ELIXIR Annual Report 2016

ELIXIR Annual Report 2016

ELXIR Annual Report 2016

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Contents 2 3

Foreword by Torsten Schwede, Chair of ELIXIR Board (2015–2016) Foreword by ELIXIR Director

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ELIXIR Platforms and Use Cases Structure of ELIXIR activities Tools: Services and connectors to drive access and exploitation Data: Sustaining Europe’s life science data infrastructure Compute: Access, exchange and storage Interoperability: Integration of data and services Training: Professional skills for managing and exploiting data Human data: Use case Rare diseases: Use case Marine metagenomics: Use case Plant sciences: Use case Platfrom and Use case leaders

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ELIXIR members Introducing ELIXIR UK Introducing ELIXIR Germany ELIXIR Nodes updates

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2016 highlights

35 EU projects 36 ELIXIR-EXCELERATE 39 Collaboration with other Research Infrastructures 41 42 43 44 46 47

Supporting activities Capacity building and Node development Governance Industry engagement International collaboration ELIXIR Working Groups

49 50 52

ELIXIR Hub activities ELIXIR Communications ELIXIR Hub staff

53 54 57 60

Governance Committees and financial data ELIXIR Committees Financial data Commissioned Services: ELIXIR Implementation studies

Foreword by Torsten Schwede I have watched ELIXIR develop since its conception and have been delighted to see its continued growth, year on year, since the Preparatory Phase.

Yet 2016 was in many ways transformative for ELIXIR. The number of activities taking place in ELIXIR Nodes and across ELIXIR Platforms and Use Cases simply exploded.

Four new Implementation Studies were initiated, five ELIXIR Node applications were approved and three Collaboration Agreements concluded. ELIXIR’s first ELSI (Ethical, Legal and Societal Issues) policy was developed in 2016, and the work to define indicators for ELIXIR Core Data Resources concluded.

ELIXIR became the largest ESFRI research infrastructure in terms of membership, with 20 members in 2016. This rapid expansion of activities and membership is a clear indication of ELIXIR’s success, and shows the increasingly widespread recognition of bioinformatics as a driving force in the life sciences. 2016 also marked the maturity of ELIXIR: the European Strategy Forum on Research Infrastructures (ESFRI) recognised ELIXIR as a ‘landmark’ infrastructure in its 2016 Roadmap.

I have had the privilege of sitting on the ELIXIR Board since its formation in 2014, serving the past two years as Chair.

ELIXIR has achieved a great deal during that time, and I am looking forward to seeing it build and develop further.

To realise the potential of computational biology to address the most pressing challenges we face, we must continue to develop ELIXIR at pace so that it may support new and emerging communities.

Looking at the energy and commitment of our members, I continue to be enthusiastic about the achievements we can make together in 2017 and beyond.

Torsten Schwede Chair of ELIXIR Board, 2015–2016

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Foreword by ELIXIR Director The year 2016 marked the midway point in ELIXIR’s first Scientific Programme (2014– 2018), and was indeed transformational.

Our two flagship projects, ELIXIREXCELERATE and CORBEL, were in full swing, allowing us to concentrate fully on infrastructure delivery and integration.

This Annual Report highlights major achievements that illustrate the growth and maturity of our research infrastructure, which represents the combined efforts of 20 members.

Integrated services Our goal is to establish a coordinated, integrated infrastructure for life-science data, and in 2016 we took major steps towards achieving just that.

Our work on ELIXIR Core Data Resources was strategically important. These resources are essential to the wider lifescience community, and to the long-term preservation of biological data. The ELIXIR Data Platform defined criteria for identifying Core Data Resources as well as the process by which they will be selected in 2017. These Core Data Resources will drive ELIXIR’s sustainability strategy, and serve as a basis for policy-level discussions.

We launched the ELIXIR Authorisation and Authentication Infrastructure (AAI), a critical component of the ELIXIR Compute Platform for both users and service providers.

AAI facilitates seamless access to ELIXIR services for researchers, and it gives ELIXIR service providers better control and management of access rights. Our Intranet was among the first services to use the ELIXIR AAI, so our partners can now share information more easily with one another from over 180 institutes.

Other services that integrated the ELIXIR AAI were ELIXIR Beacons, discovery services that make human genomic datasets and cohorts discoverable and accessible by the global biomedical research community. The Beacons, developed in collaboration with the Global Alliance for Genomics and Health, define a global standard in data discovery. By the end of 2016, ELIXIR Beacons facilitated access to genomics data from six ELIXIR Nodes. In 2016 our members will engage more deeply in the Beacons project, new Nodes will participate and the ELIXIR-GA4GH collaboration will be expanded.

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Expanding membership Five new members joined ELIXIR in 2016: Italy, Slovenia, Ireland, Luxembourg and Germany. With these additions, we became the largest ESFRI Research Infrastructure in terms of membership. In the three years since our December 2013 launch, our membership has surged from the six founding members to 20.

Looking ahead The second half of our current Scientific Programme focuses on expanding our efforts to accelerate the exploitation of open biological data. In 2017 we will further consolidate the ELIXIR's portfolio of services and initiate discussions about the next programming period (2019–2023).

There are over 600 people actively contributing to ELIXIR, and each one has played a part in its success. We owe a lot to those whose hard work and dedication contributed to the development of ELIXIR in 2016: the ELIXIR Heads of Node, Technical and Training Coordinators, Platform and Use Case Leaders and everyone in ELIXIR Nodes.

The achievements of 2016 have laid the foundations for accelerated progress in 2017 and beyond, and I look forward to continued success in this transformative era in the life sciences.

Niklas Blomberg ELIXIR Director

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ELXIR Annual Report 2016

ELIXIR Platforms

and Use Cases

Structure of ELIXIR activities ELIXIR activities are structured according to five Platforms and four Use Cases.

These form the basic units of operation within ELIXIR, and draw on expertise and resources from ELIXIR Nodes.

The ELIXIR Platforms comprise: • Data: Sustaining Europe’s life-science data infrastructure • Tools: Services and connectors to drive access and exploitation • Interoperability: Supporting the discovery, integration and analysis of biological data • Compute: Storage, compute and authentication/ access services • Training: Professional skills for managing and exploiting data The four Use Cases service domain-specific research communities: • Human data: Developing long-term strategies for managing and accessing sensitive human data • Rare diseases: Supporting the development of new therapies for rare diseases • Marine metagenomics: Developing a sustainable metagenomics infrastructure to nurture research and innovation in marine science • Plant science: Developing an infrastructure to facilitate genotype-phenotype analyses for crop and tree species

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ELXIR Annual Report 2016

ELIXIR Platforms are built on the real and changing needs of established research communities. The four Use Cases drive the work of the ELIXIR Platforms by defining their bioinformatics needs and requirements. This close collaboration ensures that the services developed by the ELIXIR Platforms are fit for purpose.

Senior scientists at the ELIXIR Nodes lead each of the Platforms and Use Cases, which are primarily funded by the ELIXIR-EXCELERATE project, in which each Platform and Use Case is represented by a Work Package. Additional activities are funded through other grants and through the ELIXIR Hub as Implementation Studies.

Human data

Rare diseases

USE CASES

Tools

Data

Compute PLATFORMS

Interoperability

Marine metagenomics

Training

Plant science

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Tools Services and connectors for access and exploitation The Tools Platform is working to deliver a discovery portal that collects and curates computational tools and data services for the life sciences. It is also developing a framework for benchmarking and evaluating bioinformatics tools from a scientific and technical perspective.

Bio.tools: ELIXIR tools and services registry In 2016 the Tools Platform focused on developing content, the underlying ontology (EDAM), portal software, sustainability strategy and applications for the bio.tools portal (launched in 2015). By the end of 2016, the portal had 6,205 entries and 45,357 EDAM annotations, including contributions from over 30 countries. The data is freely available under open license (CC BY 4.0).

The Tools Platform organised 15 events in 2016 to collect the content, anchor the portal development within the broad community, and raise awareness of bio.tools.

They also engaged other research infrastructures and infrastructure projects, many of which now use or evaluate the data from bio.tools. These include the NIH Big Data to Knowledge (BD2K) programme and AZTEC.bio in the US; Instruct, EuroBioimaging, BioEXCEL, Common Workflow Language and EU-ToxRisk in Europe, and the EMBLAustralia BioResource.

The Tools Platform also collaborated with the ELIXIR Interoperability Platform on the Common Workflow Language. The collaboration focused on enabling interoperability between different workflows, and the use of the EDAM ontology and bio.tools for tool description.

1. Continuous Automated Model EvaluatiOn (CAMEO), https://cameo3d.org 2. The Quest for Orthologs is a joint initiative to benchmark, improve and standardize orthology predictions, http://questfororthologs.org/ 3. Critical Assessment of PRediction of Interactions (CAPRI), http://www.ebi.ac.uk/ msd-srv/capri/capri.html

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Benchmarking Bioinformatics methods must be assessed for quantitative performance and user friendliness to ensure they are fit for purpose. Benchmarking is thus a basic element of the ELIXIR infrastructure. These methods are so diverse in their design and purpose that it is necessary to abstract the scientific benchmark and technical monitoring processes in order to design an effective approach. This is an important part of the ELIXIR Tools Platform work programme, which is developing guidance and infrastructure for benchmarking and monitoring bioinformatics tools, web servers and algorithms.

In 2016, the Tools Platform mapped the needs of relevant stakeholders and selected several user scenarios on which to base the development of the ELIXIR Benchmarking Platform. In 2016 the group started a stepwise implementation of the ELIXIR Benchmarking Platform, releasing the first demonstrators in early 2017.

ELIXIR supports community-driven benchmarking efforts, and in 2016 the Tools Platform provided such support through by engaging with bioinformatics initiatives such as CAMEO1, Quest for Orthologs2 and CAPRI3. This will provide a strong connection between the ELIXIR infrastructure and the communities carrying out benchmarking exercises within their expert knowledge domains. In the long term, it can lead to community agreements on data standards, submission formats and evaluation methods for quality assessment of bioinformatics tools.

The ELIXIR Tools Platform is funded through the ELIXIR-EXCELERATE project (Work Package 1: Tools Interoperability and Service Registry, and Work Package 2: Benchmarking).

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Data Sustaining Europe’s life-science data infrastructure The ELIXIR Data Platform provides a framework for developing ELIXIR’s lifescience data resources in a sustainable manner. Operated by ELIXIR Nodes, these resources serve a myriad purposes, ranging from databases that archive research outputs (e.g. DNA sequences) to dynamic, value-added knowledge bases, manually curated by experts, that aggregate, process and visualise data.

ELIXIR Core Data Resources are central to Data Platform activities. This select set of European data resources is of fundamental importance to the broader life-science research community, and to the long-term preservation of biological data.

One of the goals of ELIXIR is to ensure that these resources are available over the long term, and that they continue to support biomedical and biological research.

Figure 2: Indicators reflecting the multiple facets of Core Data Resources Scientific focus and quality of science Community served Quality of service Legal and funding infrastructure, and governance Impact and translational stories

INDICATORS

1. Durinx C, McEntyre J, et al. (2016) Identifying ELIXIR Core Data Resources.

F1000Research 5. pii:ELIXIR-2422; (doi: 10.12688/f1000research.9656.2) 2. Venkatesan A, Kim JH, et al. (2016) SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data. Wellcome Open Res 1:25; (doi: 10.12688/wellcomeopenres.10210.1)

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ELXIR Annual Report 2016

Establishing ELIXIR Core Data Resources In 2016 the Data Platform focused on establishing the ELIXIR Core Data Resources portfolio. A landmark paper published in September 2016 describes the structures, governance and processes required for identifying and evaluating ELIXIR Core Data Resources, and presents key indicators that formalise the scientific, technical and governance requirements1 (Figure 2). In October 2016, the process of selecting the ELIXIR Core Data Resources started with the collection of nominations from ELIXIR Nodes. The final portfolio of Core Data Resources will be published in Summer 2017, following extensive review.

Linking literature with data Another objective of the Data Platform is to explore how text mining and other literature-based disciplines can contribute to the sustainable curation of data resources.

Many bioinformatics resources are useful precisely because they are manually curated by experts who review published experimental data and extract relevant information. The Data Platform is exploring how this work can be further enhanced and supported by text mining approaches, which can generate more granular links between articles and the data underlying them. This is essential for removing bottlenecks to quality assurance as high-throughput data generation increases the rate of research publication.

This work resulted in the launch of SciLite, a platform that overlays text-mined annotations on research articles to link articles to related resources or tools2.

Long term sustainability of life science knowledge bases The long-term funding of data resources is a constant concern for those who are managing them, with only a very small minority of databases having secured funding over five years or more. In September 2016, the Data Platform launched an ELIXIR Implementation Study to evaluate the different funding models of knowledgebases, and propose a funding model that ensures their long-term sustainability. UniProt, the Universal Protein Resource, a key resource for protein sequences and functional information knowledge, serves as a use case in this evaluation. The final recommendations are planned for the second half of 2017.

The work on the ELIXIR Core Data Resources and linking data with literature were funded through the ELIXIR-EXCELERATE project (Work Package 3: Data Resources and Services). The Implementation Study on long term sustainability of knowledge bases is supported through the ELIXIR Hub budget.

Compute Access, exchange and storage The Compute Platform is building a robust technical infrastructure for accessing, transferring, exchanging and analysing biological data. It aims to provide cloud, compute, storage and access services for the research community.

The objective is to integrate the individual technical components provided by ELIXIR Nodes into a seamless service provision system for the life science research community. The Compute Platform works closely with the four scientific Use Cases and the ELIXIR Training Platform to ensure the technical solutions fit their specific needs.

ELIXIR Authentication and Authorisation Infrastructure (AAI) To ensure that people are identified accurately when accessing sensitive data, even when they move between organisations, a reliable system of user identification is an absolute necessity for controlled-access services and resources. In 2016 the Compute Platform developed the ELIXIR AAI, which provides an ELIXIR ID for accessing ELIXIR services in a federated manner. Using ELIXIR AAI, researchers may use their existing, verified academic, corporate and social media identities. The service providers connected to the ELIXIR AAI benefit from a centralised user identity and access management services.

Compute Demonstrator with ELIXIR Marine Metagenomics Use Case The first ELIXIR Technical Service Demonstrator, a package of compute-related services, was applied to the ELIXIR Marine Metagenomics Use Case in 2016.

The demonstrator comprises scientific-software pipelines for analysing marine metagenomics data into containers and images, which increases portability and usage of these services across ELIXIR’s distributed infrastructure. The Demonstrator used ELIXIR’s AAI to identify and authenticate researchers accessing the Marine metagenomics analysis pipeline (META-pipe, run by ELIXIR Norway) and improved the output of the data analysis.

The work of the ELIXIR Compute Platform was funded through the ELIXIR-EXCELERATE project (Work Package 4: Compute, Data access and exchange services). The development of the ELIXIR AAI was informed by close collaboration with the AARC (Authentication and Authorisation for Research and Collaboration) project.

In its first six months of its operation, ELIXIR AAI users created 584 ELIXIR IDs (in 101 ‘groups’), linked 292 identity providers and provided access to 16 relying ELIXIR services (e.g. ELIXIR Beacon in Finland). ELIXIR AAI credentials are accepted by the European Grid Infrastructure (via CheckIn) and the EUDAT e-infrastructure (via B2ACCESS).

ELIXIR Technical Services Roadmap The Compute Platform published the ELIXIR Technical Services Roadmap1, which sets out the needs of the ELIXIR Use Cases. The Roadmap defines ‘Technical Use Cases’ (TUCs), which serve as generic templates for technical activities within the Compute Platform. The Roadmap also identifies technologies that will be used to provide consistent compute infrastructure services.

1. Lars AB, Borg M, Cornelis A, Gonzalez M, et al (2016). A Technical Services Roadmap for supporting Life Science Research in Europe. Zenodo (doi: 10.5281/zenodo.60291)

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Interoperability Integration of data and services The ELIXIR Interoperability Platform (EIP) is developing and implementing a framework to support people and machines in the discovery, access, integration and analysis of biological data. The Platform implements the FAIR principles of Findable, Accessible Interoperable and Reusable data stewardship, and extends these to include APIs, ontology, standards and workflow stewardship. The Platform is driven by biological Use Cases including rare genetic diseases, marine metagenomics, plant biology and others.

ELIXIR Interoperability Platform Roadmap A key output of the Platform in 2016 was the development of the Interoperability Roadmap. The Roadmap defines both the technical and scientific strategy and outlines requirements for ELIXIR’s Interoperability services and related activities: Standards and services • Bioschemas - A new initiative delivering lightweight ‘Findability’ of ELIXIR resources and their content • Identifiers - core services and common standards for unique identification of data • Metadata – core services and common standards for dataset and sample level metadata for interoperability and reusability available from Biosharing • Ontology services enabling semantic interoperability available from Ontology Lookup Service Approaches to interoperability • Identification and integration of core services supporting interoperability • Interoperability through connecting tools and resources with workflows: API standards and metadata to describe and compare workflows using Common Workflow Language (CWL) Capacity building and support • Knowledge Hub for know-how, BYODs (Bring Your Own Data) events, and best practices

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Core services: Biosharing, Identifiers, Ontology Lookup Service The ELIXIR Interoperability Roadmap has identified the first components of the interoperability service framework: Identifiers.org, Biosharing.org and Ontology Lookup Service.

Biosharing is the ELIXIR curated metadata and standards registry. It is run by ELIXIR UK Node (University of Oxford) and endorsed by a community of 68 organisations, including publishers, standardisation groups, and data management support initiatives. In 2016 the Platform conducted a community user survey that showed that Biosharing is a core and critical resource for standards, databases and policies.

Identifiers.org is an identifier resolution service run by EMBL-EBI Node that provides unique, stable, resolvable and location independent compact URIs to identify and locate scientific data. In 2016, the Platform started an ELIXIR Implementation Study to establish Identifiers.org as a stable ELIXIR system for uniform identifier resolution to major bioinformatics resources.

Ontology Lookup Service is a repository for biomedical ontologies developed by the EMBL-EBI Node, which provides access to biomedical ontologies for use by ELIXIR partners. In 2016, its list of over 130 ontologies was extended to include key ontologies used by the ELIXIR Plant Science and Human Data Use Cases.

Bioschemas

In 2017-2018, the Platform will continue to advance the Interoperability Roadmap. This includes work on the community development and adoption of BioSchemas, and on pilot implementations in metadata validation and workflow interoperability through CWL. The vision is to continue to work closely with international interoperability services and efforts and embed Core Interoperability Services across all of the ELIXIR Platforms.

Bioschemas is a flagship project of the ELIXIR Interoperability Platform. It supports the use of schema.org markup in life sciences and streamlines the discovery, curation and analysis of distributed data.

BioSchmas enables ELIXIR registries as well as standard web search engines to harvest and exploit metadata provided by content providers and data generators.

After a successful pilot with training materials and the ELIXIR training portal (TeSS) in 2016, the Interoperability Platform has expanded the approach to datasets, running four hackathons 2016 and launching an Implementation Study in 2017. The study brings together datasets and registries across ELIXIR and focuses on datasets for protein annotation, samples, plant phenotyping, and sensitive human data (Beacons).

The work of the ELIXIR Interoperability Platform was funded through ELIXIR-EXCELERATE project (Work Package 5: the ELIXIR Interoperability Backbone). The work on Identifiers and Ontology Lookup Service was funded by CORBEL. Work on identifiers was funded

by CORBEL and ELIXIR-EXCELERATE. The Bioschemas initiative was jointly funded by the ELIXIR Hub (through ELIXIR Implementation Study), ELIXIR-EXCELERATE and CORBEL.

Figure 3: Interoperability Platform Services Framework Standards and APIs

Applications

Intergrated services

Pipelines

Identifier, resoution, versioning, provenance

Standards registry

Ontology services: Ontology Lookup Service (OLS)

API description

Identifier mapping

Tools registry: bio.tools

Linked data services

Tools and workflow descriptions

Citation implimentation

Prefix commons

Search services

Dataset description: DATS: DatA Tag Suite

Annotation services

Validation services

Identifier authorities

BYOD

BYOW

BYOAPI

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Training Professional skills for managing and exploiting data The ELIXIR Training Platform is building a sustainable training infrastructure for the wider life science community. The scope of the Platform is broad, covering the training tools and resources, training expertise, quality assurance and monitoring.

ELIXIR Training portal

The ELIXIR training infrastructure comprises four components: (1) training evaluation methods and metrics, (2) ELIXIR Training Portal , (3) ELIXIR eLearning Platform and (4) Virtual Coffee Room .

Training events in ELIXIR Nodes and third-party training providers are now aggregated automatically in the TeSS portal, using the Bioschemas event specification (in collaboration with the ELIXIR Interoperability Platform).

A crucial part of the training infrastructure is the combined expertise of the ELIXIR Training Platform members, notably the ELIXIR Training Coordinators representing each of the ELIXIR Nodes.

The TeSS portal team joined forces with the ELIXIR Tools and Interoperability Platforms to facilitate integration with the bio.tools and Biosharing.org registries, which will allow curators to link tools, databases and standards to relevant training resources.

ELIXIR Training programme In 2016, the ELIXIR Training Platform organised 36 training events according to five different streams: e-Learning, Train the Researcher, Train the Trainer, Train the Developer, and TeSS. In 2016 the Training Platform carried out a training gap analysis to identify training needs in ELIXIR Nodes. The results showed (1) the need to prioritise ELIXIR Use Cases in planning and delivering bioinformatics training, and (2) the need to improve training capacity in ELIXIR Nodes in order deliver this training effectively.

The Train the Trainer programme in 2016 trained 53 instructors from 12 ELIXIR Nodes; the plan for 2017 is to extend the pool of trainers, also in collaboration with the Software and Data Carpentry communities.

The Training eSupport System, TeSS, allows scientists to browse, discover and organise life-science training events and materials that have been aggregated from ELIXIR Nodes and third-party providers (e.g. RI-Train, BioEXCEL).

The production version of the portal was released in June 2016.

ELIXIR e-Learning The ELIXIR Training Platform released the ELIXIR e-Learning platform with six newly developed e-learning courses1 . In collaboration with GOBLET, the Platform published a white paper2 which presents a consensus of what the ELIXIR and GOBLET communities mean by ‘e-learning’. This is a necessary first step towards formulating e-learning strategies for ELIXIR and GOBLET. The ELIXIR Training Platform is funded through the ELIXIREXCELERATE project (Work Package 11: ELIXIR Training Programme).

The Platform also actively collaborates with partner initiatives and projects (GOBLET, BD2K, Software and Data Carpentries, CORBEL, RITrain and others).

Impact and quality To measure the impact and quality of ELIXIR training, the ELIXIR Training Platform defined what constitutes an ELIXIR training event, and agreed a set of Key Performance Indicators (KPIs). This work provided a solid basis for continuous monitoring of the quality of all ELIXIR training events.

To further promote standardisation and reuse of bioinformatics course material, the Platform established a common framework for the curation of training materials (in collaboration with GOBLET, the Global Organisation for Bioinformatics Learning, Education and Training).

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1. https://elixir.mf.uni-lj.si 2. Attwood, TK., Leskosek, Brane L., Dimec, Jure, Morgan, Sarah, Mulder, Nicola, van Gelder, Celia W.G., & Palagi, Patricia M. (2016). Defining a lingua franca for the ELIXIR/ GOBLET e-learning ecosystem. Zenodo. (doi: 10.5281/zenodo.166378)

Train the Trainer

eLearning • ELIXIR/GOBLET workshop: defining an e-learning lingua franca

• Train the Trainer UK and Portugal events

Train the Researcher • RNA-seq and ChIP-seq data analysis with Chipster

• RNA-seq data analysis with Chipster

• Variant Analysis Workshop Train the Developer

Train the Researcher

• Workshop for developers: Software faster: From months to minutes

• Software and Data Carpentry Instructor Training Workshop

• Data Curation Training for tranSMART

• Managing and Integrating Life Science Information

Train the Trainer

Train the Researcher

• Train the trainer Slovenia event

• ELIXIR Data and Software Carpentry Instructor Training

eLearning Train the Trainer

• Linux command line course

• EXCELERATE train the trainer and training impact workshop

Dec '15 Feb

Jan Sep '15

Mar '16

Apr Jun '16

Sep May'16

Dec Jun '16

eLearning • RNA-seq data analysis with Chipster

Train the Trainer • Using clouds and virtual machines in bioinformatics training

Train the Trainer • Train the trainer Italy event

TeSS • "Training" and "metadata searching" meetings

Train the Researcher • BIIT web-tools for highthroughput data analysis from ELIXIR-Estonia • Data Carpentry Workshop

Train the Developer • ELIXIR and DARIAH "AAI Workshop for service and resource providers" • Hackathon Bioinformatique

TeSS • TeSS workshop with training standards group BioSchemas

eLearning • Genome Assembly and Annotation • Unix Command Line SE • CASyM/EASyM tutorial

Train the Developer • ELIXIR Technical Hackathon: Tools, Workflow and Workbenches

Train the Trainer • Train the trainer event

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Human data Use case The ELIXIR Human Data Use Case is tasked with building the technical infrastructure required for researchers to discover, combine and exchange controlled-access human data, while complying with dataprivacy and data-security requirements.

The backbone of the Human Data Use Case is the European Genome-phenome Archive (EGA). The Use Case extends and generalises the EGA system of access authorisation and secure data transfer, and makes it available to researchers across the ELIXIR Nodes.

The Use Case works closely with the ELIXIR Compute Platform, particularly around systems for authorising and authenticating access to sensitive data (i.e. AAI). It is also informed by the security framework, tools and APIs developed by the Global Alliance for Genomics and Health (GA4GH).

Local EGA Local instances of the EGA will enable the storage of sensitive, controlled-access data that may not leave their country of origin for a variety of reasons. Integration of the associated metadata in EGA will ensure that such data are discoverable by researchers everywhere.

The Human Data Use Case developed a functional demonstrator of the Local EGA in 2016, including successful integration of ELIXIR AAI with the corresponding AAI services in EGA. The demonstrator was tested by ELIXIR Nodes on their local infrastructures.

The further development of the demonstrator will focus on the case of biobank data from Finland’s National Institute for Health and Welfare (THL).

ELIXIR Beacons The Beacon Project develops an open sharing platform that helps genomic data centres make their data more discoverable. Beacons allow researchers to query individual datasets – without disclosing any sensitive information – to determine whether they contain a specific genetic variant of interest.

ELIXIR’s fruitful collaboration on Beacons with the Global Alliance for Genomics and Health (GA4GH) resulted in six ELIXIR Nodes making their genomics data available for discovery during 2016. Beacons were ‘lit’ in Sweden, Finland, France, Switzerland and Belgium, and in the EGA. Each ELIXIR Beacon makes one or more genomics datasets discoverable to the international research community.

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In 2017, ELIXIR and GA4GH expand their partnership to add new security measures and create a network of ELIXIR Beacons. The goal is to make sure biomedical research data generated in Europe can be found by any researcher worldwide.

Facilitating re-use of human data The Human Data Use Case collaborated with the Dutch Center for Translational Medicine (TraIT) on a scoping study to develop IT infrastructure for translational research. This collaboration connected the EGA with TraIT’s data analysis platform (Galaxy) and data portal (tranSMART), and enabled Dutch researchers to use EGA as the long-term storage solution for raw data1 .

ELIXIR also collaborated on the Innovative Medicines Initiative (IMI) project OncoTrack, exploring options for long-term storage and discovery services for the cancer research data (e.g. from human, animal, cell lines) generated by the project.

The work of the ELIXIR Human Data Use Case was funded through the ELIXIR-EXCELERATE project (Work Package 9: Secure archiving, dissemination and analysis of human access-controlled data). The ELIXIR Beacon project and collaborations with TraIT and OncoTrack were supported by the ELIXIR Hub budget though three ELIXIR Implementation Studies (ELIXIR Beacons, Genomic data management for TraIT using the EGA, and ELIXIR – IMI OncoTrack scoping study on long-term data handling).

1. Hoogstrate Y, Zhang C, et al. (2016) Integration of EGA secure data access into Galaxy.

F1000Research 5(ELIXIR):2841; (doi: 10.12688/f1000research.10221.1)

Rare diseases Use case The ELIXIR Rare Diseases Use Case is building a portfolio of ELIXIR resources to address the needs of the rare diseases research community.

During 2016 the Use Case worked in close collaboration with the ELIXIR Tools, Data, Compute and Training Platforms as well as several rare-disease initiatives (RDConnect, BBMRI, FAIR-dICT and ODEX4ALL) to map and connect existing resources relevant to the rare-disease research community.

Portfolio of resources and tools for rare diseases research Following a survey of current tools and data resources for rare diseases research, the Use Case identified 51 ELIXIR services and tools that are important to rare disease research, and added them to the ELIXIR Tools and Services Registry (bio.tools). In collaboration with the ELIXIR Tools Platform, the Use Case started to develop benchmarking and standards for reporting quality for these resources.

Linking rare diseases data The rare disease data linkage plan emphasises data interoperability as the critical factor to boost research in the rare disease domain. Because each rare disease field is limited in size, the single most important way to gain new insights is to combine data across registries, biobanks and -omics databases. To achieve the goal of treatment and access to care for all rare diseases, exponential growth in the efficiency of combining data for analysis is required. An ecosystem of FAIR resources can bring this goal closer to this goal.

The comprehensive ‘rare disease data linkage plan’ for selected biobanks and registries within the rare disease community was established by the Use Case in 2016. The purpose of the plan is to make the data in these biobanks and registries more Findable, Accessible, Interoperable and Reusable (FAIR). The development of this technical framework will continue throughout 2017.

The work of the Rare Disease Use Case was funded through the ELIXIREXCELERATE project (Work Package 8: ELIXIR infrastructure for Rare Disease research).

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Marine metagenomics Use case The ELIXIR Marine Metagenomics Use Case is building a stable, sustainable infrastructure for the marine science community. Marine metagenomics resources range from deposition archives with research data outputs (e.g. DNA sequences), to highly dynamic knowledge bases that aggregate and process research data through manual curation and complex, scalable metagenomics analysis pipelines.

Metagenomics data standards environment for the marine domain In 2016 the Use Case - with input from the wider metagenomics community - proposed standards for provenance data throughout the data life cycle, covering the description of processes around sampling, sequencing, analysis and archiving of analysis results.1

Establishment of marine-specific data resources The Use Case released three new reference databases: MarRef, MarDB and MarCat. These were made public in early 2017 through the Marine Metagenomics Portal2.

These databases provide robust, richly annotated datasets with highly accurate, detailed information.

MarRef is a manually curated marine microbial reference genome database that contains completely sequenced genomes. MarDB includes all sequenced marine microbial genomes regardless of level of completeness. MarCat is a catalogue of uncultivable and cultivable marine genes and proteins derived from metagenomics samples.

‘Gold standards’ for metagenomics analysis To enrich the analysis output and improve computational performance, the Use Case developed new versions of the two existing metagenomics analysis pipelines: EMG (EMBL-EBI’s Metagenomics resource) and METApipe (ELIXIR Norway), based on the new standards and databases developed by the Use Case.

1. This work is captured in a paper, The Metagenomics Data Life-cycle: Standards and Best Practices accepted for publication in Gigascience in early 2017 2. http://mmp.sfb.uit.no

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EMG and META-pipe analysis pipelines were deployed within a cloud infrastructure, so they can be offered via ELIXIR cloud resources, using the ELIXIR AAI. The distribution and scheduling of computing jobs for METApipe and EMG was developed in collaboration with the ELIXIR Compute Platform as a proof of concept, and can be run on cloud providers including EMBL-EBI’s Embassy Cloud, Google Cloud Platform, Amazon Web Services, cPouta (ELIXIR Finland) and CESNET (ELIXIR Czech Republic).

The activities of the ELIXIR Marine Metagenomics Use Case in 2016 were funded through the ELIXIR-EXCELERATE project (Work Package 6: Marine Metagenomics Infrastructure as Driver for Research and Industrial Innovation).

Plant science Use case The ELIXIR Plant science Use Case is building a common infrastructure for systematic publication and programmatic access to genotypic and phenotypic data from crop and forest species. The major goal is to facilitate the discovery of plant data and streamline their analysis.

The range of bioinformatics services for the plant science community cover standards for presentation of genotypic and phenotypic plant data, plant data management, and data discovery and access.

Data description standards and annotation of key datasets Drawing on the outcomes of a major workshop1, the Use Case developed a first set of recommendation guidelines with agreed vocabularies, based on the extension and revision of the MIAPPE standards (Minimum Information about Plant Phenotyping Experiment). The evolution of the MIAPPE standard will be proposed to the MIAPPE governing body in May 2017.

Following the development of the initial set of data standards, the Use Case began annotating ten exemplar datasets from ELIXIR Nodes in Belgium, France, Netherlands, Slovenia, Portugal and the UK. Six of those exemplar datasets were fully annotated and submitted to the BioSamples database; the remaining annotated dataset was submitted to Gene Expression Omnibus.

The common API is an extension of Breeding API (BrAPI), which is being developed independently by many groups worldwide to enable access to plant-breeding data.

The Use Case contributed its experience with exemplar datasets and specific user needs to help adjust the BrAPI specification. The first proof of concept of the common API was developed during a joint BrAPI-ELIXIR workshop organised in Montpellier, France, in December 2016.

The activities of the ELIXIR Plant Science Use Case in 2016 were funded through the ELIXIR-EXCELERATE project (Work Package 7: Integrating Genomic and Phenotypic Data for Crop and Forest Plants).

Methods for plant data discovery and access To support access to reference databases, the Use Case proposed and began implementing an architecture for access to distributed datasets. The goal is to develop a common API for programmatic access to data, and implement it at each partner genotypic, phenotypic and sample repository. This will allow users to query multiple databases from a single endpoint by integrating results from distributed resources.

1. Five-day workshop Semantics for Harmonization and Integration of Phenotypic and Agronomic Data (PhenoHarmonis) in May 2016 in Montpellier, France, which brought together around 80 specialists in data standardisation, data managers and data producers. The Use Case contributed to the workshop organisation.

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Platform leaders

Tools

Søren Brunak

Data

Jo McEntyre

Alfonso Valencia

Compute

Tommi NyrĂśnen

Ludek Matyska

Steven Newhouse

Chris Evelo

Helen Parkinson

Chris Ponting

Rita Hendricusdottir

Interoperability

Carole Goble

Training

Patricia Palagi

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Celia van Gelder

Christine Durinx

Use case leaders

Human data

Serena Scollen

Tom Keane

Jordi Rambla

Rare diseases

Ivo Gut

Marco Roos

Marine metagenomics

Nils Peder Willassen

Rob Finn

Plant sciences

Paul Kersey

Celia Miguel

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ELIXIRÂ members

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Introducing ELIXIR UK Since its formation in September 2013, ELIXIR UK focused its service provision on bioinformatics training.

In 2016, ELIXIR UK expanded the consortium and its portfolio of services to better represent the activities of the UK bioinformatics community. The remit of ELIXIR UK services has been extended from its original training focus to include Data, Tools and Interoperability. It has added ten new services and three specialist training centres (University of Birmingham, Cambridge University and the Roslin Institute in Edinburgh) to its portfolio. In addition, two discovery portals developed by ELIXIR UK (ELIXIR TeSS portal1, and the Biosharing portal for data standards and related policies2) have become official ELIXIR services.

The ELIXIR UK structure is now divided into six categories: Interoperability and standards, Protein Structure and Function, Expression Atlases, Human Health and Disease, Agri Data and Training.

The new structure is the result of an open and transparent review process carried out throughout 2015-2016. The process brought in external experts to evaluate the submission, which was then reviewed by the ELIXIR’s Scientific Advisory Board. The experience gained during the expansion was summarised in an article published on the ELIXIR F1000Research channel in December 20163. www.elixir-uk.org

1. https://tess.elixir-europe.org 2. https://biosharing.org 3. Hancock JM, Game A, Ponting CP and Goble CA. (2016) An open and transparent process to select ELIXIR Node Services as implemented by ELIXIR-UK. F1000Research 5(ELIXIR):2894 (doi: 10.12688/f1000research.10473.2)

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Introducing ELIXIR Germany Germany became a full member of ELIXIR on 2 August 2016, when the Federal Minister of Education and Research signed the ELIXIR Consortium Agreement. The ELIXIR Germany Node was established by the German Network for Bioinformatics Infrastructure (de.NBI). de.NBI coordinates the management and provision of bioinformatics services across Germany, bringing together expertise and resources through dedicated service centres in areas such as microbes, integrative bioinformatics, data management, crop bioinformatics, human genomics and proteomics. It is led by the Bielefeld University and includes over 20 partner institutes across the country.

As ELIXIR Member, de.NBI focused on developing the German Node Application to specify which bioinformatics services will become part of ELIXIR. This will ensure the integration of de.NBI into ELIXIR. To celebrate Germany’s membership in ELIXIR, de.NBI organised a special session dedicated to ELIXIR at the International de.NBI Symposium in Heidelberg, where the members of the ELIXIR Germany leadership and the ELIXIR Director, Niklas Blomberg, presented ELIXIR in general and the plans and activities in ELIXIR Germany. www.denbi.de

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ELIXIR Nodes updates Members Belgium Czech Republic Denmark EMBL-EBI Estonia Finland France Germany Israel Ireland

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Observers Italy Luxembourg Norway Netherlands Portugal Slovenia Spain Sweden Switzerland United Kingdom

ELXIR Annual Report 2016

Greece

Belgium

Denmark

• Launched the ELIXIR Belgium website: www.elixirbelgium.org

• Further developed the ELIXIR registry of bioinformatics tools and data services (https://bio.tools), with addition or improvement of over 6500 entries in total from 486 contributors and 244 institutes

• Launched the ELIXIR Belgium Training platform, following a community meeting with Belgian universities and research centers • Organised a workshop on how to handle genomics data in a more efficient way • Launched the ELIXIR Belgium Beacon to provide access to exome variant frequencies from patients with rare genetic disorders • Secured a regional grant of €1 million to further develop the ELIXIR Belgium Node services; expand the portfolio of existing Node services; provide training for the life-science community; and develop a strategy for establishing a state-of-the-art data-storage and analysis infrastructure for life science research in Flanders.

• Developed comprehensive documentation for bio.tools (http://biotools.readthedocs.io/en/latest/), including details of how to get involved in the community-driven process behind the registry development • Organised, led or participated in an intensive series of 14 events around the development and use of bio.tools.

• Launched a studentship scheme to support students to work on curation-focused ‘mini-projects’ that improves the quality of the bio.tools content and its growth • Organised the second annual Danish Bioinformatics Conference

EMBL-EBI

Czech Republic

• Organised five training courses as part of CORBEL and ELIXIR-EXCELERATE

• Developed and launched the ELIXIR Authentication and Authorisation Infrastructure (AAI) together with ELIXIR Finland

• Contributed to three knowledge-exchange workshops organised by ELIXIR

• Launched Galaxy and Chipster (see ELIXIR Finland) instances for the Czech life science community • Organised ELIXIR-EXCELERATE Structural Funds workshop • Launched the ELIXIR-EXCELERATE Data Nodes Network (in collaboration with ELIXIR Sweden) • Organised a workshop and an e-learning course on RNASeq in Chipster • Organised workshop on Genome Assembly and Annotation • Presented ELIXIR CZ at the Czech National Bioinformatics Conference 2016 (ENBIK), a meeting supported by the Node • Presented ELIXIR CZ at an information day on national Research Infrastructures organised by the Czech Ministry of Education, Youth and Sport • Organised a staff exchange programme with EMBL-EBI to train ELIXIR Czech Republic staff in annotation of protein data

• Trained six postgraduate students from ELIXIR Czech Republic on protein annotation and curation as part of ELIXIR Staff Exchange pilot scheme • Launched new Implementation study on Data Identification and Interoperability (https://www.elixireurope.org/activities/identifiers)

Estonia • Launched the Virtual Coffee Room (https://cafe.elixir. ut.ee), a tool for sharing knowledge across the ELIXIR community • Launched ClustVis, a simple web tool for statistical analysis (PCA, clustering, visualisation) of tabular data • Contributed to three training courses on highthroughput data analysis (in Paris, Cambridge and Oxford) • Secured national funding for ELIXIR Estonia for 2017– 2022, with an overall budget of €1.3 million

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Finland

Germany

• Represented ELIXIR in the EU-funded AARC (Authentication and Authorisation for Research and Collaboration) project

• Signed the ELIXIR Consortium Agreement and became a full Member of ELIXIR in August 2016

• Launched an ELIXIR-FI Beacon to make available the Finnish samples sequenced in the 1000genomes project. The first beacon connected to the ELIXIR AAI developed by the ELIXIR Compute Platform • Launched Chipster (http://chipster.csc.fi) a versatile, scalable data-analysis and visualisation platform with a selection of popular bioinformatics tools • Organised one Compute Platform workshop and two training events • Successfully demonstrated cross-border extension of secure clouds as part of the Tryggve project, a collaboration between ELIXIR Nodes in Finland, Denmark, Norway and Sweden to establish a Nordic platform for sharing sensitive data • Co-developed the ELIXIR AAI with ELIXIR Czech Republic as part of the ELIXIR Compute Platform

France • Launched the ELIXIR France e-learning service for computational and experimental researchers. At the time of printing, six training courses are available on the platform • Launched Cloud Marketplaces, a catalogue of bioinformatics cloud appliances (https://biosphere. france-bioinformatique.fr/catalogue) • Launched more than 15 Public Galaxy servers • Launched BioShadock, a curated Bioinformatics container registry (http://bioshadock.genouest.org) • Organised two hackathons to register ELIXIR France tools in the ELIXIR Tools and Services Registry, and to support collaboration and technical developments between bio.tools and the French bioinformatics community • Held the first Summer School in metagenomics

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• Hosted an ELIXIR Tools and Service Registry Hackathon and registered ELIXIR Germany tools in the Registry • Organised the first International de.NBI Symposium on ‘Bioinformatics for Human ‘Health and Disease’, with a special session dedicated to de.NBI / ELIXIR Germany

Israel • Continued to develop the national Node in Israel with a focus on genomics, disease-oriented bioinformatics services, proteomics and storage and retrieval of data

Ireland • Became member of ELIXIR in July 2016 • Started to develop the ELIXIR Ireland Node

Italy • Launched a HCP resource for researchers in ELIXIR­Italy and other ELIXIR Nodes (ELIXIR-IIB HPC@Cineca) • Registered ELIXIR Italy bioinformatics services in the ELIXIR Tools and Services Registry: Pathway Inspector, (MICrobial Community Analysis, micca), VESPUCCI, COLOMBOS, ASSIsT, DisProt, VHLdb, RepeatsDB 2.0, RING, FELLS, MobiDB lite, Argot 2.5, Funtaxis • Organised nine bioinformatics training courses • Formally launched ELIXIR Italy at a launch meeting in Bologna in November • Secured a national grant with a total budget of €400,000

Luxembourg • Became member of ELIXIR in July 2016 • Organised a data curation training course in Luxembourg, in collaboration with the eTRIKS research infrastructure for translational data sharing

Norway • Submitted Service Delivery Plan with four services (LiceBase, META-pipe, Genomic HyperBrowser and BioXSD / GTrack)

• Co-organised the European Conference on Computational Biology 2016 in Den Haag (with the Netherlands bioinformatics and systems biology research school, BioSB) • Organised six bioinformatics training courses within BioSB • Co-organised a joint hackathon in Montpellier, France, with the ELIXIR Plant Use Case and the Breeding API consortium • Organised three ‘Bring Your Own Data’ (BYOD) meetings

• Organised eight training workshops on the Norwegian e-Infrastructure for Life Sciences (NeLS) platform, NGS data analysis, meta-analysis and data storage

• Placed on the National Roadmap for Large-Scale Research Facilities of the Netherlands Organisation for Scientific Research (NWO)

• Organised two developer workshops on NeLS • Organised course on tools for NGS data analysis, including ELIXIR resources

• Co-launched the European Metabolomics Training Coordination Group (EmTraG) to implement a training strategy in this area

• Hosted the ELIXIR Innovation and SME Forum, “Datadriven innovation in the aquaculture and marine industries”

• Successfully completed two Implementation studies: ELIXIR–TraIT–EGA and the Rare Disease Implementation Study

• Co-organised the "Technologies for Digital Life" meeting in Bergen and the Data management workshop in Trondheim

Portugal

• Established a close collaboration with Digital Life Norway for coordination of research infrastructures in biological and medical science, data management and innovation in biotechnology

• Launched ELIXIR Portugal Compute services, based on OpenStack, made available to researchers in Portugal • Organised a number of training events, including 13 hands-on bioinformatics training courses (attended by 167 researchers) and one Train-the-Trainer event

• Expanded to include 125 research partners in 45 partner institutions

• Contributed to the development of plant data standards and data management best practices, namely the Plant Experimental Assay Ontology and the MIAPPE and BrAPI specifications

• Co-organised a conference with other Dutch research infrastructures to kick-start the national initiative ‘Health Research Infrastructure (Health-RI)’

• Initiated a project on precision medicine, which aims at improving the diagnosis and treatment of stroke and some rare diseases

Netherlands

• Organised the ELIXIR track at the Dutch Bioinformatics conference BioSB2016

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Slovenia

Sweden

• Completed preparations for signing the ELIXIR Consortium Agreement and became a full ELIXIR Member in February 2016

• Organised three Capacity Building Workshops, two of which were on genome annotation and assembly (held in Barcelona and Prague)

• Launched the ELIXIR-SI eLearning Platform to offer bioinformatics courses and webinars (http://elearning. elixir-slovenia.org)

• Launched the ELIXIR-EXCELERATE Data Nodes Network (June 2016) in collaboration with ELIXIR Czech Republic

• Established Bioinformatics ELIXIR-SI Entity (BEE) as a core national group in Slovenia that will provide bioinformatics services to the wider life science research community in Slovenia

• Launched the Cell Atlas: part of the open-access Human Protein Atlas, featuring an interactive database with unparalleled high-resolution images that visualises, for the first time, the location of over 12 000 proteins in cells (December 2016)

• Formally launched the ELIXIR Slovenia Node at a major event for national policymakers, funders and scientific leaders

• Launched an ELIXIR Beacon, giving access to the wholegenome variant frequencies for 1000 Swedish individuals generated within the SweGen project

• Co-organised three training courses and two hackathons

• Received a national grant from the Swedish Research Council for the Human Protein Atlas contribution to ELIXIR (~€200,000 per year, 2016–2017)

• Placed in the 2016 Revision of the National Research Infrastructure Roadmap (originally published in 2011) • Received an €80,000 research grant from the Slovenian Research Agency

Spain • Broadened the ELIXIR Spain portfolio, including specific resources aligned with ELIXIR Use Cases • Developed and submitted a proposal for national funding of the INB/ELIXIR-ES to the National Institute of Health Carlos III with the double objective of consolidating the alignment with ELIXIR and increasing the translational impact on the Spanish National Health System • Launched ELIXIR Beacon servers including the whole genome variant frequencies of 790 unrelated Spanish individuals as part of the CSVS project • Supported of different events and activities, including the INB/ELIXIR-ES Annual Meeting, and the joint workshop between ELIXIR and BioCreative on text mining • Organised a training workshop on High-Performance Computing for the ELIXIR community

Switzerland • Awarded two Innovative Medicines Initiative (IMI) grants: “BEAt-DKD - Biomarker Enterprise to Attack Diabetic Kidney Disease” (2016–2021) and RHAPSODY - Risk Assessment and ProgreSsion of Diabetes (2016–2020) • Organised 57 courses on bioinformatics-related topics, spanning 113 days of teaching and training nearly 1350 researchers • Hosted the ELIXIR Software Carpentry/Data Carpentry instructors' training in Lausanne (January 2016) and three Software Carpentry/Data Carpentry workshop • Led and contributed to the ELIXIR white paper "Defining a lingua franca for the ELIXIR/GOBLET e-learning ecosystem" and to the report on the training needs identified across the ELIXIR community • Organised a series of conferences to celebrate the 30th anniversary of UniProtKB/Swiss-Prot and the 30th anniversary of The Eukaryotic Promoter Database • Launched an ELIXIR Beacon for the arrayMap cancer genome data repository

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United Kingdom • Extended the scope of the Node to include Data, Tools and Interoperability • Added ten new services and three specialist training centres (University of Birmingham, Cambridge University and the Roslin Institute in Edinburgh) to the portfolio • Launched the production of the ELIXIR TeSS portal (tess.elixir-europe.org). The Biosharing portal for data standards and related policies (biosharing.org) became official ELIXIR service • Launched a website for developing training activity in statistics (www.statschoices.org.uk), offering a growing set of resources and information about the wider Statistics Training Signposting project • Received a national grant to support the ELIXIR-UK Coordination Office (total budget of £767,420 over four years) • Organised four training workshops and two meetings for the ELIXIR UK community

Greece (Observer) • Organised Symposium "Infrastructures for Life Science’s Big Data – and the role of ELIXIR" in Athens • Developed and submitted ELIXIR Greece Node Application to the ELIXIR Scientific Advisory Board (SAB), and received a positive review • Developed and submitted a proposal for national funding of the Greek ELIXIR Node to the Ministry of Education, Research and Religion

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2016 highlights Membership Slovenia joins ELIXIR

Activities ELIXIR OncoTrack collaboration ELIXIR started a collaboration with OncoTrack, an Innovative Medicine Initiative project to improve the diagnosis and treatment of colon cancer. They will explore options for providing long-term storage of and discovery services for data generated within the project Open Data in Action: Life Science Data Infrastructure for Innovation conference Researchers, policy makers, research infrastructure operators and industry representatives gathered on 4 February in Brussels for the ELIXIR Conference 'Open Data in Action' to discuss the impact of open data in the life sciences on innovation.

Robert-Jan Smits, Director-General of the Research and Innovation DG of the European Commission (EC), opened the conference by highlighting the Open Data and Open Access policies in the Horizon 2020 funding programme. He spoke about the EC’s goal to make data management plans a requirement for all Horizon 2020 grants.

Jan

Feb

Activities ELIXIR Training Platform kicks off the ‘Train the Trainer’ programme ELIXIR’s ‘Train the Trainer’ programme, designed for ELIXIR trainers, was kicked off at the ELIXIR-EXCELERATE Workshop in Hinxton, UK. The programme takes inspiration from the EMBL-EBI programme and Software and Data Carpentry initiatives.

Mar

Apr

Activities Second ELIXIR All Hands meeting The second ELIXIR All Hands meeting was held in Barcelona, Spain on 7-10 March, with over 200 attendees. It presented the full breadth of EXCELERATE activities, with keynotes from the Centre of Genomics Regulation in Barcelona, the Malaspina 2010 Expedition and the NIH Big Data to Knowledge initiative.

Membership Italy joins ELIXIR

ELIXIR: A Landmark in the 2016 ESFRI roadmap The 2016 ESFRI Roadmap classified ELIXIR as a ‘Landmark’, as it reached its implementation phase by 2015.

The Roadmap describes the role and impact of ELIXIR as “essential for European life science research, as the enhanced technical architecture will facilitate access to well-curated data, international collaboration and ultimately play an integral role in the transformation of bio-industries”.

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Activities ELIXIR Industry Strategy The ELIXIR Industry Strategy provides a comprehensive overview of the current and future actions to stimulate innovation and ensure industry uptake of ELIXIR’s services in companies of all sizes.

ELIXIR Innovation and SME Forum: Data-driven innovation in the aquaculture and marine industries Hosted by ELIXIR Norway in Oslo on 1213 May, the event showcased free tools and services offered through ELIXIR and highlighted research-intensive companies already making use of ‘big data’ in their respective life-science fields.

May

Jun

Activities ELIXIR launches its Data Nodes Network A Data Nodes Workshop in Prague on 13-14 April 2016 marked the launch of ELIXIR’s Data Nodes Network. The Network brings together ELIXIR Nodes with large data collections and databases to develop guidelines and good practices to facilitate collection and linking of data to international deposition archives run by ELIXIR Nodes such as EMBL-EBI.

Activities EMBL-EBI teams up with Czech ELIXIR Node to build annotation capacity EMBL-EBI and Masaryk University (ELIXIR Czech Republic) started a collaboration to train researchers from Masaryk University in the annotation of data in the Protein Data Bank in Europe (PDBe). The project was part of ELIXIR’s capacity-building activities and served as a pilot for the development of the ELIXIR Staff exchange programme.

Activities ECCB 2016 in The Hague, Netherlands ELIXIR was the main organising sponsor of the 15th European Conference on Computational Biology (ECCB) held on 3-7 September in The Hague, Netherlands. The programme featured a track dedicated to ELIXIR Applications, which showcased 12 projects in ELIXIR Use cases and Platforms. The ELIXIR poster session featured over 40 posters.

Activities ELIXIR Policy for Ethical, Legal and Societal Issues (ELSI) ELIXIR adopted an overarching policy for ethical and legal aspects of accessing and re-using sensitive lifescience data. Covering Ethical, Legal and Societal Issues (ELSI) around the provision of sensitive human data in research, the policy provides guidance on key principles and clarifies how these will be handled in the context of ELIXIR services.

Three new Implementation Studies ELIXIR kicked off three new Implementation Studies, covering the Interoperability and Data Platforms as well as the Human Data Use Case.

The three new projects complemented four on-going Implementation studies in 2016. The 2016 portfolio of ELIXIR Implementation studies included seven projects and 9 ELIXIR Nodes.

ELIXIR AAI launches The ELIXIR Compute Platform launched the ELIXIR Authentication and Authorisation Infrastructure (AAI).

AAI introduced a common ELIXIR identity that allows researchers to sign-on to multiple services across ELIXIR using their institution or university accounts, or using their ORCID ID, Google or LinkedIn accounts.

Membership Germany joins ELIXIR

Jan Jul

Aug Feb

Mar Sep

Oct Apr

Nov May

Dec Jun

Membership Luxembourg and Ireland join ELIXIR

Activities The ELIXIR TeSS portal ELIXIR UK launched ELIXIR’s Training e-Support System, TeSS. The portal collects, disseminates and organises information about bioinformatics training from ELIXIR Nodes and thirdparty providers. By the end of 2016, the portal contained over 1000 resources (training events and materials) from more than 30 providers. tess.elixir-europe.org

Activities The ELIXIR International Strategy ELIXIR published its International Strategy, which defines ELIXIR's objectives in collaboration beyond Europe and ensures that ELIXIR engages with the relevant major international initiatives. The Strategy was presented at the International Conference on Research Infrastructures (ICRI), hosted in Cape Town, South Africa on 3-5 October.

Nominations for Core Data Resources ELIXIR opened the process for Nodes to propose databases as ELIXIR Core Data Resources, which are those considered to be of fundamental importance to the wider life-science community and the long-term preservation of biological data.

Core Data Resources are exemplars both within ELIXIR and the global bioinformatics community. They represent the community consensus on data resources that are of utmost importance to research. They drive ELIXIR’s sustainability strategy, provide policymakers with insights into quality and impact, and serve as a quality benchmark in ELIXIR capacity building.

Activities Five new ELIXIR Beacons The first stage of the ELIXIR Beacon project (2015-2016) resulted in the ‘lighting’ of Beacons in five ELIXIR Nodes: Sweden, Finland, France, Switzerland and Belgium, and in the European Genome-phenome archive run jointly by EMBL-EBI and ELIXIR Spain. Each ELIXIR Beacon makes one or more genomics datasets discoverable to the international research community.

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EU Projects

ELXIR Annual Report 2016

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ELIXIR-EXCELERATE ELIXIR-EXCELERATE is a €19 million Horizon 2020 project to help implement ELIXIR by coordinating national data infrastructures and ensuring the delivery of life-science data services through its Platforms and Use Cases.

Basic facts • €19.8 million • four years (2015-2019) • 41 partners in 17 countries

Overall goals • Implement the ELIXIR Scientific Programme • Develop and connect resources and services across ELIXIR Nodes • Build bioinformatics capacity in Europe The ELIXIR-EXCELERATE project is fully embedded into ELIXIR’s operations. This means that all EXCELERATE activities and objectives reflect and complement the objectives of ELIXIR’s Scientific Programme 2014– 2018. The five ELIXIR Platforms and four Use Cases are represented in EXCELERATE as Work Packages (WPs), complemented by Work Packages on Capacity Development, Operations, Communications and Ethics: Platforms • WP1: Tools Platform: Tools Interoperability and Service Registry • WP2: Tools Platform: Benchmarking • WP3: Data Platform: Data Resources and Services • WP4: Compute Platform: Compute, Data access and exchange services • WP5: Interoperability Platform: The ELIXIR Interoperability Backbone

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Use Cases • WP6: Marine Metagenomics Use Case: Marine metagenomics infrastructure as driver for research and industrial innovation • WP7: Plant Sciences Use Case: Integrating Genomic and Phenotypic Data for Crop and Forest Plants • WP8: Rare Disease Use Case: Use Case: ELIXIR infrastructure for Rare Disease research • WP9: Human Data Use Case: Secure archiving, dissemination and analysis of human access-controlled data Node Capacity • WP10: ELIXIR Node Capacity Building Programme Training • WP11:Training Platform: ELIXIR Training Programme Operations and outreach • WP12: Excellence in ELIXIR Management and Operations • WP13: Communications, Industry and Community Engagement • WP14: Ethics requirements In 2016, the EXCELERATE project held its first annual meeting in Barcelona on 7–10 March 2016, as part of the ELIXIR All Hands meeting. The theme of the meeting was ‘User communities', with the programme focusing on activities in the ELIXIR four Use Cases: Marine metagenomics (WP6), Rare diseases (WP7), Human data (WP8) and Plant Sciences (WP9).

The main EXCELERATE outputs in 2016 • Launched the ELIXIR Authentication and Authorisation Infrastructure to enable individual researchers to access different services across ELIXIR, through a single sign-on process1 (WP4) • Established the ELIXIR Data Nodes Network – a network of Nodes with key data resources, developing guidelines and good practices to facilitate linking to international archives (WP10) • Released the ELIXIR Training Portal to disseminate training resources from ELIXIR Nodes and third-party providers2 (WP11) • Published ELIXIR Technical Services Roadmap3 that map specific scientific needs of different communities to technical and infrastructure solutions (WP4)

• Extended the ELIXIR Tools and service registry (https:// bio.tools) with benchmarking capabilities (WP1), ensuring it is a gateway to databases and tools for lifescience data analysis • Developed indicators to assess quality and impact of data resources4. These indicators will be used to identify ELIXIR Core Data Resources and support excellence in resource development and operation (WP3) • Developed reference implementation of descriptors, service management and API for datasets (WP5) • Use Cases: specific marine databases launched (WP6); released first set of ontologies for annotation of phenotype in crop and forest plants (WP7); organised rare-disease community workshop (WP8); defined requirements for human access-controlled data (WP9) • Developed and adopted the ELIXIR ELSI Policy (WP14)

Re-using life-science data ethically Clear governance of Ethical, Legal and Societal Issues (ELSI) is an integral part of the provision of ELIXIR Services, so the adoption of ELIXIR’s ELSI policy was a major milestone within both EXCELERATE and ELIXIR generally. The policy is centred around the provision of sensitive human data for use in research, and provides guidance on key principles in the context of ELIXIR-EXCELERATE Services.

ELIXIR Services offer data for secondary use - they do not produce data and are not involved in getting informed consent from research participants. Their role centres around data stewardship as a service

to both data generators and data users. ELIXIR’s ELSI Policy supports the process of making scientific data available in an ethically and legally sound manner by consolidating requirements shared across all ELIXIR Members and Services.

As distributed infrastructure, ELIXIR Services are delivered by ELIXIR Nodes. This means that each ELIXIR Service must have its own ethics and regulatory oversight in place as the complexity and diversity of regulations around data can vary significantly between or even within individual countries.

Developed in consultation with Heads of Nodes and technical personnel,

ethics experts on the ELIXIR Scientific Advisory Board and external experts, the ELSI Policy addresses the concerns of key stakeholders such as ethics committees and ethics advisory boards (e.g. of large projects), funders, data providers, data users and patients or patient groups.

As it defines a model that clarifies specific responsibilities of databases and other services offering human data for secondary use, the ELIXIR ELSI Policy is also of use to other research infrastructures and database providers currently going through the process of assessing or developing their own policies.

1. www.elixir-europe.org/aai 2. http://tess.elixir-europe.org 3. Bongo LA, Borg M, Cornelis A et al (2016). A Technical Services Roadmap for supporting Life Science Research in Europe. Zenodo (doi: 10.5281/zenodo.60291) 4. Durinx C, McEntyre J, et al. (2016) Identifying ELIXIR Core Data Resources.

F1000Research 5. pii:ELIXIR-2422 (doi: 10.12688/f1000research.9656.2)

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Figure 4: Scope of the ELIXIR ELSI Policy Submission

Access ELIXIR Node

Data generator (researcher, consortium)

Patient

ELIXIR SERVICE

User (researcher, consortium)

Consent ELIXIR ELSI Policy • Data transfer agreement • Data access agreement • Terms of use Scope of the ELIXIR ELSI Policy: An ELIXIR Service (e.g. an archive) providing data for research. When implemented the ELSIs policy only influences the DTA (e.g. as "Terms of Use" or "Terms of Service") at the "data in) (submission) and "data out" (use) ends. The Node retains full responsibility for having a sustainable ELSI framework in place for the ELIXIR Service in question

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The Data Transfer Agreement ensures that data providers and users are aware of their obligations. The responsibility for implimenting the obligations is cascaded down to the date provider and/or user.

Collaboration with other Research Infrastructures ELIXIR both collaborates in and runs major EU projects, which in turn helps to fund specific activities in ELIXIR Platforms and Use Cases. These projects also enable ELIXIR to collaborate with key international initiatives in the life sciences, other ESFRI Research Infrastructures and e-Infrastructures.

Authentication and Authorisation for Research and Collaboration (AARC) The AARC project brings together 20 partners from across Europe with the goal to harmonise approaches to authentication and authorization in different e-infrastructures and research collaborations.

Represented by ELIXIR Finland (CSC- IT Center for Science), ELIXIR focuses on developing training materials on AAI (Authentication and Authorization Infrastructure) integration and leads the work on Level of Assurance. In March, it organised a training workshop on AAI integration for the ELIXIR community; furthermore, ELIXIR Finland led the working group to develop a Level of Assurance framework for research services.

The AARC and CORBEL projects were working together towards a common AAI for life sciences. An initial workshop was organised in May and hosted by ECRIN to discuss the possibilities of having a common AAI for the participating research infrastructures. The different use cases for a common AAI were gathered and compared in Autumn.

European Marine Biological Research Infrastructure Cluster (EMBRIC) EMBRIC – initiated in 2015 and, financed with €9 million from the Horizon 2020 programme – connects marine biotechnology initiatives that focus on science, industry and regional growth. In EMBRIC, ELIXIR partners with research infrastructures such as the European Marine Biological Resource Centre (EMBRC), Microbial Resource Research Infrastructure (MIRRI) and EU-OPENSCREEN, to drive at stronger connections between science and industry through a number of “workflows” including bioproduct discovery, leverage of microbiological culture collections and aquaculture breeding strategies informed by genomics.

Achievements in 2016 include: • Launch of the EMBRIC “Configurator” service , a structured consultancy service that translates incoming proposed blue biotechnology studies into effective configurations of data infrastructure from the portfolio of ELIXIR resources, setup and operation guides and data management plans • Checklist reporting standards, deployed within ELIXIR, for biomolecular data sets derived from strains in microbiological collections and for shellfish aquaculture applications • Mapping of services and requirements around chemical biology, including profiling of reference-level and other ELIXIR resources, unmet requirements (typically around laboratory management), future training needs and data integration across small molecules, culture collections and genomics databases

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ENVRIplus

CORBEL

ENVRIplus 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, interdisciplinary and interoperable cluster of Environmental Research Infrastructures.

CORBEL is collaboration between 11 ESFRI Biological and Medical Research Infrastructures funded through EU’s Horizon 2020 programme. The goal of CORBEL is to establish a framework of shared services between the participating infrastructures (BMS RI), which enhances the efficiency, productivity and impact of European biomedical research and its translation into medicine. The CORBEL consortium is led by ELIXIR as the coordinator and the Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) as co-coordinator.

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.

To date, ELIXIR work has included: • Support for a mapping exercise between the established ENVRI Reference Model and resources within ELIXIR, including the provision of a number of ELIXIR use cases from ELIXIR Greece and EMBL-EBI • Presentation of ELIXIR outreach and dissemination practices

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In the first half of 2016 the project set up its governance and administrative structures, established user and stakeholder forums, and carried out technology and gap analysis to set the direction for the project’s technical and scientific development.

The project also established the BMS RI Innovation Office to help the European Biological and Medical Research Infrastructures with collaboration with industry and technology transfer, providing legal support and partnering advice.

In the second half of the year, the project started the technical and research effort to develop CORBEL platform for shared infrastructure services. In October CORBEL launched the first Open Call for research projects to access integrated research infrastructures. The call offered four different Access Tracks: (1) Genotype to phenotype analysis, (2) Predictive systems pharmacology for safer drugs and chemical products, (3) Structure-function analysis of large protein complexes and (4) Marine Metazoan developmental models. The project received 80 proposals which were reviewed by external experts and by the service providers requested by the applicant.

Supporting activities

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Capacity building and Node development The ELIXIR Capacity Building Programme (1) supports ELIXIR Nodes in their organisation and governance, including sharing best practices in accessing EU Structural Funds (ESIF) and (2) develops and coordinates ELIXIR-wide ‘communities of practice’ for management, administrative and technical services in ELIXIR Nodes.

ELIXIR Node Handbook In 2016 the Capacity Building Programme developed the ELIXIR Node Handbook which provides a basic reference for organisational, legal and governance aspect of ELIXIR Nodes’ functioning. Building on and extending the ELIXIR Handbook of Operations, the Node Handbook will be regularly updated to reflect the experience from individual ELIXIR Nodes.

Data Nodes Network The ELIXIR Data Nodes Network focuses on establishing guidelines and good practices to facilitate efficient data collection from national data resources and channeling these into international archives. The goal is to create routes for uniform data publishing across ELIXIR, including repositories for replication of reference data and secure storage of sensitive data.

The network was launched at the Capacity Building Workshop held in April in Prague, Czech Republic. The first component of the Data Nodes Network was the Local EGA developed by the ELIXIR Human Data Use Case. The release and full implementation of the Local EGA in the Data Nodes Network is planned for 2017.

Genome assembly and annotation Genome assembly and genome annotation are two areas of bioinformatics analysis that require considerable time, resources, and knowledge. These resources are unevenly distributed throughout Europe, with only a few centres dealing with these analyses regularly. The ELIXIR Capacity Building Programme supports the transfer of genome annotation and assembly know-how from those centres across ELIXIR Nodes.

One training course on genome annotation and assembly was organised in October 2016 in Prague, Czech Republic, attended by 24 participants. The course content is now available on the ELIXIR eLearning platform. Two more courses are planned in 2017.

ELIXIR Sweden and ELIXIR Czech Republic also started a pilot project to investigate how the experts centres could supply genome assembly and genome annotation as a service in Europe. The project is scheduled to finish in 2017.

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Governance To ensure the integration of bioinformatics services into a coherent distributed infrastructure, it is critical to create effective links between the national institutes that make up ELIXIR Nodes, and between those institutes and the ELIXIR Hub. This is done through the signature of Collaboration Agreements, which allows the ELIXIR Nodes to receive funding from the ELIXIR Hub for Commissioned Services.

In 2016, the ELIXIR Hub worked closely with ELIXIR Nodes on the development of Collaboration Agreements – three Collaboration Agreements (France, Portugal and Spain) were signed during the period. By the end of 2016, a total of twelve ELIXIR Nodes had their Collaboration Agreements in place. Negotiations will continue with the remaining Nodes in 2017.

In parallel with the development of Collaboration Agreements, the ELIXIR Hub begun working on ELIXIR Node Service Delivery Plans (SDPs), which describe the scientific and service provision content that each ELIXIR Node provides through ELIXIR. In 2016 the Hub prepared ten SDPs (Czech Republic, Denmark, Estonia, EMBLEBI, Finland, France, Netherlands, Norway, Sweden and Switzerland) and submitted them for review and approval to the ELIXIR Board during its 2016 Autumn session (21–22 November) in Hinxton, UK.

Commissioned services Following the signature of Collaboration Agreements, the ELIXIR Hub can conclude Commissioned Services Contracts with ELIXIR Nodes. These are short-term projects funded through the ELIXIR budget (currently carried out through Implementation Studies) run by ELIXIR Nodes. The Commissioned Service Contract is signed between the ELIXIR Hub and the entity that represents the ELIXIR Node in each country.

In 2016, the total of 37 contracts were approved across nine ELIXIR Nodes. The goal for 2017 is to increase the number of Nodes with Commissioned Service Contracts and perform the first pilot for internal tendering of long-term Infrastructure Services, which will go beyond the current short-term duration of Implementation Studies.

Handbook of Operations To formalise existing procedures and policies and support governance and administrative practices throughout ELIXIR, the ELIXIR Hub in 2016 developed the ELIXIR Handbook of Operations. The document is the authoritative source of information on ELIXIR procedures, recommendations and guidelines, strategies and reference documents. It is aimed at the whole ELIXIR community, including all staff in ELIXIR Nodes, ELIXIR Hub staff, ELIXIR Board members and national funders. The topics covered by the Handbook include Governance, Nodes and Service provision, ELIXIR Programme cycle, Project management, Communications and External relations, and Technical operations.

The services included in Nodes Service Delivery Plans now form the initial portfolio of ELIXIR services .

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Industry engagement

In 2016, ELIXIR appointed a dedicated Industry and International Officer, Pablo Román García. Pablo leads the implementation of ELIXIR's Industry Strategy and runs the ELIXIR Innovation and SME programme.

The ELIXIR Industry Strategy, published in May 2016, sets five objectives in order to increase awareness and promote open innovation.

• Increase industry usage of ELIXIR resources and ensure the name is synonymous with quality • Enable Open innovation by Europe’s SMEs • Build effective partnerships with key industry stakeholders and initiatives • Ensure effective communication between industry and ELIXIR • Support the bioinformatics training needs of industry Each objective is met by a set of actions, carried out by ELIXIR partners. The strategy itself will be reviewed annually against metrics and updated regularly to include new activities.

An industry brochure1 was also produced, featuring some of the major activities and relevant initiatives within the five ELIXIR Platforms.

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Innovation and SME events

ELIXIR’s Industry Advisory Committee

In May 2016, an ELIXIR Innovation and SME forum was held in Norway, focusing on metagenomics and marine aquaculture. Organised in collaboration with ELIXIR Norway and the ELIXIR Marine Metagenomics Use Case, it featured talks from companies such as MarineHarvest, AquaGen and ArticZymes, who rely on access to public data to run their analysis pipelines. The Programme Technical tracks presented some of the free resources offered through ELIXIR such as Ensembl, EBI Metagenomics portal, LiceBase, SalmoBase and genomic resources for Atlantic cod.

The ELIXIR Industry Advisory Committee (IAC) met for the second time in early 2016, issuing a set of high-level recommendations for ELIXIR, including the need to keep developing good links with other successful industryacademia initiatives such as the Innovative Medicines Initiative. The IAC also recommended continuing to increase awareness through presence at conferences and the promotion of ELIXIR Node services (see page 54 for IAC members).

During 2016, ELIXIR prepared a calendar of four upcoming Innovation and SME forums to take place in 2017. Starting with Helsinki in February, followed by Barcelona (June), Brussels (October) and Paris (November), the events will focus on health, microbiome and rare diseases respectively.

ELIXIR at industry networking events ELIXIR was presented at several industry focused events: the IMI Stakeholder Meeting in Brussels, Belgium, BioEurope in Cologne, Germany, and the Target Validation Using Bioinformatics Conference in Heidelberg, Germany.

During the last part of 2016, ELIXIR further expanded its engagement with local biotechnology clusters in Spain, Finland, UK and with the Council of European BioRegions.

Industry projects Throughout 2016, ELIXIR built up collaborations with key industry initiatives.

ELIXIR and the IMI-funded OncoTrack project developed their collaboration around using the European Genomephenome Archive as a solution for long-term storage of data. OncoTrack uses large-scale genomics to generate new data to power research that will improve the early diagnosis of colon cancer. The final report published at the end of the collaboration also explains the benefits of ELIXIR services to industry.

ELIXIR kept on developing Bioschemas as a flagship project. This community-driven initiative encourages people, including industry users (e.g. Google and repositive.io2) in life science to use schema.org markup, so that their websites and services contain consistently structured and machine readable information.

1. Available via http://www.elixir-europe.org/industry 2. https://repositive.io

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International collaboration ELIXIR International strategy

ELIXIR on the global stage

In October 2016, ELIXIR published its International Strategy, which sets out ELIXIR's role on the global stage.

The strategy defines ELIXIR's objectives in international collaboration and will ensure that ELIXIR engages with major international initiatives in bioinformatics and key countries outside Europe.

Collaboration with the US Big Data to Knowledge (BD2K) initiative stepped up in 2016. Several ELIXIR representatives gave talks at the BD2K Annual Meeting in Bethesda, USA, presenting ELIXIR’s International Strategy, Training and Interoperability initiatives.

The four objectives of the ELIXIR International Strategy are to: • Ensure ELIXIR serves life-science users and communities across the globe • Support collaboration between ELIXIR and relevant global bioinformatics and data initiatives • Shape global science policy discussions around data and research infrastructures • Develop formal collaboration with those countries outside Europe where there is a mutual benefit ELIXIR is recognised by the G7's Group of Senior Officials to be a Global Research Infrastructure with a potential for membership by countries outside of Europe. At the heart of ELIXIR’s International Strategy is a commitment to realise this potential and drive bioinformatics collaboration at the global level.

ELIXIR Platforms and groups continued their collaboration with global initiatives such as GOBLET (Global Organisation for Bioinformatics Learning, Education and Training), Global Alliance for Genomics and Health, and the Research Data Alliance.

At the policy level, ELIXIR began global discussions around the sustainability of life science databases with representatives from North American, European and Asian funding bodies, facilitated by the Human Frontiers Science Programme.

The International Conference on Research Infrastructures ELIXIR was presented at the International Conference on Research Infrastructures (ICRI) in Cape Town, South Africa, on 3-5 October 2016. ICRI is a global forum for research infrastructures operators and managers to discuss collaboration on research infrastructures across countries and scientific domains.

ELIXIR presented its International Strategy; ELIXIR’s External Relations Manager, Andrew Smith, gave a talk on Inclusive Research Infrastructures for Development and Capacity building.

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ELIXIR Working groups The ELIXIR Working Groups gather experts around a specific theme or a problem and actively engage with ELIXIR Nodes, ELIXIR Platforms and Use Cases. Their mandate and scope are defined by the ELIXIR Heads of Node Committee; their outcomes range from policy recommendations and white papers to review articles and scoping studies.

In 2016 ELIXIR had three working groups in operation: the Galaxy Recommendation Working Group, the Software Development Best Practices Working Group and the Data Management Plans Working Group.

Galaxy Recommendations Working Group

ELIXIR Working Group on Data Management Plans The ELIXIR Data Management Plans (DMP) Working Group received a 6-month mandate in December 2015 to explore potential actions in developing a strategy for supporting good data management practices in life sciences.

Following a survey and a discussion held at the ELIXIR AllHands meeting in March 2016, the Working Group became part of the ELIXIR Training Platform, tasked to develop the ELIXIR Data Management Portal. The development was led by ELIXIR Netherlands and ELIXIR Czech Republic; the first testing version of the portal was released in December 2016.

The goal of the Data Management Portal is to provide guidance to life science researchers on data stewardship and help them to create Data Management Plans for their research projects.

The Galaxy Recommendation Working Group was established in 2015 to evaluate to evaluate the use of the online platform Galaxy in the ELIXIR Nodes, and its applications in ELIXIR Platforms and Use Cases. In 2016 the Working Group presented its work at the Galaxy Community Conference in Bloomington, USA1, and organised Galaxy DevOps Workshop in Heidelberg, Germany.

Software Development Best Practices Working Group The Software Development Best Practices Working Group was launched in December 2015 to deliver guidelines on best practices and quality assessment in software development. Following the kick-off workshop in Amsterdam, the group proposed and published a set of metrics to monitor and assess good practices in software development2. The set represents a consensus of experts from different organisations that have potential to get adopted by the communities they represent.

The group also worked on recommendation for Open Source software development. The research paper to present these recommendations and a corresponding website are planned for publication in were published in Summer 2017.

1. Coppens F. ELIXIR: a distributed infrastructure for life-science information.

F1000Research 2016, 5:1569 (poster) (doi: 10.7490/f1000research.1112469.1) 2. Artaza H, Chue Hong N, Corpas M et al. Top 10 metrics for life science software good practices. F1000Research 2016, 5(ELIXIR):2000 (doi: 10.12688/f1000research.9206.1) 3. http://dmp.fairdata.solutions

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ELIXIR Hub activities

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Mathias Uhlén (ELIXIR Sweden) in the ELIXIR profile video

ELIXIR Communications

Following an ELIXIR Communications expert workshop held in December 2015, the ELIXIR Hub (with input from partners) developed ELIXIR’s first Communications Strategy. The purpose of the Communications Strategy is to act as a reference point for all aspects of ELIXIR’s communications work. It provides a comprehensive overview of existing communications channels and policies, including main messages and primary target groups. Annexed to the strategy contain more detailed guidance documents on specific aspects of ELIXIR communications (ELIXIR social media strategy, ELIXIR writing style guide and others).

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The ELIXIR Intranet was formally launched in December 2015; in 2016 the focus was on expanding functionality and attracting more active users from within ELIXIR. By the end of 2016, the ELIXIR intranet had nearly 400 users.

The ELIXIR Intranet was also the first service to use the newly developed ELIXIR Authorisation and Authentication Infrastructure (AAI): this enabled intranet users to use their institutional account as well as their ORCID ID or LinkedIn account to log in.

In October, the ELIXIR Hub released the ELIXIR profile video to present its structure, mission and objectives. The video includes interviews with partners and presents many of ELIXIR’s current activities. It will be followed by three more videos presenting specific aspects of ELIXIR. The video is available on the ELIXIR YouTube channel1 .

In 2016 the ELIXIR Hub continued with the ELIXIR Webinar Series and organised 15 webinars to present the work of ELIXIR Implementation Studies, ELIXIR Platforms and Use Cases.

ELIXIR at ECCB 2016

ELIXIR Gateway on F1000Research

ELIXIR was the main organising partner of the European Conference for Computational Biology (ECCB), the main European event for bioinformatics and computational biology in 2016, held from 3–7 September in The Hague, Netherlands.

The ELIXIR Gateway on F1000Research was launched in December 2015 as a platform to collect and capture ELIXIR’s research and technical outputs. In 2016, the ELIXIR channel published nine articles, all transparently peer-reviewed through the F1000Research invited post publication peer review process.

As part of the ELIXIR-ECCB 2016 partnership, the programme of the conference featured a dedicated track to showcase ELIXIR activities and services. The ELIXIR Application Track session presented twelve projects from across ELIXIR infrastructure, which were selected from over 40 submissions from ELIXIR Nodes, Platforms and Use Cases.

The full breadth of ELIXIR activities was presented in the ELIXIR Poster session that showcased nearly 50 posters.

“As one of the major initiatives in Europe and globally, we were delighted to give ELIXIR a venue to present its work to the international and multidisciplinary audience at ECCB. It was for the first time that we included an Applications track in the programme and it proved to be a success! It was great to see the interest the ELIXIR Track created and the feedback we received from the delegates was overwhelmingly positive.”

— Jaap Heringa, Chairman of the ECCB 2016 Organising Committee and Head of the ELIXIR Netherlands The ECCB 2016 was organised by the Dutch Techcentre for Life Sciences (ELIXIR Netherlands) and the BioSB research school.

The most successful article published in the ELIXIR Gateway was by Durinx, McEntyre, Appel et al.2, which presented the criteria and process for identifying and selection of ELIXIR Core Data Resources. This has been viewed by over 16,000 readers. Other important publications include articles by Bousfield, McEntyre, Velankar et al. exploring patterns of database citation in articles and patents3 and by Artaza, Chue Hong, Corpas et al., presenting top ten metrics for life science software development good practices4.

The editorial oversight of the ELIXIR Gateway is provided by an Advisory Board who review all papers submitted to the Gateway and ensure all materials are relevant to the ELIXIR community. The members of the Advisory Board also worked as a review panel for the ELIXIR Applications Track organised as part of the ECCB 2016 (see above).

The members of the Advisory Board of the ELIXIR Gateway are: • Niklas Blomberg, ELIXIR Director • Inge Jonassen, University of Bergen, Head of ELIXIR Norway • Barend Mons, Leiden University Medical Center, Netherlands • Arlindo Oliveira, Instituto Superior Técnico, Head of ELIXIR Portugal • Bengt Persson, Uppsala University, Sweden, Head of ELIXIR Sweden

1. https://youtu.be/stTY6fxwonY 2. Durinx C, McEntyre J, Appel R et al. Identifying ELIXIR Core Data Resources.

F1000Research 2017, 5(ELIXIR):2422 (doi: 10.12688/f1000research.9656.2) 3. Bousfield D, McEntyre J, Velankar S et al. Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.

F1000Research 2016, 5(ELIXIR):160 (doi: 10.12688/f1000research.7911.1) 4. Artaza H, Chue Hong N, Corpas M et al. Top 10 metrics for life science software good practices. F1000Research 2016, 5(ELIXIR):2000 (doi: 10.12688/f1000research.9206.1)

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ELIXIR Hub staff In 2016, the ELIXIR Hub expanded its team and recruited experts for technical, coordination and leadership positions.

Serena Scollen joined the Hub in June as the Head of Human Genomics and Translational Data to lead the development and implementation of an ELIXIR-wide Human Data strategy.

Serena joined ELIXIR from Pfizer where she was Director and Head of UK Genetics. In this role, she led and implemented a genetic and precision medicine strategy to support drug target selection and clinical programmes for the Pain and Sensory Disorders Research Unit.

The technical expertise and coordination capacity was strengthened by two new Technical Coordinators.

Montserrat González joined the Hub team in March as ELIXIR Technical Officer to implement the quality assurance processes for ELIXIR services and support the coordination of the ELIXIR Compute Platform (Montserrat left the ELIXIR Hub at the end of 2016 and took up a new position at EMBL-EBI). Norman Morrison joined the ELIXIR Hub in July to work as Technical Lead for the ELIXIR Interoperability Platform. Norman works closely with the Interoperability Platform leadership team, driving the development of a long-term interoperability strategy and architecture for ELIXIR. Norman took over responsibilities from Andy Jenkinson who left his temporary assignment at ELIXIR at the end of June.

The ELIXIR Hub External Relations team expanded with the arrival of Pablo Román García as ELIXIR Industry and International Officer. Pablo leads the implementation of ELIXIR's Industry strategy, including running the ELIXIR Innovation and SME programme; He also supports ELIXIR’s collaboration with countries outside Europe and relevant global initiatives.

Melissa Balzano joined the Hub in March as ELIXIR Events Officer, replacing Joy Friesner.

To support the administration of EU grants, the Project Management team recruited Elenko Anastasov as ELIXIR Grants Administrator. Elenko supports the financial monitoring and administration of the ELIXIREXCELERATE and CORBEL projects.

The ELIXIR Hub also hosted three interns. Roberto Preste spent six months (March - August) supporting the Bioschemas initiative; Federico López Gómez joined the Hub in October and worked on several short-term projects for the ELIXIR Events portal and the Bioschemas initiative.

Marine Gabory joined the External Relations team to support ELIXIR’s work on long term funding strategies and consultation responses.

ELIXIR Hub staff in 2016. From left to right: Federico López Gómez, Nicola Kay, Přemysl Velek, Steffi Suhr, Melissa Balzano, Pablo Román García, Phyllida Hallidie, Norman Morrison, Serena Scollen, Andy Smith, Niklas Blomberg, Marine Gabory and Martin Cook. (Not pictured: Susanna Repo, Rafael Jimenez, Friederike Schmidt-Tremmel, Mikael Linden, Montserrat González, Elenko Anastasov, Roberto Preste)

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Governance committees and financial data

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ELIXIR Committees ELIXIR Board Chair Torsten Schwede, Switzerland

Vice Chairs Anna Wetterbom, Sweden Prof Rein Aasland, Norway

Country

Scientific delegate

Administrative delegate

Belgium

Laurence Lenoir (from July 2016) François Guissart (until June 2016)

Michele Oleo Didier Flagothier

Czech Republic

Jaroslav Koča

Jan Burianek

Denmark

Anders Krogh

Troels Tvedegaard Rasmussen

Estonia

Pärt Peterson

Toivo Räim Priit Tamm

Finland

Per Öster

Riina Vuorento Jarmo Wahlfors

France

Claudine Medigue

Eric Guittet

Germany (from August 2017)

Roland Eils Alexander Goesmann

Johannes Mohr

Ireland (from July 2017)

TBA

Marion Boland Dara Dunican

Israel

Yossi Kalifa

Ilana Lowi

Italy

Anna Tramontano

Salvatore La Rosa

Luxembourg (from June 2016)

TBA

Lynn Wenandy Pierre Misteri

Netherlands

Ruben Kok

Bea Pauw

Norway

Rein Aasland Stig Omholt

Jacob E Wang (until March 2016)

Portugal

Ana Teresa Freitas

Andreia Feijão Tiago Saborida

Slovenia

Damjana Rozman

Albin Kralj

Spain

Ferran Sanz

Cristina Bauluz Dr Rafael de Andres-Medina

Sweden

Ulf Gyllensten (Until October 2016) Björn Andersson (From October 2016)

Karl Gertow (from October 2016) Anna Wetterbom (stepped down end of 2016)

Switzerland

Torsten Schwede

Isabella Beretta

UK

Chris Rawlings

Mark Palmer Amanda Collis

EMBL

Iain Mattaj Janet Thornton

Silke Schumacher

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Heads of Node Committee Chair Niklas Blomberg, ELIXIR Director Country

Head of Node

Belgium

Yves Van de Peer

Czech Republic

Jiří Vondrášek

Denmark

Søren Brunak

Estonia

Jaak Vilo

Finland

Tommi Nyrönen

France

Jean‐François Gibrat

Germany (from August 2016)

Alfred Pühler

Ireland (from July 2016)

Walter Koch

Israel

Michal Linial

Italy

Graziano Pesole

Luxembourg (from June 2016)

Reinhard Schneider

Netherlands

Barend Mons (until September 2016) Jaap Heringa (from September 2016)

Norway

Inge Jonassen

Portugal

Arlindo Oliveira

Slovenia

Brane Leskošek

Spain

Alfonso Valencia

Sweden

Bengt Persson

Switzerland

Ron Appel

UK

Carole Goble

EMBL-EBI

Rolf Apweiler Ewan Birney

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Scientific Advisory Committee

Industry Advisory Committee

Chair Robert Gentleman, 23andMe, USA

Chair Angel Pizarro, Amazon Web Services, USA

Vice Chair Janet Kelso, Max Planck Institute for Evolutionary Anthropology, Germany

Vice Chair Philippe Sanseau, GlaxoSmithKline, UK

Members Alan Archibald, University of Edinburgh, UK Pascal Borry, University of Leuven, Belgium Kate Bushby, Newcastle University, UK Elina Ikonen, University of Helsinki, Finland Larry Hunter, University of Colorado, USA (from November 2016) Edward Marcotte, University of Texas at Austin, USA Nicola Mulder, UCT Computational Biology Group (NBN), South Africa Francis Ouellette, Ontario Institute for Cancer Research, Canada (from April 2016) Juni Palmgren, Karolinska Institutet, Sweden (from November 2016) Susan E. Wallace, University of Leceister, UK Jérôme Wojcik, Quartz Bio, Switzerland

ELIXIR Scientific Advisory Board, from left to right: Francis Ouellette, Alan Archibald, Nicola Mulder, Robert Gentleman, Juni Palmgren, Susan E. Wallace, Larry Hunter (not pictured: Janet Kelso, Pascal Borry, Kate Bushby, Elina Ikonen, Edward Marcotte and Jérôme Wojcik)

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Members Belinda Clarke, Agri-Tech East, UK (from April 2016) Martin Ebeling, Hoffmann-La Roche, Switzerland Anita Eliasson, Biocomputing Platforms Ltd, Finland Iain Hrynaszkiewicz, Springer Nature, UK Natalia Jiménez Lozano, Atos, Spain Claus Stie Kallesøe, Grit42, Denmark Sara Paulina de Oliveira Monteiro, P-BIO, Portugal (from April 2016) Christian Paulitz, Bayer CropScience, Germany (from November 2016) Angel Pizarro, Amazon Web Services, USA Liz Reynolds, General Bioinformatics, UK Sándor Szalma, Takeda Pharmaceuticals, USA Jerry Lanfear, Pfizer, UK (until June 2016) Mark Foster, Syngenta, UK (until July 2016)

ELIXIR Industry Advisory Committee, from left to right: Pablo Román García (ELIXIR Industry and International Officer), Natalia Jiménez Lozano, Philippe Sanseau, Martin Ebeling, Niklas Blomberg (ELIXIR Director), Anita Eliasson, Christian Paulitz, Liz Reynolds, Angel Pizarro, Iain Hrynaszkiewicz (not pictured: Belinda Clarke, Claus Stie Kallesøe, Sara Paulina de Oliveira Monteiro, Sándor Szalma, Jerry Lanfear and Mark Foster).

Financial data In its 2014 Summer meeting, EMBL Council unanimously approved ELIXIR’s legal framework, including its status within EMBL as a "Special Project” as well as EMBL's membership of ELIXIR (EMBL/2013/16/Rev 1).

As of 31 December 2016, the total number of signatories to the ECA stood at 20 (with France and Spain as Provisional Members) with Greece additionally making contributions to its financing as an Observer.

As of 31 December 2015, the total number of signatories to the ECA stood at 15 (with France and Spain as Provisional Members) with Slovenia additionally making contributions to its financing.

The budget of ELIXIR is set annually by the ELIXIR Board and all funds related to its activities, including its surplus, are ring-fenced within EMBL's accounts.

Income

2016 2016 2015 Actual Budget Actual €000

ELIXIR Member state contributions

Ordinary contributions

€000

€000

(a)

3.710

2.759

Foreign exchange gain on sterling contributions

(b)

50

Grant income

(c)

899

1.042

150

Other income

1

-

3

Provision for unpaid member state contributions

-

-

2.217

2.064

Net Income

4.660

3.801

Expenditure

Technological activities

Salaries

195

440

112

Running costs

151

260

79

Equipment and depreciation

-

8

-

Commissioned services (see page 58-59)

435

940

Total expenditure Technological Activities

781

1.648

Directorate and Administrative expenditure

Salaries

640

1.161

800

Running costs

260

452

463

Equipment and depreciation

-

4

-

900

1.617

1.263

Support and Admin Infrastructure costs

342

534

405

Grant expenditure incurred

899

-

150

Total expenditure Directorate and Administration

191

Total expenditure

2.922

3.799

2.009

Surplus/(Deficit)

1.738

2

208

ELXIR Annual Report 2016

57

ELIXIR Member state contributions

(a) ELIXIR Member state contributions

2016 2015 Actual Actual â‚Ź000

â‚Ź000

123

116

Czech Republic

46

43

Denmark

79

74

Estonia

5

4

Finland

61

58

France

719

226

Belgium

Germany 376 Greece

22

-

Ireland 20 Israel

56

53

Italy 531 Luxemburg

4

Netherland

205

193

Norway

113

107

Portugal

54

51

Slovenia

10

11

372

265

Sweden

125

118

Switzerland

159

151

United Kingdom

630

594

3.710

2.064

-

-

3.710

2.064

Spain

Total Less provision for unpaid member state contributions Net ELIXIR member state contributions

58

ELXIR Annual Report 2016

(b) The ELIXIR Board approved that, from January 2016, the UK will pay its member state contributions in Sterling (ELIXIR/2015/28). The difference between the value of these contributions valued in Euros at the date of payment and the date of the approval of the 2016 budget was €50k.

(c) Grant income

2016 2015 Actual Actual

€000

€000

Grant funding awarded

5.832

5.941

Grant income earned

899

150

Expenditure incurred

(899)

(150)

4.892

5.791

Unutilised grant income

(d) The following countries have amounts due or prepaid at 31 December 2016: Values in € 000 Greece Germany Israel ELIXIR member state receivables

Contribution 2016

Contribution 2015–2013

Total

-

45

45

376

-

376

-

53

53

376

98

474

ELXIR Annual Report 2016

59

Commissioned Services: ELIXIR Implementation studies Implementation Studies are short-term projects carried out by ELIXIR Nodes addressing key scientific and technical issues within ELIXIR. The outcome of an Implementation Study may be a description of service requirements, a piece of software, or a technical deliverable with an accompanying report.

Implementation Studies are funded through the budget of the ELIXIR Hub and form part of ELIXIR’s ongoing activities Name

in a particular Platform or Use Case. They are proposed

by Platforms, agreed with the ELIXIR Heads of Nodes Committee and approved by the ELIXIR Board.

In 2016 ELIXIR ran nine Implementation Studies , with three additional studies approved in 2016 with a start date in early 2017. Ongoing and completed Implementation Studies are listed at https://www.elixir-europe.org/aboutus/implementation-studies

Sector

Nodes

Leads

Metrics discovery and implementation in life-sciences

Tools

United Kingdom

Manuel Corpas, UK John Hancock, UK

Genomic data management for translational and biomarker research using the European Genome-phenome Archive (EGA)

Human Data

Netherlands EMBL-EBI Spain

Sanne Abeln, NL Dylan Spalding, EMBL-EBI

Rare disease interoperability backbone

Rare Disease

Netherlands France EMBL-EBI

Marco Roos, NL

Bringing European data forward for international data discovery

Human Data

France Switzerland Spain Belgium EMBL-EBI The Netherlands Sweden

Ilkka Lappalainen, FI Jordi Rambla, ES

Building the foundation for Data Carpentry and Software Carpentry within ELIXIR

Training

United Kingdom Norway Finland Italy Belgium Switzerland The Netherlands Slovenia Estonia Czech Republic France Israel Portugal

Alexandra Pawlik, UK

Finished in 2016

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ELXIR Annual Report 2016

Name

Sector

Nodes

Leads

Implementation Study on Data Identification and Interoperability

Interoperability

EMBL-EBI

Henning Hermjakob, EMBL-EBI

Data Resource Implementations for the Global Alliance for Genomics and Health Data Schema

Human Data

Switzerland France EMBL-EBI

Michael Baudis, CH

The scientific and economic impact of ELIXIR Data Resources – Towards a sustainable funding model for the UniProtSwissProt use case

Data

Switzerland

Christine Durinx, CH

Solutions for IMI data management

Human Data

EMBL-EBI ELIXIR Hub IMI OncoTrack Spain

Dylan Spalding, EMBL-EBI Susanna Repo, ELIXIR Hub David Henderson, IMI OncoTrack

Integrating distributed resources in Ensembl Genomes

Data

EMBL-EBI Sweden Norway

Paul Kersey, EMBL-EBI

Microbial metabolism resource for Systems Biology

Data

France Switzerland EMBL-EBI

Claudine Medigue, FR

Proteomics infrastructure service

Data

EMBL-EBI Germany

Juan Antonio Vizcaino, EMBL-EBI

Ongoing in 2016

Approved in 2016 (to start early 2017)

ELXIR Annual Report 2016

61

Credits and acknowledgements

Produced on the direction of the ELIXIR Board in May 2017.

With special thanks to all of those who contributed to the development of ELIXIR infrastructure in 2016, most notably Heads of Nodes, Platform and Use Case leads, Technical and Training Coordinators and members of the various Working Groups. Š 2017 ELIXIR This publication was produced by the External Relations team at the ELIXIR Hub For more information about ELIXIR please contact info@elixir-europe.org

Art direction and design: Design Science Illustration: Jai Wilson

ELXIR Annual Report 2016

63

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 Kingdon +44 (0)1223 492 670 +44 (0)1223 494 468 info@elixir-europe.org www.elixir-europe.org