1. ELIXIR - Capacity Building
ISMB/ECCB Prague, 2017
J.Vondrášek, B. Persson, B.Leskošek

2. ELIXIR - Nodes of European infrastructure for biological information
Data infrastructure for Europe life-science
research:
21 Members
1 Observer
ELIXIR Hub based
in the UK
Data Interoperability Tools Compute Training
ELIXIR Nodes build local bioinformatics capacity throughout Europe
Over 180 institutes involved in ELIXIR Nodes
@ELIXIREurope

3. Platforms of ELIXIR Infrastructure
Integration and interoperability of data and services
Compute
Data
Standards
Tools
Training
Services & connectors to drive access and exploitation
Access, Exchange & Compute on sensitive data
Sustain core data resources
Professional skills for managing and exploiting data
Capacity Building at Nodes
– mostly covers all platforms 3

4. Build ELIXIR capacity – Node development programme
Sustainability
Legal agreements
Organisation
National Community
Data Nodes Network
Genome Annotation Network
Staff mobility
National Funding and Roadmaps
Accessing Structural Funds
Strengthen Bioinformatics throughout Europe
Node Operations & Management
Data Nodes Network (Task 2)
Genome Annotation Network (Task 3)
Genome Assembly and Annotation Courses (CZ, SI …)
(Task 1)
Nodes handbook as Wiki linked with ELIXIR Handbook of Operations
(Tasks 4 and 5)
14 nodes involved:
BE, CZ, EE, EMBL-EBI, ES, FI, FR, GR, IL, PT, NO, SE, SI, UK
Laboratory level
National level
European level
EGA
EGA-SE
SciLifeLab
EGA-NL
DTL
EGA- … …

5. ELIXIR - Capacity Building Strategy
TeCG/TrCG
Capacity Building
Training
Training courses/wrkshps (Training Platform/TrCG)
Identification of needs, expertises, resources on existing areas at a Node
Technical Solution
(Technical Platform/TeCG)
Sustainability
(identification of funds)
Capability of a Node

6. Capacity Building Main goals
ELIXIR goal:
Increase bioinformatics capacity and competence across Europe
ELIXIR- Excelerate goals:
Node Capacity Building, supporting the formation of an ELIXIR community, shaping ELIXIR as an efficient pan-European infrastructure
Capacity Building in selected areas:
Data Nodes Network
Genome Annotation and Assembly
Sustainability enabled by regular turn-over of focus areas
Organisational Capacity Building enabling utilisation of Smart Specialisation Strategies and accessing EU Structural and Investment Funds (ESIF)
Funded under the Horizon 2020 Framework Programme, grant agreement no

7. ELIXIR Node Capacity Building
ELIXIR Node Handbook linked with the ELIXIR Handbook of Operations

8. Data Nodes Network ELIXIR Europe ELIXIR Nodes
Institutional repository
National data centre
International resources
Usage , Value, Permanence, Curation and Standards
Aim to establish guidelines and good practices to facilitate efficient data collection into core data resources and making them FAIRified.
A first step is to facilitate data management/ stewardship, where common European efforts have resulted in creation of templates for data management plans.
We have initiated the creation of a data nodes network, applied on the use case based on local EGA (cf. WP9). Workshop and Designathon arranged in 2016.
Plan for architectural alignment is validated and simple API inter- operability test has been conducted.
Need for local Genome-phenome data archives is growing every year because of exponential data generation of human data that in many cases cannot leave the country unless access is granted via data access committees.

9. Data Nodes Network European level National level Laboratory level EGA
EGA-SE
SciLifeLab
EGA-NL
DTL
EGA- … …

10. Coordinated infrastructure for data management

11. Capacity Building in Genome Assembly and Annotation
The specialised expertise at multiple ELIXIR Nodes would benefit from capacity building through competence- spreading advanced workshops and staff exchange.
The capacity-building efforts will benefit the Use Cases in WP6 on marine organisms and in WP8 on plant Use Cases.
The genome annotation groups will contribute with domain- specific knowledge about different species, e.g. marine organisms, woody plants and crop plants.
Deployment of web services to enable genome projects in the scientific community to efficiently interact with the data.

12. Capacity Building in Genome Assembly and Annotation
Advanced Genome Assembly and Annotation Courses
First hosted at IOCB in Prague
Teachers from 4 nodes (SE, NO, FR, BE)
24 participants, all from Czech Republic
3 days; 2 days assembly + 1 day annotation
Lectures and practical computer exercises
eLearning platform (EeLP) was used to host presentations, instructions, and survey – provided by ELIXIR-SI
Two more courses in 2017
June in Ljubljana (Slovenia)
Oct in Lisboa (Portugal)
Advanced Workshops
Preparatory in Uppsala Oct 2015
Barcelona April 2016
The Hague Sept 2016
Best Practices Document
A printed publication and an online wiki
Publication to be submitted to Faculty1000 mid-2017.
European “Advanced Help Desk”
Pilot project where the Swedish node is providing high-level expert support to a project from the Czech Republic with genome assembly and annotation.

13. Impact

14. Sustainability of capacity building
The main goal is periodical and long-term discovery of users with specific capacity needs at ELIXIR Nodes and/or research groups within Nodes, especially in specialised areas where the number of experts is small and the competences are to be found across Europe.
Our current efforts on capacity building in data management and in genome annotation and assembly (tasks 10.2 and 10.3) will serve as models for capacity building efforts in other areas.

15. Potential new areas
Control data with EGA in box and Bioschema; local EGA
HPC/Cloud Computing
Supporting uptake of standards across ELIXIR, especially by new node resources.
Data protection issues
GPDR, SOP's for data access, best practise for implementing data security schemas, train people on these issues
Metabolomics
Linked Data(bases)
Structural biology
Distributed Ensembl
Metagenomics
Atlases and their use for data “annotation”, integration, query, and analysis.
Computational Biology
Systems Medicine
FAIR data management, FAIR- compliant tooling and compute; training
Training/e-learning

16. Smart Specialisation Strategies
Structural Funds workshop organised in Brno, 8–9 October 2015
Structural funds break out session organised during ELIXIR All-hands meeting in Barcelona, March 2016
Meeting of the structural funds working group at the ELIXIR All-hands meeting in Rome, 22 March 2017
2 Grants Awarded in CZ, €
1 Proposal Submitted Interreg Cross Border Program Belgium- Netherlands
Calls open in Greece, Estonia and Slovenia