Competence centre ELIXIR
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CC Coordinators: Tommi Nyrönen and Kimmo Mattila (CSC)
CC members' email list: cc-elixir AT mailman.egi.eu
ELIXIR is a pan-European RI supported by 17 European governments united in a vision to build a sustainable European infrastructure for biological information, supporting life science research and its translation to medicine, agriculture, bioindustries and society. Members of the ELIXIR Competence Centre (CC) will select key life science use case workflows between partners that are representative of many in the community and will have high impact for scientist end-users and use these as drivers to develop demonstrators that will assess the use of EGI cloud resources for tool and/or data services recognised within the ELIXIR community. The CC will also create best practices materials for life science service providers using the experience gained in those tasks and organise events to facilitate discussions between e-Infrastructure and life science communities. The goal is that by the end of the two-year effort ELIXIR service providers feel motivated to use Big Data tools coming from e-Infrastructures, and that e-Infrastructure providers have established processes to support particular life science data analyses. OSG, as an associate partner will organise collaborative discussions co-located with existing events to discuss life science drivers for virtual organisations and research groups.
- CC project duration: 18 months, from M6 until M24 of EGI-Engage (1. August 2015 - 28. February 2017)
- CC members from the EGI-Engage project:
- ELIXIR Finland hosted at CSC (coordinator) - 9PM
- ELIXIR Czech Republic hosted at CESNET - 9PM
- ELIXIR node hosted at EMBL-EBI and hosting ELIXIR Hub - 5PM
- ELIXIR France hosted at CNRS IFB-core - 6PM
- ELIXIR Netherlands (DTL) CC hosted at SURFsara - 2PM
- ELIXIR Greece part of the node hosted as GRNET - 4PM
- University of Indiana representing Open Science Grid - 1.5PM (Unfunded)
The CC is open for other members to join.
Concept and approach
An incremental and iterative approach will be used to build the Competence Centre excellence by bringing together designated life science experts from ELIXIR, and technical experts from EGI’s Federated Cloud. The combined team will be driven by the short term delivery of small and medium size use case objectives as identified through the intersection of the EGI legacy for life science support and the requirements from life science community represented by ELIXIR. Regular meetings among all involved parties will showcase presentations from the ELIXIR technical work program and complementary initiatives such as GEANT’s Enlighten Your Research, and from e-Infrastructure resource providers that respond to the agreed use case objectives.
Task 1 is to agree on life science use cases with high impact with the EGI and ELIXIR communities that can bring new competitive element for Europe. When this work is complete, the project is ready to extend further towards Tasks 2 and 3. The joint use cases need match the skill-base and resources of the CC to deliver them.
Task 1 - Life Science community integration
- Goal: Community networking, use cases specification and critical services identification
- EGI-Engage M6.3: Life science requirements analysis and driver use case(s) with implementation roadmap are agreed (DOC), in EGI-Engage M12 i.e. February 2016 to EC. (Deliver to review by end of Jan 2016)
- Description: This task will establish the liaison between EGI (user community board and technical experts), and ELIXIR (cloud task force and the broader ELIXIR community) representatives in order to make an analysis of life science community needs and relevant EGI technical offering based on specific use cases. Task leads to a selection of scientific problem use cases of high impact with the ELIXIR community where a tool or a data provider can potentially use the EGI Federated Cloud.
Task 2 - Life Science community support
- Goal: Use cases porting, compatibility analysis and experience acquisition
- EGI-Engage D6.10: Infrastructure tests and best usage practices for life science service providers (DOC), in EGI-Engage M15 i.e. May 2016
- EGI-Engage D6.15: Demonstrator for ELIXIR workflows implemented in the EGI Federated cloud (DEM), in EGI-Engage M24 i.e. Feb 2017
- Description: This task will port the identified use cases to resolve scientific problems selected in Task 1 using the EGI Federated Cloud infrastructure. It will deal with properly controlling the infrastructure, considering the scale needed for implementing the targeted cases by drawing on the resources provided by the partners in the CC and those from the rest of the EGI Federated Cloud. This Task will run in parallel to Task 1, in order to establish a feedback loop for evaluating each proposed use case across several different key aspects (including technical feasibility within the CC lifetime, potential impact, technical expertise etc). The experience gained through the execution of the individual subtasks will be summarized in a best practise document. The final workflows will be released at the end of the CC activity.
Task 3 - Life Science community training
- Goal: Dissemination and community engagement
- Description: This task will run continuously to disseminate the experience gained with use cases implementation and large-scale infrastructure testing. In collaboration with EGI-Engage NA2.1 and SA2.1 it will produce materials for dissemination, communication and training and will perform dissemination and training activities towards the ELIXIR community.
- M6.3 milestone document: Life science requirements analysis and driver use case(s) with implementation roadmap (end of Feb 2016): https://documents.egi.eu/document/2675
- D6.10 deliverable document: Infrastructure tests and best usage practices for life science service providers (June 2016): https://documents.egi.eu/document/2841
- D6.15 deliverable document: Demonstrator for ELIXIR workflows implemented in the EGI Federated cloud: https://documents.egi.eu/public/ShowDocument?docid=3019
The Competence Centre has setup a Virtual Organisation in EGI for ELIXIR. The VO contributes to the effort of building a sustainable European infrastructure for biological information, supporting life science research and its translation to medicine, agriculture, bioindustries and society. The Virtual Organisation is part of the ELIXIR Compute Platform and federates cloud computing sites from ELIXIR and EGI institutes.
- BioMedBridges SYMPOSIUM: Open bridges for life science data, 17-18 November 2015, Wellcome Genome Campus, Hinxton, UK
- ELIXIR All Hands 2016, Barcelona, 2016. March 7-10
- EMBL Conference: CTLS 2016 - Core Technologies for Life Science, Heidelberg, 12-15 June, 2016
- Digital Infrastructures For Research 2016, Krawkow, 28-30 September 2016