
Carole Goble,
ELIXIR UK
The primary goals of the ELIXIR Interoperability Platform
are to:
• Deliver interoperability services that underpin ELIXIR
use cases, technical platforms and applications;
• I dentify and promote interoperability best practices
and policies for data providers and data integrators.
2015 highlights:
• E
stablished contacts and collaboration with partner
initiatives (BioCADDIE, and BioSharing), including
external liaisons and working groups;
Barend Mons,
ELIXIR Netherlands
• D
eveloped platform management structure and
communication tools;
• S
tarted to draft work plans for the Identifiers and
Services working groups, in preparation for the 2016
review of existing implementation services and
interoperability guidelines;
• O
rganised a series of 'Bring Your Own Data' (BYOD)
workshops and developed BYOD guidelines and
training materials;
• I n the context of ELIXIR’s participation in the Research
Data Alliance (RDA), a global forum to enable open
data across disciplines, technologies and countries,
established an ELIXIR Bridging Force Interest Group to
connect with groups working on agricultural data, Big
Data analysis, federated identity management, marine
data, structural biology, toxicogenomics and data
publishing. Within RDA, ELIXIR contributed knowledge
and solutions to challenges relating to sensitive data in
the life sciences.
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Helen Parkinson,
EMBL-EBI
Tools: Services and connectors to drive access
and exploitation
The ELIXIR Tools Platform supports
accessability and discoverability of
bioinformatics tools and ‘bottom-up’
community efforts to benchmark and
enhance their scientific quality.
The cornerstone of this platform is the ELIXIR Tools and
Data Services Registry (bio.tools), a discovery portal for data
and analysis tools. The registry is curated through a series
of community-driven hackathons, knowledge-exchange
workshops and cross-domain strategy workshops.
Søren Brunak,
ELIXIR Denmark
The main goals of the ELIXIR Tools Platform are to:
• P
rovide tools to help end-users find, understand and
compare the resources they need in their research;
• S
upport resource providers and developers to
contribute to an emerging, globally distributed
biocurator network.
2015 highlights
• L
aunched the ELIXIR Tools and Data Services Registry
run by ELIXIR Denmark;
• O
rganised five hackathons (two in Denmark, one in
the Netherlands, Czech Republic, and Estonia), which
resulted in over 70,000 annotations and over 2,000
entries in the registry. The registry now contains over
2,300 entries from over 200 contributors;
Alfonso Valencia,
ELIXIR Spain
• P
ublished two articles describing different aspects
of the registry in peer-reviewed scientific journals
including Nucleic Acids Research (November 2015).
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Compute: Access, exchange and storage
The ELIXIR Compute Platform aims
to develop and help implement
geographically and organisationally
distributed cloud, compute, storage and
authentication/access services.
It collaborates closely with e-infrastructures such as GÉANT,
EUDAT and EGI as well as translational, biobanking and
imaging infrastructures to facilitate access to effective
services for secure access and data exchange.
2015 highlights:
Tommi Nyrönen,
ELIXIR Finland
• P
ublished a reference document, Technical Services
Architecture for Supporting Life-Science Research,
which resulted from a workshop on mapping ELIXIR’s
use cases to its technical platforms (Amsterdam, the
Netherlands, March 2015). The document identifies
technical aspects of the use cases and proposes a series
of 27 policy and technical recommendations concerning
the strategic objectives of ELIXIR’s compute services.
• W
orked on developing the ELIXIR Authentication and
Authorisation Infrastructure (AAI), in parallel with
the GÉANT-led Horizon 2020 Authentication and
Authorisation Research and Collaboration (AARC)
project. The ELIXIR intranet, launched in December
2015, was the first service to use the ELIXIR AAI.
Luděk Matyska,
ELIXIR Czech Republic
Steven Newhouse,
EMBL-EBI
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Training: Professional skills for managing and
exploiting data
The mission of the ELIXIR Training Platform
is to establish an interactive, ELIXIR-wide
training community to deliver ELIXIR-related
training across Europe.
ELIXIR Training aims to provide developers, researchers
and trainers within the ELIXIR Nodes with the skills to
effectively exploit the data, tools, standards and compute
infrastructure offered by ELIXIR. The platform also focuses
on researchers in the ELIXIR use cases and topics identified
as training gaps.
The Training Platform activities align with and build on
national training activities in ELIXIR Nodes. The ELIXIR
Training Coordinators Group is composed of training
coordinators from ELIXIR Nodes.
Chris Ponting,
Patricia Palagi,
ELIXIR UK
SIB Swiss Institute of
Bioinformatics
Celia van Gelder,
Rita Hendricusdottir,
ELIXIR Netherlands
ELIXIR UK
The main goals of the ELIXIR Training Platform are to:
• B
uild a sustainable training infrastructure for the ELIXIR
community consisting of a training portal for sharing
training content and events (TeSS), relevant e-learning
solutions, and a developers’ forum;
• I ncrease the number of trainers (training capacity
building) with a dedicated Train the Trainer programme;
• D
evelop good training practices and guidelines,
standards, metrics and evaluation systems;
• D
evelop and deliver training to researchers, developers
and infrastructure operators and trainers in topics
selected as gaps within the ELIXIR community and in
the ELIXIR use cases.
2015 highlights
• O
rganised hackathon 'Best practices for training in
Next Generation Sequencing Analysis', Norwich, UK;
• S
tarted the development of the Virtual Coffee Room,
a forum for communicating training needs and sharing
technical solutions (launch planned for 2016);
• L
iaised with ELIXIR platforms, use cases and partner
initiatives, such as RItrain, U.S. Big Data to Knowledge
(BD2K) and RDA-CODATA;
• L
aunched the TeSS portal for sharing training resources
collected by ELIXIR Nodes and third-party providers
(production version planned for 2016);
• W
ith the Global Organisation for Bioinformatics
Learning, Education and Training (GOBLET), published
a Joint Training Strategy (May);
• O
rganised two joint GOBLET/ ELIXIR workshops (in
Ljubljana, Slovenia and Cape Town, South Africa) to
develop guidelines for e-Learning in bioinformatics
(ELIXIR white paper on e-learning to publish in 2016);
• C
o-organised an education workshop and presented
at ISMB in Dublin, Ireland. Co-organised a workshop at
the Galaxy Community Conference in Norwich, UK
• O
rganised eleven Software and Data Carpentry (SWC/
DC) workshops in ELIXIR Nodes to introduce Software
and Data Carpentry’s curriculum and training model
to ELIXIR. The workshops trained around 240 lifescience researchers from 13 ELIXIR Nodes. In addition,
it created a pool of new SWC/DC instructors within
ELIXIR, which will continue to grow in the future.
researchers and trainers from 13 ELIXIR Nodes.
10
Use Cases
ELIXIR Use Cases link the technical
activities taking place in ELIXIR to
the real needs of user communities
in the life sciences. They represent
designated application areas,
and serve to both demonstrate
the impact of services and
activities run by ELIXIR’s technical
platforms and provide the context
for scientific questions that must
be accommodated by the ELIXIR
infrastructure.
In preparation for the ELIXIR-EXCELERATE project, the
ELIXIR Heads of Node Committee identified four highimpact exemplar Use Cases:
Human data
Rare diseases
Marine metagenomics
Plant sciences
In 2015, these ELIXIR Use Cases established their
organisation and governance structures and developed their
work plans.
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Use Case: Human data
As sequencing becomes increasingly
relevant to medicine, the demand for
secure transfer, storage and analysis tools
for human biomedical data consented for
research has risen substantially. The Human
Data Use Case brings together ELIXIR’s
experts from partnering Nodes to develop
a long-term management policy for human
data, and to provide standardised tools for
data discovery and access.
Arcadi Navarro,
ELIXIR Spain
The supporting infrastructure and services developed by
this use case will allow the producers of data to focus on
their unique areas of data generation and analysis expertise,
confident that they can rely on ELIXIR to provide sustainable
infrastructure for their data storage (e.g. for ‘omics data),
coordination and distribution needs within appropriate
legal frameworks.
Ilkka Lappalainen, ELIXIR Human Data Coordinator,
initiated work on ELIXIR’s Human Data strategy in 2015.
This involved developing new activities to support pilot
projects, and building collaborations with external partners
to understand their long-term data-management needs.
TraIT (Translational research IT) is a project by the Dutch
Center for Translational Molecular Medicine (CTMM) to
implement an IT infrastructure for translational biomedical
research. In 2015 ELIXIR initiated a collaborative project
with TraIT with two main goals: (1) to connect TraIT’s data
analyses platform and the data portal TranSMART with the
European Genome-phenome Archive (EGA), a joint project
between EMBL-EBI and the CRG in Barcelona; and (2) to
enable the Dutch researchers to use the EGA as the longterm storage for raw data from all TraIT projects. Once this
project is completed, the TraIT data stored in EGA will be
available on demand to the TraIT researchers for further
analysis in a cloud service, using the Galaxy workflow.
OncoTrack, an Innovative Medicine Initiative (IMI) project
pioneering the use of large-scale genomics to improve the
early diagnosis of colon cancer, began working with ELIXIR
on a joint feasibility project to explore options for the
provision of long-term storage and data-discovery
services for data generated within the project.
ELIXIR will help OncoTrack store and manage
the research and clinical data it generates
by ensuring it is deposited safely and
securely in the EGA, and ensuring that
OncoTrack data are released only to bona
fide researchers following an access review
by the Data Access Committee.
Justin Paschall,
EMBL-EBI
Lighting beacons: A collaboration
with the Global Alliance for
Genomics and Health
‘Beacons’ provide a single point of access to datasets that
are available through many participating institutions. In
2015, ELIXIR initiated the ELIXIR Beacon project with the
GA4GH to provide data-discovery services for genomics that
balance efficient data sharing and data protection. The goal
of the project is to provide consent-based access to genomic
data in the EGA and national resources by implementing
GA4GH Beacons that will scale to support data discovery
across all the ELIXIR Data Nodes. Designed to be technically
simple so that they can be implemented widely,
Beacons represent an important step towards
collaborative, responsible sharing of human
genomic data in Europe.
12
Use Case: Rare diseases
The main objective of the Rare Disease Use
Case is to support the development of new
therapies for rare diseases. This use case
interacts directly with data generators and
curators, researchers and clinicians, SMEs
and the pharmaceutical industry.
The main goals of the ELIXIR Rare Disease Use Case are to:
•
Build an ELIXIR portfolio of data resources and analysis
tools critical for the rare disease research community;
•
Implement a technical framework for the comparison
and standardisation of services useful for this
community;
•
Arrange training courses, workshops and hackathons
to train rare disease researchers to use ELIXIR services
and capture the specific service requirements of this
community.
Ivo Gut, ELIXIR Spain
2015 highlights:
Access to multiple biological and clinical resources, without
too many barriers, is of critical importance in the rare
diseases field. In 2015 ELIXIR launched a joint initiative with
RD-CONNECT, Biobanking and Biomolecular Resources
Research Infrastructure – the Netherlands (BBMRI-NL) and
BBMRI-ERIC to create a federated infrastructure for access
to rare-disease repositories throughout Europe.
Because each rare-disease field is limited in size, the
single most important way for researchers to find source
materials and gain new insights is to combine data across
registries, biobanks and -omics databases. ELIXIR will
test different technologies and find those best suited to
link different resources and tools to better serve the rare
disease community. This work will feed into the ELIXIREXCELERATE Rare Disease Use Case.
ELIXIR Finland (CSC – IT Center for Science) began a
collaboration with BBMRI, becoming the main partner and
supplier of IT infrastructure services to the BBMRI national
centre in Finland (BBMRI.fi). In 2015 ELIXIR Finland began to
run the software that BBMRI uses (e.g. sample availability,
consent register, research access management service,
REMS) within 'ePouta', the secure cloud offered by
ELIXIR Finland.
13
Marco Roos,
ELIXIR Netherlands
Use Case: Marine metagenomics
The ELIXIR Use Case on Marine
metagenomics will develop a sustainable
metagenomics infrastructure to enhance
research and innovation within the
marine domain.
This use case aims to expand the potential of metagenomics
for research and industry while addressing challenges in
standardisation, develop marine reference databases and
deploy bioinformatics tools in cloud environments.
The specific objectives for the ELIXIR Marine Use Case
are to:
•
Develop and implement selected standards for the
marine domain;
•
Develop and implement databases specific to marine
metagenomics;
•
Evaluate and implement tools and pipelines for
metagenomics analyses;
•
Develop a search engine for the interrogation of marine
metagenomics datasets;
•
Organise training workshops for end users.
2015 highlights:
•
Successfully completed a pilot study to gain
deeper insights into challenges related to marine
metagenomics, and to harmonise existing
metagenomics pipelines (i.e. the EMBL-EBI
Metagenomics portal and META-pipe, operated by
ELIXIR Norway);
•
In the context of the pilot project, explored the
potential of available technologies for establishing a
sustainable research and e-infrastructure for marine
metagenomics to help manage the rapid expansion of
metagenomics data. For example, in 2015 alone EMBLEBI Metagenomics analysed three trillion nucleotides–
an increase of 98% over the previous year;
•
Gained a better understanding of how to transfer and
replicate metagenomics data, optimise algorithms
used in metagenomics pipelines and assess the need
for hardware to address computing and storage
capacity issues.
Rob Finn, EMBL-EBI
Nils Peder Willassen,
ELIXIR Norway
14
Use Case: Plant sciences
The Plant sciences Use Case (Genotype
and phenotype in crop and tree species) is
developing an infrastructure to facilitate
genotype–phenotype analyses for crop
and tree species, using standard-compliant
services to allowing integrated querying of
potentially dispersed data.
The main objectives of this use case are to:
•
Design, implement and recommend standards
(minimum information, vocabularies, and file formats)
for the representation of genotypic and phenotypic
data, through coordination with the crop and forest tree
research communities.
•
Make data discoverable and interoperable (in line with
the FAIR data principles specified in the Interoperability
Platform) through the use of common APIs, through
which any researcher can advertise the availability of
their data;
•
Annotate and submit key exemplar datasets to relevant
public archives;
•
Develop re-usable modules for the visualisation of
these data;
•
Disseminate best practice and supporting tools to
national projects and researchers.
Priorities for 2016 are the annotation of initial data sets,
and the investigations of relevant ontologies and tools,
resulting in the establishment of minimum information
guidelines and the specification for further annotation and
API development.
2015 highlights:
• E
stablished working groups to commence work
on metadata representation, the development of
standardised APIs, the definition of biomaterials, and
use cases for genotype-phenotype data.
• B
egan discussion of requirements and approaches with
the ELIXIR platforms.
15
Paul Kersey, EMBL-EBI
Celia Miguel,
ELIXIR Portugal
Highlights from ELIXIR Nodes
Joint Nordic services for human
data: The Tryggve project
In 2015 the ELIXIR Nodes in Finland, Denmark, Norway and
Sweden joined forces to develop IT services for human data.
Supported by the Nordic e-Infrastructure Collaboration
(NeIC), the work has been carried out in the Tryggve project
(https://wiki.neic.no/tryggve), which aims to provide
researchers with a trusted set of services to store and
process sensitive biomedical data across Nordic countries
based on the capacities of the ELIXIR Nodes. Ultimately,
Tryggve aims to produce solutions that are applicable for the
whole ELIXIR community.
Improving the mobility of sensitive, human-based
data,users and tools amongst ELIXIR countries requires that
human data can be moved beyond national borders. Ideally,
the processing tools used for analysis would also be moved
easily to any system the user wants to utilise. In 2015 the
Tryggve worked on the development of secure processing
environments, and achieved technical advances that support
joint use of these environments amongst the partner
countries. The secure computing systems include TSD2.0
at USIT, ELIXIR Norway; Mosler at NBIS, ELIXIR Sweden;
ePouta at CSC – IT Center for Science Ltd, ELIXIR Finland;
and Computerome at Denmark Technical University (DTU),
ELIXIR Denmark. Tryggve project partners also worked
actively on enhancing the portability of tools, notably using
Docker Containers, and on facilitating secure data transfer
between countries.
The Tryggve project supports a research use case concerning
genetic and environmental risk factors in schizophrenia.
This research has combined both genetic and environmental
data from several countries to create larger sample size,
enriching the research. In 2016, the Tryggve project plans to
set up additional collaborations with the Nordic life-science
community.
New secure cloud in
ELIXIR Finland
ELIXIR Finland (www.elixir-finland.org), run by the CSC – IT
Center for Science Ltd (www.csc.fi), provides training and IT
e-Infrastructure services for researchers in the life sciences.
These services are based on cloud and storage resources,
with integrated computational access to very large
biological data resources.
ELIXIR Finland was officially inaugurated on 4 May 2015
at the Museum of Natural History in Helsinki. The event
brought together life scientists, national funders and
policymakers from all over Europe, providing an opportunity
to introduce the full scope of ELIXIR Finland activities and
its service portfolio. The event spotlighted the ePouta cloud,
a new service of CSC – IT Center for Science. Created to
handle sensitive data, ePouta is a secure compute cloud
that meets high-level information security regulations.
Successfully piloted in 2015 by top research centres in
Finland, it was made ready for roll-out to the ELIXIR
community in 2016.
Together with ELIXIR Czech Republic, the Finnish Node
is also leading work on the ELIXIR Authentication and
Authorisation Infrastructure (AAI), which will provide
federated access support for ELIXIR services scheduled to
launch in early 2016. ELIXIR Finland also represents ELIXIR in
the CORBEL and AARC projects, as well as the proposal for
an AARC2 project to develop an integrated cross-discipline
AAI framework for scientific research.
Introducing ELIXIR Czech Republic
ELIXIR’s Czech national Node (www.elixir-czech.org) was
officially established on 4 March 2015, when representatives
of 11 Czech universities and research institutes met in
Prague to sign the consortium agreement. ELIXIR Czech
Republic focuses on three areas, where it serves as a
connection between national and European research
structures: structural bioinformatics, curated databases and
IT-dedicated solutions for life-science research.
In collaboration with ELIXIR Finland, the Czech Node started
working in 2015 on the ELIXIR AAI, providing the national
Identity and Access Management system (PERUN).
Along with ELIXIR Sweden, ELIXIR Czech Republic also
leads ELIXIR’s Capacity Building and Node development
programme to boost organisational capacity in newly
formed ELIXIR Nodes, and to create an ELIXIR-wide Genome
Annotation Network. In 2015 the Czech Node supported
two knowledge-exchange workshops: one hosted by
CEITEC in Brno, Czech Republic, and the other hosted by the
Prague House in Brussels, Belgium (See Capacity Building
Programme for more information).
ELIXIR Czech Republic was also successful in the evaluation
of the Czech research infrastructures, a project conducted
by the Ministry of Education, Youth and Sports. The Czech
National Roadmap, published in October 2015, awarded
ELIXIR Czech Republic a ranking of A1, indicating the highest
priority for public funding in 2016-2022. It was among the
three infrastructures in the biomedical sector to receive the
highest priority mark.
16
ELIXIR Members and Observers
(as of 31 December 2015)
Members
Observers
17
Expanding membership of ELIXIR
Members
Observers
18
ELIXIR Member updates
Belgium
France
• R
eleased five new resources for plant science: plant
genomics, genome annotation, plant data mining and
variant discovery;
• T
rained over 2,000 people in over 80 courses for
life-science researchers and 25 courses for university
students;
• O
rganised and hosted a Data Carpentry workshop in
Brussels (November);
• C
ompleted work towards becoming an ELIXIR Member
(October);
• C
ompleted work towards signing the ELIXIR
Consortium Agreement, becoming a full Member in
November;
• W
elcomed Orphanet, the European reference portal
for information on rare diseases and orphan drugs, to
ELIXIR France (November).
• S
ecured a national grant (€200,000) to bring together
the Belgian bioinformatics community and develop the
Belgian ELIXIR Node.
Denmark
• L
aunched the ELIXIR Tools and Data Services Registry
(January 2015);
• H
eld the first annual Danish Bioinformatics Conference,
sponsored by ELIXIR Denmark (August);
• M
ade Computerome, ELIXIR Denmark’s supercomputer
for life sciences, available to users outside Denmark;
• P
ublished two papers presenting the ELIXIR Tools
and Data Registry in peer-reviewed journals (July,
November);
• H
eld two hackathons: the EDAM Development &
Governance and RNA Analysis (March, September);
• P
resented the Danish ELIXIR Node in BioZoom,
a journal published by the Danish Society for
Biochemistry and Molecular Biology.
Estonia
• H
eld ELIXIR’s first thematic hackathon: NextGeneration Sequencing (NGS), in Tallinn (August).
EMBL-EBI
• C
o-organised ELIXIR’s Software Sustainability
workshop (December);
• H
eld two webinars to present new tools and services
developed by BioMedBridges (BioSamples Database,
RDF, UniChem);
• R
eleased five online training courses as part of
BioMedBridges.
Netherlands
• H
eld the first Green Genetics’ Bring Your Own Data
(BYOD) workshop (January);
• O
rganised the first BYOT (Bring Your Own Template)
meeting, in association with BioMedBridges, the
FAIRport initiative, BBMRI-NL and CTMM/TraIT
(March);
• H
eld two hackathons, two webinars and one training
course;
• H
eld the ELIXIR Innovation and SME Forum DataDriven Innovation in the Agri-Food Industries in
Wageningen (March);
• I ntroduced in a dedicated track at the BIoSB 2015
Conference (May);
• C
o-organised the Empowering Personalized Medicine &
Health Research Conference in Amersfoort (November
2015);
• C
ongratulated Barend Mons, Head of the Dutch ELIXIR
Node, on his appointment to Chair of the European
Commission’s High Level Expert Group on the
European Open Science Cloud;
• E
xpanded the Dutch ELIXIR Node, Dutch Techcentre
for Life Sciences (DTLS), to include over 100 research
groups in 36 partner institutions.
Norway
• O
rganised training activities including two workshops,
ten short training courses and one university course on
the effective use of the bioinformatics tools offered by
ELIXIR Norway;
• M
ade new set of state-of-the-art analysis workflows for
analysing high-throughput sequencing data available
on the Norwegian e-infrastructure for Life Science;
• L
aunched a new collaboration with Biobank Norway on
sensitive data access and management;
19
• A
s part of the marine metagenomics pilot project
supported by EMBL-EBI, devoted considerable efforts
to exploring the potential for establishing a sustainable
research and e-infrastructure for marine metagenomics
to help manage the steep increase of data in this
emerging area.
Portugal
• I nitiated the development of a bioinformatics training
programme for woody plants;
• E
stablished ELIXIR’s Plants Use Case as the platform
co-leader alongside EMBL-EBI;
• L
aunched the ELIXIR Portugal website (www.elixirportugal.org);
• A
ppointed Professor Arlindo Oliveira as new Head of
Node (June).
Spain
• C
ompleted work towards supporting Spain to become
an ELIXIR member, resulting in Spain joining in
October;
• I n collaboration with Intel and Atos, organised
a conference to facilitate academia–industry
collaboration in bioinformatics.
Sweden
• P
resented the Human Protein Atlas in Science
(January);
Switzerland
• H
osted the ELIXIR-SIB Innovation and SME Forum:
Data-driven innovation in the pharma and biotech
industries, in Basel (June);
• H
eld 41 short workshops and 11 long-block courses,
training nearly 1,000 researchers.
• P
ublished an article in Nucleic Acid Research
introducing curated resources at the SIB Swiss Institute
of Bioinformatics (December).
Israel
• C
o-organised an ELIXIR e-Learning workshop in
Slovenia (September).
United Kingdom
• E
stablished a Scientific Development Group to provide
guidance on ELIXIR UK’s future development of its
remit and portfolio (December);
• C
oordinated ELIXIR’s Software and Data Carpentry
Pilot Action, a project featuring the collaboration
between ELIXIR and Software and Data Carpentry;
• E
stablished a collaboration with NIH BD2K in
interoperability, data and training;
• A
dministered the first international survey on the
metabolomics community’s training needs;
• A
ppointed John Hancock, TGAC, as ELIXIR UK Node
Coordinator (February).
• L
aunched Pcons.net, the Protein Structure Prediction
Meta Server (executed in the federated cloud of EGI);
• H
osted the Human Protein Atlas workshop
(November);
• A
s part of the Tryggve project, was awarded a new
grant by NeIC- NordForsk for systems development for
sensitive data;
• F
eatured in Science and Technology (Pan European
Networks Publishing) (September);
• C
oncluded an ELIXIR Pilot Action, featuring the
integration of raw data repositories for mass
spectrometry proteomics data run by ELIXIR Sweden
and ProteomeXchange via the PRIDE database, in
collaboration with EMBL-EBI.
20
ELIXIR Observer updates
Greece
• L
aunched two new tools: Mouse Resource Browser
(MRB), providing interactive view of mouse resources
available worldwide, and CuticleDB, a relational
database of Arthropod cuticular proteins;
• H
eld the ELIXIR Greece partners’ meeting to prepare
the launch of the Greek ELIXIR Node (December).
Italy
• S
ecured four new EU grants totaling over €500,000
for research in food and health, marine science and
biodiversity;
• O
rganised four bioinformatics training events for lifescience researchers;
• C
oncluded ELIXIR Italy’s preparatory phase, joining
ELIXIR as a full member in January 2016.
Ireland
• J oined ELIXIR as Observer in October 2015, presently
working on establishing ELIXIR’s Irish Node.
Slovenia
• R
eceived support from Horizon 2020 (totaling nearly
€500,000) to develop the Centre of Excellence for
Translational Medicine (CETM);
• L
aunched ELIXIR Slovenia’s eLearning Platform,
including a series of hands-on tutorials;
• C
o-organised the SysBioMed conference in Ljubljana,
in collaboration with ISBE and CASYM (June-July);
• O
rganised four training workshops and meetings as
part of ELIXIR’s Training Platform;
• C
ompleted ELIXIR Slovenia’s preparatory phase at
the AGM meeting in December, becoming an ELIXIR
Member in February 2016.
21
Accelerating implementation
ELIXIR-EXCELERATE
ELIXIR-EXCELERATE is a major EU Horizon
2020 grant to help ELIXIR implement its
Scientific Programme.
Basic facts:
•
€19.8 million
•
4-year project (2015-2019)
•
41 partners across 17 countries
ELIXIR was invited to apply to a dedicated call within
Horizon 2020 following the ESFRI and European Council’s
decision in 2014 to name ELIXIR as one of Europe’s three
priority new Research Infrastructures. ELIXIR-EXCELERATE
represents ELIXIR’s submission to this call.
•
Start: 1 September 2015
With a budget of nearly €20 million and including well over
40 partners from ELIXIR Nodes, ELIXIR-EXCELERATE will
accelerate the implementation of the ELIXIR Platforms and
integrate ELIXIR bioinformatics resources into a coherent
infrastructure.
•
Accelerate the implementation of ELIXIR;
•
Develop and connect resources and services (across
ELIXIR Nodes);
•
Build bioinformatics capacity across Europe (through
Capacity Building and Training).
ELIXIR-EXCELERATE’s structure reflects the scientific
and technical priorities set out in ELIXIR’s Scientific
Programme 2014-2018. The impact of the infrastructure
services delivered within the five technical Platforms
established within ELIXIR (Data, Tools, Interoperability,
Compute and Training) will be informed by four Use Cases:
marine metagenomics, crop and forest plants, rare disease
and sensitive human data. The technical and scientific
activities will be complemented by a pan-European training
programme, which will increase bioinformatics capacity
and competency.
Overall goals:
On 10 December, the project kick-off meeting brought
together over 90 representatives across ELIXIR to
Cambridge, UK. Project partners presented their plans and
expected outcomes for each of the project tasks, discussing
challenges and actions that cut across the Work Packages.
The activities and first results include a series of hackathons
to expand the ELIXIR Tools and Services Registry (http://
bio.tools), establishing a common identity to access
ELIXIR services (e.g. AAI), setting up the first Data Nodes
(i.e. those with large data collections and databases), the
first workshop on genome annotation, and activities to
strengthen the ELIXIR Training programme.
Delegates at the ELIXIR-EXCELERATE kick-off meeting at Murray Edwards College, University of Cambridge, UK, December 2015.
22
Highlights from Technical Coordinators
The Technical Coordinators Group (TeCG)
comprises technical experts representing
each of the ELIXIR Nodes and is chaired
by ELIXIR’s Chief Technical Officer, Rafael
Jimenez. The group’s role is to identify
challenges and existing gaps in ELIXIR’s
scientific and technical aspects and
coordinate the technical activities across
the individual Nodes. The TeCG also explores
technical opportunities and issues providing
advice and recommendations to the Heads
of Nodes.
In 2015, the TeCG worked together with the Compute
Platform on the Reference Technical Services Architecture
for supporting Life Science Research, which provided
strategic objectives for the Compute Platform, on ELIXIR’s
AAI Strategy, and on the Storage and data transfer strategy.
The TeCG also established a new Working Group for
Galaxy Recommendations. Galaxy is an online platform
for data-intensive biomedical research, designed for lifescience researchers who do not have extensive computer
programming experience. The working group aims to
collect information on the Galaxy Platform and evaluate
its use across ELIXIR Nodes and its applications in ELIXIR
Platforms. The Heads of Nodes Committee adopted
the group’s recommendations on training, especially on
technical training for Galaxy operators and service providers
in ELIXIR Nodes.
The TeCG launched the Software Development Best
Practices Working Group to deliver guidelines on best
practices and quality assessment in software development.
In collaboration with the Software Sustainability Institute,
the Working Group will address issues such as quality and
sustainability metrics, open source policies or software
licensing. The group is open to any organisation in lifescience research, especially to biomedical research
infrastructures, and its objective is to find and define
common aspects in software development that could be
adopted across the life sciences.
The kick-off meeting of this initiative took place on 14
December 2015 in Amsterdam. The main goals are to
develop a white paper on best practices and quality
assessment in software development in life-science and
present it to the Heads of Node Committee in Autumn 2016.
23
Rafael Jimenez, ELIXIR
Chief Technical Officer,
Chair of the Technical
Coordinators Group
Industry engagement
ELIXIR Innovation and
SME programme
In 2015 the ELIXIR Innovation and SME programme
expanded, holding two events in the Netherlands and
Switzerland. Hosted by DTL and Wageningen University,
the interactive, two-day event in March focused on datadriven innovation in the agri-food sectors. The 80 delegates
included representatives from companies such as Bayer,
Syngenta and FrieslandCampina; smaller plant-breeding and
food companies such as Enza Zaden, Bejo Zaden and Nizo;
IT companies including Microsoft; and research-intensive
SMEs such as Keygene, Genetwister and EdgeLeap.
Richard Finkers, Wageningen University and Research
Centre commented: “I am delighted that such a large
number of companies attended the meeting. This is
testament to the importance of a high-quality public
infrastructure for life science data. I am equally pleased that
there was such deep interaction and discussion between
delegates during the two days and I am confident that
it will lead to further collaboration between industry
and academia.”
The June event, hosted by the SIB Swiss Institute of
Bioinformatics (ELIXIR Switzerland) and held alongside the
Basel Computational Biology Conference (BC2), focused
on pharma and biotech. Over 70 participants attended,
representing Novartis, Sanofi, Lonza Bioscience, 4-Antibody
AG, ALK, IBM, QIAGEN and many other companies.
Delegates heard about many relevant services and resources
and interacted with the SIB experts who run them.
"I made good connections, and expect
to start several new translational
bioinformatics projects as the result
of the meeting.”
John Castle, Senior Director, Bioinformatics;
4-Antibody AG & Agenus
Industry projects
Throughout 2015, ELIXIR developed collaborations with key
industry initiatives, which will continue during 2016.
ELIXIR began a collaboration with the Pistoia Alliance to
map the links between academia and industry. Through
BioSchemas, the community-driven initiative to extend
the standards within schema.org, this collaboration aims
to standardise the description of content including events,
training, training materials, people and organisations in the
life sciences. This will ensure more effective information
sharing across the sector. All of the data gathered in the
project will be made available for reuse.
ELIXIR and the IMI-funded OncoTrack project began
to plan collaboration around the long-term storage of
data. OncoTrack uses large-scale genomics to generate
new data to power research that will improve the early
ELIXIR Innovation & SME forum at Wageningen University in
the Netherlands.
diagnosis of colon cancer. As part of the collaboration,
ELIXIR will examine the provision of safe data storage and
management via the European Genome-Phenome Archive.
The project is scheduled to run throughout 2016.
Understanding the needs
of industry
ELIXIR’s Industry Advisory Committee (IAC) met for
the first time in early 2015, issuing a set of high-level
recommendations including the need to develop a set of
core resources of industry standard and to ensure that data
services within ELIXIR remain interoperable, open and
sustainable.
IAC Members in 2015:
•
Martin Ebeling, Hoffmann-La Roche, Switzerland
•
Anita Eliasson, Biocomputing Platforms Ltd, Finland
•
Wendy Filsell, Unilever R&D, UK (Vice Chair)
•
Mark Forster, Syngenta, UK (Chair)
•
Iain Hrynaszkiewicz, Nature Publishing Group Macmillan, UK
•
Natalia Jimenez Lozano, Atos, Spain
•
Claus Stie Kallesøe, Gritsystems A/S, Denmark
•
Angel Pizarro, Amazon Web Services, USA
•
Philippe Sanseau, GlaxoSmithKline, UK
•
Montserrat Vendrell, Biocat, Spain
•
Jakob de Vlieg, Bayer CropSciences Innovation Center,
Belgium
24
Highlights from 2015
29 January 2015
Launch of the ELIXIR Tools and Data services registry: A portal to bioinformatics resources worldwide
ELIXIR’s Tools & Data Services Registry (bio.tools) provides essential information to help users find the right
resource for their research. By the end of 2015 this community-driven curation effort, coordinated by ELIXIR
Denmark, offered over 2,000 consistently described resources, all conforming to an emerging common standard.
4 March 2015
ELIXIR Czech Republic is established officially
Representatives of 11 Czech universities and research institutes met in Prague to sign a consortium
agreement setting up the Czech ELIXIR Node. ELIXIR Czech Republic include structural bioinformatics,
genomics data on microorganisms and plants, and cheminformatics. With ELIXIR Finland, the Czech Node
started to build an Authentication and Authorisation Infrastructure (AAI) to for all ELIXIR services.
30-31 March 2015
JU
N
M
AY
AP
R
M
AR
FE
B
JA
N
ELIXIR holds its first All-Hands meeting
ELIXIR’s first All-Hands meeting, held in Hinxton, UK, welcomed over 150 members of ELIXIR Nodes and
collaborators from partner organisations. Topics included data management plans, Node development,
database metrics, human research data and training. The keynote presentation was given by Prof. Geoffrey
Boulton of the University of Edinburgh.
26 February 2015
20 April 2015
11 June 2015
ELIXIR establishes its Industry Advisory
Committee: First recommendations made
This Committee held its first meeting on 26
February 2015 in Hinxton, UK. Mark Forster of
Syngenta was elected Chair of the Committee
and Wendy Filsell of Unilever was elected
Vice Chair. The committee published its first
recommendations, introduced examples of
value generated by open life-science data
resources, and outlined how ELIXIR can help
industry make better use of these resources.
ELIXIR and GOBLET launch global
training strategy
ELIXIR and the Global Organisation for
Bioinformatics Learning, Education and
Training (GOBLET) published a Joint Training
Strategy to establish a collaboration
framework. ELIXIR and GOBLET organised
workshops on e-Learning in Ljubljana,
Slovenia, and Cape Town, South Africa.
Beacon project: ELIXIR
partners with the Global
Alliance for Genomics
and Health
During the third plenary
meeting of the Global Alliance
for Genomics and Health
(GA4GH), ELIXIR and GA4GH
discussed a joint project to
provide data-discovery services
for genomics. The project
centres on establishing GA4GH
Beacons in the European
Genome-phenome Archive
(EMBL-EBI and CRG Barcelona)
and national resources in
Finland, Sweden and the
Netherlands. The ELIXIR Beacon
project started on 1 September.
4 May 2015
ELIXIR Finland Node launches officially
ELIXIR Finland was launched at an event in the
Natural History Museum of Helsinki. The event
featured an address by Finland’s Ministry of
Education and Culture.
25
9 October 2015
22 October 2015
G7 report highlights ELIXIR as a global
research infrastructure
The G7 Group of Senior Officials (GSO) on
Global Research Infrastructures published
its 2015 Progress Report following a
meeting of the G7 Science Ministers held on
8-9 October 2015. The report named ELIXIR
as a Global Research Infrastructure with the
potential for collaboration with countries
across the globe.
France and Spain join ELIXIR
In October and November 2015, the
ELIXIR Board approved the membership
applications of France, Spain and Belgium.
ELIXIR Spain is funded by the
National Institute of Health Carlos
III and coordinated by the National
Bioinformatics Institute (INB), which
maintains core resources in functional
genomics, transcriptomics with RNA-Seq,
genotyping, genomic medicine, structural
bioinformatics and molecular dynamics
simulations.
ELIXIR France is led by the French Institute
of Bioinformatics (IFB), which provides
well-curated specialised databases,
on-line tools and services, dedicated IT
infrastructures, support to life-science
projects, and training. IFB Platforms
add value to routinely produced data in
sequencing, genotyping, proteomics,
metabolomics and other areas.
DE
C
NO
V
Collaboration with Software Sustainability Institute launches
An initiative between ELIXIR and the Software Sustainability Institute,
launched in Amsterdam, aims to develop guidelines for creating a
sustainable open-source policy for software development.
O
CT
ELIXIR and BD2K explore collaboration
ELIXIR and the NIH Big Data to Knowledge initiative (BD2K)
organised a joint session at ISMB-ECCB 2015 in Dublin. This
marked the beginning of an on-going dialogue between
Europe and the US to explore shared challenges in lifescience data infrastructure. ELIXIR and BD2K collaborate on
interoperability and standards in projects such as BioCADDIE,
BioSharing and CEDAR.
SE
P
14 December 2015
JU
L
13 July 2015
24 November 2015
Belgium joins ELIXIR
ELIXIR Belgium focuses on sustainable agriculture and human health, offering databases, resources,
services and expertise in biostatistics and machine learning. It also offers expertise and resources in highperformance computing, notably computing resources for handling next generation sequencing data.
17-18 November 2015
Symposium marks the closing of BioMedBridges
At the end of BioMedBridges, the "Open Bridges for Life Science Data" symposium in Hinxton presented
the project outcomes. Members of the biomedical research infrastructure community discussed practical
challenges in data sharing and interoperability.
Symbolically, the event was followed by the kick-off meeting for CORBEL, which will build on the
achievements of BioMedBridges.
1 September 2015
EXCELERATE and CORBEL grants start
Horizon 2020 grants ELIXIR-EXCELERATE and CORBEL commenced, establishing
organisational and governance structures and developeing a timeline for delivery.
The EXCELERATE kick-off meeting took place on 10 December 2015 in Cambridge,
UK. ELIXIR and BBMRI are project coordinators for CORBEL, a collaboration of 11
biomedical research infrastructures. The CORBEL project held its kick-off meeting
on 19 November.
26
Scientific Advisory Board
ELIXIR’s Scientific Advisory Board (SAB)
plays a major role in reviewing ELIXIR
Nodes, and provides strategic scientific
advice to the ELIXIR Board. The SAB is
an independent body made up of leading
experts from around the world, and meets
twice a year.
On its meeting in October 2015 in Hinxton, the ELIXIR Board
appointed three new members to the Scientific Advisory
Board: Prof. Pascal Borry, Prof. Kate Bushby, and Dr Susan
Wallace. Kate Bushby replaces Dr Ségolène Aymé who
stepped down from the ELIXIR SAB at the end of her term in
October 2015; Pascal Borry and Susan Wallace will work in
the SAB as experts on Ethical, Legal and Social Implications
(ELSI).
Members:
• Prof. Alan Archibald, University of Edinburgh, UK
• D
r Ségolène Aymé, Institut National de la Santé Et de la
Recherche Médicale, France (until October 2015)
• P
rof. Pascal Borry, University of Leuven, Belgium (from
October 2015)
• P
rof. Kate Bushby, Newcastle University, UK (from
October 2015)
• Prof. Elina Ikonen, University of Helsinki, Finland
• P
rof. Edward Marcotte, The University of Texas at
Austin, USA
• P
rof. Nicola Mulder, UCT Computational Biology Group
(NBN), South Africa
• D
r Susan E. Wallace, University of Leicester, UK (from
October 2015)
• Dr Jérôme Wojcik, Quartz Bio, Switzerland
• Chair: Dr Robert Gentleman, 23andMe, USA
• V
ice Chair: Dr Janet Kelso, Max Planck Institute for
Evolutionary Anthropology, Germany
ELIXIR Scientific Advisory Board in 2015. From Left to right: Edward Marcotte, Susan E. Wallace, Elina Ikonen, Jérôme Wojcik, Robert
Gentleman, Alan Archibald, Ségolène Aymé, Janet Kelso, Nicola Mulder.
27
International collaboration
ELIXIR expanded its membership within
Europe during 2015, and began to develop
collaborations with key countries and
initiatives globally.
Dialogue with Australia and Canada picked up throughout
2015, with visits by the ELIXIR Director to both countries.
Discussions took place around the development of
Memoranda of Understanding, with the aim of facilitating
a path to closer collaboration or membership in the
coming years.
Expanding membership
within Europe
On the technical level, ELIXIR Platforms and groups
expanded their interaction with key global initiatives such as
the GA4GH, GOBLET and the Research Data Alliance (RDA).
Membership of ELIXIR at the start of 2015 stood at 12
(the Czech Republic, Denmark, Estonia, Finland, Israel,
Netherlands, Norway, Portugal, Sweden, Switzerland,
United Kingdom and EMBL-EBI) with six Observer countries
(France, Spain, Belgium, Italy, Slovenia and Greece).
Throughout the year, France, Spain and Belgium moved
to become ELIXIR Members, and thus be able to fully
participate in its activities, taking membership to 15, with
Italy poised to join as Member in early 2016. The progress
made in this regard has been extremely positive and is
testament to the importance ESFRI member states place on
ELIXIR and to its successful operations so far.
At the policy level, ELIXIR began global discussions around
the sustainability of databases with representatives of North
American, European and Asian funding bodies.
In 2016 ELIXIR will publish a public international strategy,
mapping out the international countries and initiatives that
will be the focus of global collaboration efforts.
Ireland became an ELIXIR Observer in Autumn 2015 and
the remaining Observer countries (Slovenia and Greece)
made good progress towards ratifying the ECA and
achieving full Membership in ELIXIR in 2016. Dialogue
continued with Ministries and scientific communities
in Germany, Luxembourg and Austria, with the aim of
facilitating Membership in the future. In particular, ELIXIR
collaborated on a joint strategy with the German Network
for Bioinformatics Infrastructure (de.NBI), with a view
to implementing this collaboration fully when a positive
decision on Germany’s membership in ELIXIR has
been taken.
Positioning ELIXIR globally
In October, the G7 Group of Senior Officials (GSO) on
Global Research Infrastructures published its 2015 Progress
Report. ELIXIR was recognised by the report as a research
infrastructure of global potential, due to the potential it has
for collaboration with, and membership from, countries
across the globe. ELIXIR was one of only a small number of
ESFRI Research Infrastructures to be categorised as such.
Collaboration with the US Big Data to Knowledge (BD2K)
initiative stepped up, with a joint workshop on standards
and interoperability in London early in the year, a joint
session at the European Conference on Computational
Biology (ECCB) in Dublin in summer, and representation
from ELIXIR members at the BD2K annual meeting later in
the year.
28
Capacity building
ELIXIR’s Capacity building and Node
development programme began in 2015. The
programme focuses on knowledge transfer
amongst ELIXIR Nodes, particularly for
newer or smaller Nodes and those in less
research-intensive regions.
Rolled out as part of ELIXIR-EXCELERATE Work Package
10, the programme aims to boost organisational capacity
in newly formed ELIXIR Nodes and create an ELIXIR-wide
Genome Annotation Network. Led by ELIXIR Czech Republic
and ELIXIR Sweden, the programme saw the organisation of
three successful knowledge exchange workshops in 2015.
Accessing EU Structural Funds
8-9 October, Brno, Czech Republic
The workshop brought together experts on EU Structural
Funds (ESIF) from across ELIXIR Nodes and organisations
such as the European Commission. Hosted by CEITEC, the
programme allowed partners understand the current rules
and opportunities for ESIF, exchange best practice in using
ESIF to fund research infrastructures and plan for an ELIXIR
Task Force on ESIF.
Genome Annotation
19-20 October, Uppsala, Sweden
Hosted by ELIXIR Sweden, the meeting brought together 26
participants, representing 11 ELIXIR Nodes. The programme
was dedicated to presenting and discussing the interests
29
and needs in genome assembly and annotation across the
Nodes and defining the work plan for 2016. In the first part,
participants presented their Nodes and their capacity and
interest in genome assembly and annotation. The second
part focused on specific tasks to support information
exchange and training within the group.
Structure and Governance of
ELIXIR Nodes
3-4 November, Brussels, Belgium
Over 20 ELIXIR representatives attended this event, held
in Brussels at Prague House. With talks from established
Nodes, such as the SIB Swiss Institute of Bioinformatics, it
focused on organisational and governance structures for
ELIXIR Nodes. Another topic for discussion was building
effective national collaboration between ELIXIR and other
ESFRI infrastructures. The meeting also included a session
from the European Commission on using the Linked Third
Party clause in Horizon 2020 grants.
Looking ahead to 2016, the Capacity Building programme
will work on developing the concept of ELIXIR Data Nodes
Network, which aims to document ELIXIR-wide good data
stewardship, such as practices for submission to archives
and practices for optimal interoperability of these archives,
as well as good practices in setting up Data Nodes enabling
secure storage of sensitive human data. Furthermore, the
programme will look at staff exchanges between ELIXIR
Nodes and facilitate Node development through exchanging
expertise on national roadmap applications.
Participants at the ELIXIR capacity building and Node development
workshop , Brussels, 3-4 November 2015.
Scientific collaborations: EU grants
ELIXIR participates in several EC-funded
projects to drive the delivery of various
bioinformatics services to the scientific
community. These projects enable ELIXIR
to collaborate with other key European
and global initiatives, as well as other
ESFRI Research Infrastructures and
e-Infrastructures.
ELIXIR, represented by ELIXIR Finland (CSC- IT Center for
Science), focuses on preparing training materials for service
providers and leads the work on Level of Assurance. In
2015, ELIXIR Finland conducted a Level of Assurance survey
among operators of research and e-infrastructures and
developed a recommendation for a minimal assurance level
for European research infrastructures, which define the
minimum authentication requirements to allow user access.
AARC benefited from ELIXIR’s requirements and design
documentation of its authentication and authorisation
infrastructure (AAI), which was used in the project’s
architecture blueprints.
ENVRIplus
ENVRIplus (www.envriplus.eu) is a Horizon 2020 project
linking Environmental and Earth System Research
Infrastructures, projects and networks together with
technical specialist partners to create a more coherent,
European Marine Biological
Research Infrastructure Cluster
(EMBRIC)
EMBRIC (www.embric.eu), financed with €9 million
from the Horizon 2020 programme, connects marine
biotechnology initiatives that focus on science, industry and
regional growth. The EMBRIC project started in September
2015 and includes four ESFRI Research Infrastructures:
European Marine Biological Resource Centre (EMBRC),
Microbial Resource Research Infrastructure (MIRRI), EUOPENSCREEN and ELIXIR. With five ELIXIR Nodes involved
(France, Greece, Italy, Norway and EMBL-EBI), ELIXIR’s role
is to provide capacities and expertise in data services and
management.
The goals of EMBRIC are to:
1. Strengthen the connection of science with industry;
2. Defragment R&D policies and involve maritime regions
with the construction of EMBRIC;
3. Accelerate the scientific discovery and innovation from
marine bioresources.
Authentication and Authorisation
for Research and Collaboration
interdisciplinary and interoperable cluster of Environmental
Research Infrastructures.
ENVRIplus covers all domains of Earth system science
(Atmospheric domain, Marine domain, Biosphere and
Solid Earth domains), and it is organised into six themes:
(1) Technical innovation, (2) Data for science, (3) Access
to research infrastructures, (4) Societal relevance
and understanding, (5) Knowledge transfer and (6)
Communication and dissemination.
ELIXIR, represented by EMBL-EBI, provides expertise and
resources in the Biodiversity and Ecosystem field and in the
‘Data for science’ theme. The project started in May 2015
and is coordinated by the Integrated Carbon Observation
System (ICOS) Research Infrastructure.
The AARC project (https://aarc-project.eu) started in May
2015, bringing together 20 partners from across Europe.
The project’s goal is to harmonise AAI approaches among
different e-infrastructures and research collaborations.
30
Collaborations with biomedical
research infrastructures
ELIXIR coordinates collaboration between many research
infrastructures in the biomedical sciences. 2015 saw the
successful conclusion of BioMedBridges, the first biomedical
science research infrastructure ‘cluster project’, and the start
of its successor, CORBEL, which is coordinated by ELIXIR.
Both BioMedBridges and CORBEL focus on simplifying
and harmonising user access to the services offered by
the ESFRI biomedical research infrastructures. Whilst for
BioMedBridges, the goal was to enable data integration
across the biological, medical, translational and clinical
domains, CORBEL aims to support users and research
projects in accessing common services run by partners,
going beyond data to also include access to physical
infrastructures, innovation and ELSI expertise.
BioMedBridges
Coordinated by EMBL-EBI on behalf of ELIXIR,
BioMedBridges (2012-2015, www.biomedbridges.eu)
brought together 12 of Europe’s biomedical sciences
research infrastructures to link the data, resources and
services provided by the individual infrastructures.
BioMedBridges’ main purpose was to facilitate the
translation of ideas into new biomedical and environmental
applications by removing technical stumbling blocks related
to interoperability of data coming from different scientific
domains. BioMedBridges built a shared data culture by
connecting data specialists and domain experts across a
large number of biomedical, biological and environmental
domains, from genomics, imaging and structural biology,
through mouse disease models and clinical trials to highly
contagious agents and chemical biology.
The project outcomes and its contribution to data
interoperability laid the foundation for the reuse,
combination and analysis of data in many different contexts
across different spatial scales (from molecules to humans
and environment), between different species (from mouse
models to humans), between different technologies, and
across different research communities (from basic molecular
biologists to clinicians and environmental researchers).
Examples of project results include the harmonisation of
standards and identifiers, guidelines for sharing sensitive
and personally identifiable data, a range of new services
to facilitate discovery in research on diabetes and obesity
by enabling better comparisons between data on mouse
models and humans, a web service to support the analysis
of low-resolution structural data, tools to enable easier
and better data annotation and annotation of images from
different organisms and at different scales and many others.
“What BioMedBridges tries to do is to ensure that the
interface between these different communities within the
life sciences gets better so that we can exchange our data,"
31
said Janet Thornton of EMBL-EBI. "It’s very clear that over
the next ten, twenty years the real novel discoveries in life
sciences will occur at the interfaces between the molecular
and the cellular, the cellular and the organismal, and that we
need to join all of this data up. Gradually (...) we will develop
much better tools, ontologies and identifiers that will allow
us to seamlessly exchange and interpret data.”
"It’s very clear that over the next
ten, twenty years the real novel
discoveries in life sciences will
occur at the interfaces between
the molecular and the cellular, the
cellular and the organismal, and that
we need to join all of this data up."
Janet Thornton, EMBL-EBI/ELIXIR,
BioMedBridges Coordinator
Open Bridges for Life-Science
Data symposium
The BioMedBridges project concluded with the final
symposium, hosted by ELIXIR at the Wellcome Genome
Campus Conference Centre in Hinxton, on 17-18
November 2015. The symposium presented the results and
achievements of the project and provided a venue for the
community to discuss real-life challenges connected to data
sharing and interoperability in the life sciences. It attracted
around 250 delegates from all over the world.
CORBEL
CORBEL (www.corbel-project.eu), the next biomedical
science cluster project, builds on and extends a number
of the resources, tools and collaborations developed in
BioMedBridges. The CORBEL consortium is led by ELIXIR as
the coordinator and BBMRI as co-coordinator.
Overall goals:
1. Set up simplified access points and joined-up service
catalogues for users across medicine and biology;
2. Integrate the capabilities of individual RIs into the
scientific workflow of advanced users;
3. Implement a portfolio of seamless, shared research
infrastructure services.
Basic facts:
• Funded with €14.5 million over four years (2015-2019);
• 1 1 participating research infrastructures in biomedical
sciences (35 partners in nine European countries);
• Start: 1 September 2015;
• C
oordination: ELIXIR (Coordinator) and BBMRI‐ERIC
(Co-coordinator).
Each of the participating research infrastructures provides
access to domain-specific research services, instruments,
data, samples, facilities and specialist knowledge and
training that collectively cover life science research,
from basic biology to medical translation. CORBEL will
integrate these services into common scientific workflows
and ensure that these respond to the needs of European
researchers. CORBEL will also set up a training programme
for research infrastructure operators and key users to drive
the rapid implementation of shared services into research
infrastructure operations.
The project started in September 2015 and its priorities
have been discussed on 19 November 2016 at the kickoff meeting held on the Wellcome Genome Campus in
Hinxton, following the BioMedBridges symposium. For
2016, priorities include linking CORBEL’s data management
efforts with other standardisation efforts globally, including
parallel efforts in the EXCELERATE interoperability Work
Package, and the development of common approaches to
Ethical, Legal and Societal Implications (ELSI).
Photos from the Open Bridges for Life-Science Data symposium,
Hinxton, UK, November 2015.
32
Activities at the ELIXIR Hub
Supporting Node development
ELIXIR Gateway on F1000Research
For a fully functional infrastructure, it is critical to implement
ELIXIR effectively at the national level and tie the institutes
and resources together in each country so that the national
Node can enter into a Collaboration Agreement with the
ELIXIR Hub. After the approval of the ELIXIR Collaboration
Agreement Template in 2014, the first agreements between
the Hub and ELIXIR Nodes (Czech Republic, Denmark,
Estonia, Finland, Netherlands, Norway, Sweden, and
Switzerland) were put into force in 2015.
In December 2015, ELIXIR launched the ELIXIR
F1000Research Gateway (http://f1000research.com/
channels/elixir) to publish its research and technical
outputs. The Gateway was introduced to the community
in an Editorial, published by the newly established ELIXIR
Editorial Board.
In 2016, we plan to conclude the negotiations with the
remaining ELIXIR Nodes and have the ELIXIR Board
to approve these agreements later in the year. Each
Collaboration Agreement will also describe the scientific and
service content that each national ELIXIR Node
exposes through ELIXIR: the work to draft these Service
Delivery Plans was initiated in 2015 and will continue
throughout 2016.
ELIXIR communications
The ELIXIR Hub launched a new HTML template and a
new Drupal installation with an ELIXIR theme that can be
adopted by ELIXIR Nodes in building their own website. The
ELIXIR Drupal installation is an out-of-the-box solution for
ELIXIR Nodes and allows for seamless navigation between
all ELIXIR websites.
ELIXIR Portugal’s new website launched in November
2015 (www.elixir-portugal.org) and was the first site to use
the ELIXIR Drupal installation. In 2015, ELIXIR UK, ELIXIR
Norway and ELIXIR Slovenia started the development of
their websites using the Drupal theme.
In 2016 we plan to update the structure and content of the
public website and improve the site’s navigation. We will
also support further Nodes in their adoption of the ELIXIR
Drupal installation.
The ELIXIR intranet launched in December 2015 to provide
a platform for information and knowledge exchange to the
ELIXIR community. It is embedded into the ELIXIR website
and provides a reference point for all information and
documents within the ELIXIR infrastructure. The intranet
was also the testing ground for the ELIXIR Authorisation and
Authentication Infrastructure (AAI)–the first service to use
the ELIXIR AAI for login and access.
In 2015, the intranet was in testing mode and has been
introduced only to a limited number of community
members. In 2016 the intranet will be rolled out to all
Platforms and Use Cases and will become the main internal
communication channel in ELIXIR.
33
ELIXIR Gateway’s Advisory Board oversees the publication
process and provides the editorial oversight to ensure
that the published materials are relevant to the ELIXIR
community. All research articles published in the ELIXIR
Reports Channel are transparently peerreviewed through
the F1000Research-invited post-publication open peerreview process. Articles accepted by independent reviewers
are indexed in PubMed and available as open access in
Europe PMC and other major bibliographic databases.
The Gateway will feature work developed through
ELIXIR’s five Technical Platforms: Tools, Data, Compute,
Interoperability and Training, as well as ELIXIR’s strategy
documents, technology developments and reviews. The
Gateway published its first research articles in early 2016.
ELIXIR Hub staff
In 2015, the ELIXIR Hub expanded its team and recruited
experts for technical, communications and project
management positions. Stephanie Suhr joined the Hub as
Senior Project Manager to lead the project management
unit for externally-funded projects. In September, Friederike
Schmidt-Tremmel joined as Project Manager for the
CORBEL project.
The technical expertise at the Hub was strengthened by
the arrival of three visitors: Ilkka Lappalainen from EMBLEBI, Mikael Linden from CSC - IT Center for Science (ELIXIR
Finland) and Andy Jenkinson from EMBL-EBI. Ilkka brought
to the ELIXIR Hub his considerable expertise on secure
sharing of genomic data, and helped shape our strategy
for managing human data. In September 2015, Ilkka took
up a new position in ELIXIR Finland as Biomedical Service
Development Manager. We wish Ilkka all the best for his
new job.
Mikael Linden has a strong expertise in authentication and
authorisation infrastructure (AAI) and will support the work
of the ELIXIR Compute Platform. In the ELIXIR-EXCELERATE
project, Mikael co-leads our work to define and implement
ELIXIR authorisation and authentication services to enable
easy and secure user access to data resources and other
ELIXIR resources.
ELIXIR Hub staff in 2015. From Left to right: Joy Friesner, Mikael Linden, Nicola Kay, Chuqiao Gong, Phyllida
Hallidie, Susanna Repo, Niklas Blomberg, Friederike Schmidt-Tremmel, Andy Smith, Steffi Suhr, Martin Cook,
Přemysl Velek. Front row: Andy Jenkinson and Rafael Jimenez. (Not pictured: Ilkka Lappalainen.)
Andy Jenkinson has extensive experience in life science
data management and at the Hub he focused on developing
ELIXIR’s data management architecture and activities.
He looked across the ELIXIR Platforms and Use Cases and
delivered a proposal for an architecture that supports
effective data distribution to users across ELIXIR Nodes and
cloud environments.
In June, Přemysl Velek joined the ELIXIR Hub as
Communication and Outreach Officer and led ELIXIR’s dayto-day communications and outreach activities supporting
the dissemination of ELIXIR-related activities. He also
initiated a network of communications experts from across
ELIXIR Nodes. To ensure the ELIXIR website, intranet and
other online services are developed to cater the growing
infrastructure, Martin Cook joined the ELIXIR Hub as Web
Developer. Charles Gaillard joined the Hub as an intern,
working on a short-term project for the ELIXIR Events portal.
Phyllida Hallidie joined us in July to take the role as Personal
Assistant to the ELIXIR Director when Branka Stekovic
moved to a new role outside of ELIXIR.
Staff exchange
In October 2015, two staff members from ELIXIR Czech
Republic (CEITEC) visited the ELIXIR Hub in Hinxton, UK,
and spent a week learning about ELIXIR Communications
activities and exchanging experience in different aspects
of science communications and outreach. Jana Silařová,
CEITEC Communications Officer and Dana Černošková,
CEITEC Events Officer met with Hub staff members–Andrew
Smith and Přemysl Velek – as well as with EMBL-EBI’s
Communications team and discussed how to facilitate
information exchange between ELIXIR Nodes.
Plans for the establishment of an official ELIXIR staff
exchange programme are underway. The programme,
expected to roll out in 2016, would enable sharing of
experience and expertise between the ELIXIR Nodes and
the Hub.
In the legal office at EMBL Heidelberg, Anna Kubalczyk
joined the team as Legal Officer to support Collaboration
Agreements and the Commissioned Services contracts.
34
ELIXIR committees
ELIXIR Board
Chair: Prof. Torsten Schwede (Switzerland)
Vice Chairs: Prof. Rein Aasland (Norway), Dr Anna
Wetterbom (Sweden)
Country
Scientific delegate(s)
Administrative delegate
Belgium (from Oct. 2015)
Dr François Guissart
Mrs Michele Oleo and Mr Didier Flagothier
Czech Republic
Prof. Jaroslav Koča
Mr Jan Buriánek
Denmark
Prof. Anders Krogh
Mr Troels Tvedegaard Rasmussen
Estonia
Prof. Pärt Peterson
Mr Toivo Räim and Mr Priit Tamm
Finland
Dr Per Öster
Ms Riina Vuorento and Dr Jarmo Wahlfors
France (from Oct. 2015)
Dr Eric Guittet and Dr Claudine Medigue
Mr François Chambelin
Israel
Dr Yossi Kalifa
Ms Ilana Lowi
Netherlands
Prof. Jaap Heringa and Dr Ruben Kok
Dr Bea Pauw
Norway
Prof. Rein Aasland and Prof. Stig Omholt
Dr Jacob E. Wang
Portugal
Dr Ana Teresa Freitas
Dr Andreia Feijão and Dr Tiago Saborida
Spain (from Oct. 2015)
Prof. Arcadi Navarro
Dr Cristina Bauluz and Dr Rafael de Andres-Medina
Sweden
Prof. Ulf Gyllensten
Dr Anna Wetterbom
Switzerland
Prof. Torsten Schwede
Dr Isabella Beretta
UK
Dr Chris Rawlings
Dr Mark Palmer and Dr Amanda Collis
EMBL
Prof. Iain Mattaj and Prof. Janet Thornton Dr Silke Schumacher
Observers
Greece
TBC
Dr Konstantina Botsi
Ireland
TBC
Dr Eamonn Cahill
Italy (member as of Jan. 2016) Prof. Anna Tramontano
Dr Salvatore La Rosa
Slovenia
(member as of Feb. 2016)
Dr Albin Kralj
35
Prof. Damjana Rozman
Heads of Node Committee
Chair: Dr Niklas Blomberg (ELIXIR Hub)
Country
Head(s) of Node
Belgium (from Nov. 2015)
Prof. Yves Van de Peer
Czech Republic
Dr Jiří Vondrášek
Denmark
Prof. Søren Brunak
Estonia
Prof. Jaak Vilo
Finland
Dr Tommi Nyrönen
Dr Jean‐François Gibrat
Israel
Prof. Michal Linial
Netherlands
Prof. Barend Mons
Norway
Prof. Inge Jonassen
Portugal
Prof. Arlindo Oliveira
Prof. Alfonso Valencia
Sweden
Prof. Bengt Persson
Switzerland
Prof. Ron Appel
UK
Prof. Chris Ponting
EMBL
Dr Rolf Apweiler and Dr Ewan Birney
Observers
Greece
Prof. Babis Savakis
Ireland
TBC
Italy (member as of Jan 2016)
Prof. Graziano Pesole
Slovenia (member as of Feb 2016)
Prof. Brane Leskošek
36
ELIXIR Technical Coordinators Group
Chair: Rafael C. Jimenez (ELIXIR Hub)
Country
Technical coordinator(s)
Dr Frederik Coppens (Deputy: Dr Lieven Sterck)
Czech Republic
Dr David Antoš (Deputy: Dr Jan Paces)
Denmark
Mr Kristoffer Rapacki
Estonia
Dr Hedi Peterson
Finland
Dr Jarno Laitinen
Dr Christophe Blanchet
Israel
Dr Jaime Prilusky
Netherlands
Dr Rob Hooft
Norway
Dr Kjell Petersen
Portugal
Dr Mário Silva
Dr Victor de la Torre
Sweden
Dr Mikael Borg
Switzerland
Dr Heinz Stockinger
UK
Dr Manuel Corpas
EMBL
Dr Steven Newhouse
Observers
Greece
Dr Theodore Dalamagas (Deputy: Dr Stelios Sartzetakis)
Ireland
TBC
Italy (member as of Jan. 2016)
Dr Federico Zambelli
Slovenia (member as of Feb. 2016)
Dr Peter Juvan (Deputy: Prof. Brane Leskošek)
37
ELIXIR Training Coordinators Group
Chair: Dr Rita Hendricusdottir (ELIXIR UK)
Country
Training coordinator(s)
Dr Alexander Botzki
Czech Republic
Dr Vojtěch Spiwok
Denmark
Dr Henriette Husum Bak-Jensen
Estonia
Dr Hedi Peterson
Finland
Dr Eija Korpelainen
Dr Victoria Dominguez del Angel
Israel
Prof. Michal Linial
Netherlands
Dr Celia van Gelder
Norway
Dr Ståle Nygård
Portugal
Mr Pedro Fernandes
Dr Oswaldo Trelles
Sweden
Dr Sara Light
Switzerland
Dr Patricia Palagi
EMBL
Dr Sarah Morgan
ELIXIR Hub
Mr Rafael C. Jimenez
Observers
Greece
Dr Theodore Dalamagas (Deputy: Dr Stelios Sartzetakis)
Ireland
TBC
Italy (member as of Jan. 2016)
Dr Federico Zambelli
Slovenia (member as of Feb. 2016)
Dr Peter Juvan (Deputy: Prof. Brane Leskošek)
38
Financial data
INCOME
2015*
2014*
Member state contributions
Ordinary contributions
(b)
2,064
1,198
External grants
(a)
150
-
3
-
-
(1)
2,217
1,197
2015*
2014*
Salaries
112
33
Running costs
79
4
-
-
191
37
Salaries
800
557
Running costs
463
265
-
-
Directorate and Administration Costs
1,263
822
Support and Admin Infrastructure Costs
405
142
Grant expenditure incurred
150
0
Total expenditure
2,009
1,001
Surplus / (Deficit)
208
196
Other income
Provision for unpaid member state contributions
(b)
Net income
EXPENDITURE
Technological Activities
Equipment and depreciation
Total expenditure Technological Activities
Directorate and Administrative expenditure
Equipment
(a) GRANT INCOME
2015*
2014*
5,941
-
Grant funding received
150
-
Expenditure incurred
(150)
-
-
-
Grant funding awarded
Unutilised grant income
*Numbers shown are expressed in thousands of euros.
39
(b) ELIXIR member state contributions
2015*
2014*
Belgium
116
76
Czech Republic
43
29
Denmark
74
51
Estonia
4
3
Finland
58
39
France
226
-
Greece
-
47
Israel
53
36
The Netherlands
193
131
Norway
107
72
Portugal
51
34
Slovenia
11
8
265
86
Sweden
118
80
Switzerland
151
102
United Kingdom
594
404
2,064
1,198
Member state
Spain
(i)
Total
Less provision for unpaid member state contributions
(ii)
Net member state receivables
(1)
2,064
1,197
(i)The Spanish contribution comprises the 2015 contribution amount of €351 000, less a credit note issued relating to the 2014 contribution
of €86 000.
(ii) The 2014 accounts included requested write-off of the outstanding balance of Switzerland’s 2013 contribution. This was a result of the
contribution being paid in Swiss francs with an ensuing difference in the foreign exchange at the time of payment causing a small currency
loss of €931.27. This has been written off in 2015.
(b) The following countries have amounts due or prepaid 31 December 2015*
Member state
Contribution 2015 Contribution 2014/2013
Total
Prepayments for 2016
Greece
-
Netherlands
-
205
Israel
-
56
Total
45
45
45
45
261
*Numbers shown are expressed in thousands of euros.
40
ELIXIR Hub
EMBL-EBI South building
Hinxton, Cambridge, UK
41
42
ELIXIR is building a
sustainable European
Infrastructure for biological
information, supporting
life science research and its
translation to:
Medicine
Environment
Bioindustries
Society
Contact
Niklas Blomberg, Director
ELIXIR
Wellcome Genome Campus
Hinxton, Cambridgeshire
CB10 1SD, United Kingdom
C
P
E
1y
+44 (0)1223 492 670
+44 (0)1223 494 468
[email protected]
www.elixir-europe.org
ELIXIR Scientific Programme 2014

- ELIXIR Europe

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