ELIXIR - Capacity Building

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Presentation transcript:

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

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 www.elixir-europe.org @ELIXIREurope

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

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- … …

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

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. 676559

ELIXIR Node Capacity Building ELIXIR Node Handbook linked with the ELIXIR Handbook of Operations https://bioinfo.uochb.cas.cz/mediawiki/index.php

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.

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

Coordinated infrastructure for data management

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.

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.

Impact

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.

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

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, €3.900.000 1 Proposal Submitted Interreg Cross Border Program Belgium- Netherlands Calls open in Greece, Estonia and Slovenia