VT ELIXIR

General Project Information

• Leader: Pavel Fibich, CESNET, Czech Republic (NGI_CZ)
• Mailing List: vt-elixir@mailman.egi.eu
• Indico page (slides and minutes from meetings)
• Schedule of national presentations (Doodle)
• Status: approved
• Start Date: 1/10/2012
• Duration: 6 months initial phase, report at EGI CF 2013
• Meetings (plan):
  • 17-21 September 2012: Informal meeting(s) at EGI Technical Forum 2012: Gathering initial ideas on coordinated approach, starting to build ELIXIR-related social network.
  • First official phone conference in the second half of October. Introductory teleconference meeting of by-that-time-known ELIXIR-related people within EGI: Setting out basic objectives, agreement on coordinated approach to ELIXIR, gathering more contacts.
  • October-March: Regular phone conferences (weekly at the beginning): Discussing details, tuning/harmonizing joint approach proposal, resolving particular issues. Further expansion of the social network.
  • November-February: Meetings with presentations on technical/organizational approaches to ELIXIR in detail in individual countries given by respective NGIs (or ELIXIR) delegates. Mutual exchange of experience.
  • End of March: Final meeting: Finalizing joint approach proposal. Report.
  • April 2013: ELIXIR VT presentation at EGI CF 2013, discussion about next phase of the interaction.
• Other information (presentations from EGI TF 2012)
  • Experiences with ELIXIR in the Czech Republic
  • VT ELIXIR proposal from NILs EGITF2012 meeting File:ELIXIR VT proposal.pdf

Motivation

ELIXIR is an emerging pan-European infrastructure for life science research support, in particular aimed for handling biological information. Due to new technologies in life sciences, the rate of production of biological data is intensely increasing. The collection, curation, storage, archiving, integration and deployment of large amounts of biomolecular data is a challenge that cannot be handled by a single organisation or by one country alone, but requires international coordination.

In the Czech Republic, universities and institutions that create or handle life sciences data are gathering together with institutions that provide IT support (especially the Czech node of EGI) to form a Czech node of ELIXIR called ELIXIR_CZ. All of these member institutions have declared their in-kind contributions statements (both in terms of working time commitments and hardware/software/data resources) and their willingness to cooperate on the country-wide level. Naturally, the mission of ELIXIR_CZ is also the implementation of ELIXIR standards throughout various life sciences infrastructures.

To our knowledge, in Netherlands, Finland, and possibly other countries, the national nodes of ELIXIR are collaborating or getting integrated with respective national grid infrastructures, too. This NGI-ELIXIR interaction could benefit coordination at the EGI level, sharing information and experience gained in individual countries and helping EGI to prepare a concise and acceptable approach towards ELIXIR. We believe this bottom up collaboration is an excellent complement to the already started collaboration at the EGI and ELIXIR HQ level.

Output

• An established social network of ELIXIR-related people within individual NGIs (ELIXIR liaisons in NGIs). This network can serve as a basis for international collaboration at both technical and organizational levels between ELIXIR and EGI.
• Proposal on coordinated approach for EGI to collaborate with and support ELIXIR.

Tasks

• Collect and analyze the current situation of NGI collaboration with ELIXIR representatives.
• Put together (create a virtual/social network) of people from NGIs who are working with or are interested in working with ELIXIR, esp. at the national level.
• Collect, exchange and document experiences and ideas about how NGIs/EGI could support ELIXIR. The document would help the EGI community to perform coordinated action with ELIXIR partners to define and facilitate the setup of the ELIXIR infrastructure.

Members

NGIs:

• Czech Republic
  • Pavel Fibich (NGI_CZ)
  • Mirek Ruda (NGI_CZ)
  • Michal Jaros (CERIT-SC)
  • Ivana Krenkova (NGI_CZ)
  • Ludek Matyska (NGI_CZ)
  • Jiri Vondrasek (Institute of Microbiology, ELIXIR_CZ)
  • Jiri Vohradsky and Jan Paces (Institute of Molecular Genetics, ELIXIR_CZ)

• Other countries (Call for participation issued, deadline October 15)
  • Hrachya Astsatryan (Armenian NGI)
  • Burcu Ortakaya (Turkey)
  • David Wallom (OXFORD, UK)
  • Andrew Lyall (UK)
  • Kalle Happonen (CSC FI)
  • Pekka Lehtovuori (CSC FI)
  • Tommi Nyronen (CSC FI)
  • Irene Nooren (UvA / eBioGrid)
  • Tom Visser (SARA NL)
  • Coen Schrijvers (SARA NL)
  • Mariusz Sterzel (CYFRONET PL)
  • Ignacio Blanquer (UPVLC Spain)
  • Tiphaine Martin (FR)
  • Daniele Cesini (ITA)
  • George Lamprinidis (Faculty of Pharmacy Athens-Greece)
  • Anders Waananen (DK)

• EGI.eu:
  • Gergely Sipos
  • Richard McLennan

We are looking initially for people with existing contacts to ELIXIR at national level. Please express interest in working in this VT through e-mail to krenkova@ics.muni.cz

Table of Participation

The following table provides details of nations that are members of the ELIXIR project and of the EGI ELIXIR VT project. The table has been compiled from data that is published via the ELIXIR website.

Note 1: see the ELIXIR Business Case (Web information valid on 1 Nov 2012).

Note 2: see the ELIXIR MoU signatories (Web information valid on 1 Nov 2012).

Nation	ELIXIR Node Exp of Interest (business case info)(Note 1)	ELIXIR MOU (website info)(Note 2)	VT ELIXIR Members
Armenia			Yes
Belgium	Yes
Croatia	Yes
Czech Republic	Yes	Yes	Yes
Denmark	Yes	Yes	Yes
Estonia	Yes
Finland	Yes	Yes	Yes
France	Yes		Yes
Germany	Yes
Greece	Yes		Yes
Hungary	Yes
Ireland	Yes
Israel	Yes	Yes
Italy	Yes
Latvia	Yes	Yes	Yes
Netherlands	Yes	Yes	Yes
Norway	Yes	Yes
Poland	Yes		Yes
Portugal	Yes
Slovenia	Yes	Yes
Spain	Yes	Yes	Yes
Sweden	Yes	Yes
Switzerland	Yes	Yes
Turkey	No		Yes
UK	Yes	Yes	Yes
European Patent Office	Yes
European Clinical Research Infrastructures Network(ECRIN)	Yes
EGI			Yes
ELIXIR Project	Yes	Yes	No

Topics for local presentations

• Local ELIXIR organization model
• Which institutions are involved?
• What activities/projects are ongoing (you are aware of)?
• Interaction between ELIXIR and NGI (or other e-infrastructures like NRENs)
• Are there any formal or informal contacts?
• Is there any actual collaboration ongoing with ELIXIR or part of its community?
• Any issues, comment on the interaction between ELIXIR and NGI?
• Anything else (relevant)

Emerging Information

• All of the ELIXIR Preparatory Phase reports can be found at:
  • http://www.elixir-europe.org/prep/reports
• The INB develops a broad training activity, including road-shows (e.g. Course on Bioinformatics for Integrative Genomics, http://bg.upf.edu/course-big/), conferences (e.g. Exascale Challenges in Computational Biology, http://mmb.pcb.ub.es/exascale2010/) and specialization courses. Furthermore, INB staff participates in the organization of the various masters in Bioinformatics (e.g. Master in Bioinformatics and Computational Biology, (e.g. the CNIO has the http://www.masterbioinformatica.com/ but most of the partners have their own master degree on bioinformatics).

In this area it is particularly relevant to mention the courses that for the last years have been organized in collaboration with the Spanish Medical Collaborative Institutes for the training of medical doctors in genomics and bioinformatics. These three to four day courses are carried out in hospitals and have been attended by more than 300 MDs. The courses on Massive Data Analysis (http://bioinfo.cipf.es/courses/mdac) and others together with the EBI are specially interesting for the scope of EGI. It is envisioned that this type of collaborative training will be increased in ELIXIR.

• The individual pages for training activities by the members of the ELIXIR node are:
  • Centre for Genomic Regulation (CRG): http://pasteur.crg.es/portal/page/portal/Internet/05_TRABCONS/Courses
  • Príncipe Felipe Research Centre (CIPF): Events: http://bioinfo.cipf.es/events, Courses: http://bioinfo.cipf.es/courses
  • Barcelona Supercomputing Centre (BSC): http://www.bsc.es/life-sciences/life-sciences-seminars
  • Spanish National Center of Biotechnology (CNB): http://www.cnb.csic.es/index.php/en/informacion-cientifica/noticias/505-ignacio-cirac-imparte-la-charla-inaugural-del-xvi-ciclo-de-seminarios-del-cnb.html
  • Hospital del Mar Medical Research Institute (IMIM-UPF): http://sbi.imim.es/web/index.php/courses