Difference between revisions of "VT ELIXIR"

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[[Category:Virtual_Teams]]
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== General Project Information  ==
 
== General Project Information  ==
  
 
*Leader: Pavel Fibich, CESNET, Czech Republic (NGI_CZ)
 
*Leader: Pavel Fibich, CESNET, Czech Republic (NGI_CZ)
 
*Mailing List: vt-elixir@mailman.egi.eu
 
*Mailing List: vt-elixir@mailman.egi.eu
*[https://indico.egi.eu/indico/categoryDisplay.py?categId=76 Indico page] (meetings, documents)
+
*Meetings: [https://indico.egi.eu/indico/categoryDisplay.py?categId=76 Indico page] (slides and minutes from meetings)
*Status: {{{VTP_Status | approved}}}
+
*[http://doodle.com/ew95nz9e8sizeuep? Schedule of national presentations (Doodle)]
 +
*Status: Finished
 
*Start Date:  1/10/2012  
 
*Start Date:  1/10/2012  
*Duration: 6 months initial phase, report at EGI CF 2013
+
<!--
 
*Meetings (plan): {{{VTP_Meetings | }}}
 
*Meetings (plan): {{{VTP_Meetings | }}}
 
**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.  
 
**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.  
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** [https://indico.egi.eu/indico/materialDisplay.py?contribId=120&sessionId=66&materialId=slides&confId=1019 Experiences with ELIXIR in the Czech Republic]
 
** [https://indico.egi.eu/indico/materialDisplay.py?contribId=120&sessionId=66&materialId=slides&confId=1019 Experiences with ELIXIR in the Czech Republic]
 
**VT ELIXIR proposal from NILs EGITF2012 meeting [[ File:ELIXIR_VT_proposal.pdf ]]
 
**VT ELIXIR proposal from NILs EGITF2012 meeting [[ File:ELIXIR_VT_proposal.pdf ]]
 
+
-->
 
== Motivation  ==
 
== 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.
 
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.
  
 +
The European Grid Infrastructure (EGI) is a collaboration of National Grid Infrastructures (NGIs) that serves scientific research across Europe and beyond. EGI can trace its routes back through over a decade of activities in distributed computing that has been co-funded by the European Commission and national research councils.
 +
 +
This EGI Virtual Team project helps EGI build a complete operational picture of the collaborations that are relevant at a national level between the NGIs and the ELIXIR nodes, and at a European level between EGI.eu (that coordinates EGI on behalf of its stakeholders) and ELIXIR itself. The project will lead us to two important outcomes:
 +
# A social network of ELIXIR-related people within the individual NGIs of ELIXIR participating nations. This network will serve as a basis for international collaboration at both technical and organisational levels between ELIXIR and EGI communities.
 +
# A set of recommendations for how a coordinated approach can be developed whereby EGI can best collaborate with and support ELIXIR. These recommendations will help the EGI community work with ELIXIR partners to define and facilitate the establishment of the ELIXIR infrastructure.
 +
 +
 +
<!--
 
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.
 
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.
 
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  ==
 
== Output  ==
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* 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.  
 
* 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.
+
* Agreement between the EGI and ELIXIR management representatives to strengthen collaborations by intensifying knowledge exchange between the NGIs and the ELIXIR nodes.  
  
 
== Tasks  ==
 
== Tasks  ==
  
* Collect and analyze the current situation of NGI collaboration with ELIXIR representatives.
+
* Collect and analyze the current situation of NGI-ELIXIR collaborations in the member countries.
* 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.
+
* Put together people (create a virtual/social network) from NGIs who are working with or are interested in working with ELIXIR.
* 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.
+
* Collect, exchange and document experiences and recommendations for how NGIs/EGI could support ELIXIR.
  
== Members  ==
+
== Virtual Team Project Members  ==
NGIs:
+
From EGI NGIs:
  
 
* Czech Republic  
 
* Czech Republic  
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! width="80"|ELIXIR MOU (website info)(Note 2)
 
! width="80"|ELIXIR MOU (website info)(Note 2)
 
! width="80"|VT ELIXIR Members
 
! width="80"|VT ELIXIR Members
! width="80"|meeting 31 Oct 12 participation
 
 
|-
 
|-
 
| Armenia
 
| Armenia
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|  
 
|  
 
| Yes
 
| Yes
| No
 
 
|-
 
|-
 
|Belgium
 
|Belgium
 
|Yes
 
|Yes
|
 
 
|
 
|
 
|
 
|
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|Croatia
 
|Croatia
 
|Yes
 
|Yes
|
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
|Czech Republic
 
|Czech Republic
|Yes
 
 
|Yes
 
|Yes
 
|Yes
 
|Yes
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|Yes
 
|Yes
 
|Yes
 
|Yes
|
 
 
|-
 
|-
 
|Estonia
 
|Estonia
 +
|Yes (during VT)
 
|Yes
 
|Yes
|
 
|
 
 
|
 
|
 
|-
 
|-
 
|Finland
 
|Finland
|Yes
 
 
|Yes
 
|Yes
 
|Yes
 
|Yes
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|Yes
 
|Yes
 
|
 
|
|Yes
 
 
|Yes
 
|Yes
 
|-
 
|-
 
|Germany
 
|Germany
 
|Yes
 
|Yes
|
 
 
|
 
|
 
|
 
|
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|Greece
 
|Greece
 
|Yes
 
|Yes
|
+
|Yes (during VT)
|Yes
 
 
|Yes
 
|Yes
 
|-
 
|-
 
|Hungary
 
|Hungary
 
|Yes
 
|Yes
|
 
 
|
 
|
 
|
 
|
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|Ireland
 
|Ireland
 
|Yes
 
|Yes
|
 
 
|
 
|
 
|
 
|
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|Yes
 
|Yes
 
|Yes
 
|Yes
|
 
 
|
 
|
 
|-
 
|-
 
|Italy
 
|Italy
 
|Yes
 
|Yes
|
+
|Yes (during VT)
|
+
|Yes
|
 
 
|-
 
|-
 
|Latvia
 
|Latvia
|Yes
 
 
|Yes
 
|Yes
 
|Yes
 
|Yes
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|-
 
|-
 
|Netherlands
 
|Netherlands
|Yes
 
 
|Yes
 
|Yes
 
|Yes
 
|Yes
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|Yes
 
|Yes
 
|Yes
 
|Yes
|
 
 
|
 
|
 
|-
 
|-
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|Yes
 
|Yes
 
|
 
|
|Yes
 
 
|Yes
 
|Yes
 
|-
 
|-
 
|Portugal
 
|Portugal
 
|Yes
 
|Yes
|
+
| Yes (during VT)
|
 
 
|
 
|
 
|-
 
|-
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|Yes
 
|Yes
 
|Yes
 
|Yes
|
 
 
|
 
|
 
|-
 
|-
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|Yes
 
|Yes
 
|Yes
 
|Yes
|No
 
 
|-
 
|-
 
|Sweden
 
|Sweden
 
|Yes
 
|Yes
 
|Yes
 
|Yes
|
 
 
|
 
|
 
|-
 
|-
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|Yes
 
|Yes
 
|Yes
 
|Yes
|
 
 
|
 
|
 
|-
 
|-
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|No
 
|No
 
|
 
|
|Yes
 
 
|Yes
 
|Yes
 
|-
 
|-
 
|UK
 
|UK
|Yes
 
 
|Yes
 
|Yes
 
|Yes
 
|Yes
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|European Patent Office
 
|European Patent Office
 
|Yes
 
|Yes
|
 
 
|
 
|
 
|
 
|
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|European Clinical Research Infrastructures Network(ECRIN)
 
|European Clinical Research Infrastructures Network(ECRIN)
 
|Yes
 
|Yes
|
 
 
|
 
|
 
|
 
|
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|
 
|
 
|
 
|
|Yes
 
 
|Yes
 
|Yes
 
|-
 
|-
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|Yes
 
|Yes
 
|Yes
 
|Yes
|No
+
|Yes
|No
 
 
|}
 
|}
 
== Topics for local presentations ==
 
== Topics for local presentations ==
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* Anything else (relevant)
 
* Anything else (relevant)
  
 +
== Emerging Information  ==
  
== Resources  ==
+
* All of the ELIXIR Preparatory Phase reports can be found at:
 
+
** http://www.elixir-europe.org/prep/reports
{{{VTP_Resources |
+
*  Letter requesting engagement with Project ELIXIR sent to Prof Soren Brunak (interim ELIXIR Board Chair) on 2 Jan 2013.
 
+
*  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.
== Progress ==
+
   
 
+
* The individual pages for training activities by the members of the ELIXIR node are:
{{{VTP_Progress|
+
** 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
[[Category:Virtual_Teams]]
+
** 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

Latest revision as of 15:07, 19 June 2015

EGI Activity groups Special Interest groups Policy groups Virtual teams Distributed Competence Centres


EGI Virtual teams: Main Active Projects Closed Projects Guidelines

General Project Information

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.

The European Grid Infrastructure (EGI) is a collaboration of National Grid Infrastructures (NGIs) that serves scientific research across Europe and beyond. EGI can trace its routes back through over a decade of activities in distributed computing that has been co-funded by the European Commission and national research councils.

This EGI Virtual Team project helps EGI build a complete operational picture of the collaborations that are relevant at a national level between the NGIs and the ELIXIR nodes, and at a European level between EGI.eu (that coordinates EGI on behalf of its stakeholders) and ELIXIR itself. The project will lead us to two important outcomes:

  1. A social network of ELIXIR-related people within the individual NGIs of ELIXIR participating nations. This network will serve as a basis for international collaboration at both technical and organisational levels between ELIXIR and EGI communities.
  2. A set of recommendations for how a coordinated approach can be developed whereby EGI can best collaborate with and support ELIXIR. These recommendations will help the EGI community work with ELIXIR partners to define and facilitate the establishment of the ELIXIR infrastructure.


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.
  • Agreement between the EGI and ELIXIR management representatives to strengthen collaborations by intensifying knowledge exchange between the NGIs and the ELIXIR nodes.

Tasks

  • Collect and analyze the current situation of NGI-ELIXIR collaborations in the member countries.
  • Put together people (create a virtual/social network) from NGIs who are working with or are interested in working with ELIXIR.
  • Collect, exchange and document experiences and recommendations for how NGIs/EGI could support ELIXIR.

Virtual Team Project Members

From EGI 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 (during VT) Yes
Finland Yes Yes Yes
France Yes Yes
Germany Yes
Greece Yes Yes (during VT) Yes
Hungary Yes
Ireland Yes
Israel Yes Yes
Italy Yes Yes (during VT) Yes
Latvia Yes Yes Yes
Netherlands Yes Yes Yes
Norway Yes Yes
Poland Yes Yes
Portugal Yes Yes (during VT)
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 Yes

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:
  • Letter requesting engagement with Project ELIXIR sent to Prof Soren Brunak (interim ELIXIR Board Chair) on 2 Jan 2013.
  • 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.