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									National e-infrastructure and ELIXIR activities in Latvia


R. Balodis, I.Opmane, L.Trukšāns, J.Vīksna




 3.11.2011

 Latvia University
 RIGA, LATVIA
Established ERIC and
National CLARIN node
                       Institute of Math&Comp.Sci
signet MoU             support national node
ELIXIR is an e-Infrastructure




                e-Infrastructure




    GÉANT, DANTE, EGI.eu, PRACE, etc
             ELIXIR – the purpose
The purpose of ELIXIR is to construct and operate a sustainable infrastructure for
biological information in Europe to support life science research and its translation
to medicine and the environment, the bio-industries and society.

Because of new technologies such as next-generation DNA sequencing, data
produced in biological experiments is doubling every few months, and this rate is
increasing. In addition, new types of data are constantly emerging that need to be
integrated meaningfully.

The collection, curation, storage, archiving, integration and deployment of
biomolecular data is an immense challenge that cannot be handled by a single
organisation or by one country alone, but requires international coordination.
     ELIXIR – the organizational structure




ELIXIR will be built on existing data
resources and services; it won’t replace
them. It follows a hub and nodes model,
with EMBL-EBI as the hub and the
nodes distributed throughout Europe.



The expectation is that it will be persistently funded
by European Member States as well as regional and
international agencies. The model is scalable, so
that new nodes, services, resources and tools can
be added and integrated as the infrastructure
grows.
        ELIXIR preparatory phase
Call for suggestions and applications for potential elixir nodes –
July 2010.

57 applications for potential ELIXIR nodes.

From Latvia – an application for a national ELIXIR node that will be based at
Institute of Mathematics and Computer Science (IMCS) and will strongly
collaborate with Latvian Biomedical Research and Study Centre (BMC).

Currently five countries plus the European Molecular Biology Laboratory (EMBL)
have signed a Memorandum of Understanding to catalyse the implementation
and construction of ELIXIR. The memorandum has been signed by:

Denmark, Finland, the Netherlands, Sweden and the United Kingdom.

More countries are planning to join in the near future. All European countries
are invited to engage with ELIXIR.
ELIXIR potential nodes
                    Red:
                    medical applications of
                    bioinformatics

                    Green:
                    agriculture and food

                    Blue:
                    environmental applications
                    of bioinformatics

                    Yellow:
                    pharmaceutical
                    applications of
                    bioinformatics.

                    Purple:
                    bioinformatics in general
     Institutions in Latvia, that support ELIXIR node




 Institute of Mathematics and Computer Science      University of Latvia
 (software development, data base maintenance, computing
 resources (cloud), GN3, ELIXIR node organizational support);


The Latvia State Institute of Fruit-Growing
(fruit crop genetic resources collection);


The Latvia State Institute of Forest “SILAVA”
 (wood plant data base);




  Latvian Biomedical Research and Study Centre
  (Latvian Genome Data Base and other biobanks);
             IMCS and EML-EBI collaboration
             (researchers from IMCS, that works in EBI)




Alvis Brazma, Senior team leader



Natalja Kurbatova, bioinformatician



Uģis Sarkans, Technical Team leader



Dace Rukliša
        Base layers for ELIXIR- more about this




Different layers of e-infrastructure are available today
to support scientific research: GÉANT network,
GRID technologies and scientific field-specific e-infrastructures (ESFRI).
Today IMCS provides for researchers in Latvia:

- networking and international connectivity to GÉANT
                  (IMCS is partner of GN3- http://www.geant.net ),

- computing environment (GRID computing environment and National Grid
Infrastructure http://www.egi.eu and EGI-InSPIRE
http://www.egi.eu/projects/egi-inspire/,

- national Cloud prototype with servers (IBM series 3500) and IBM Storage Area
Network of ½ Peta Byte capacity ); This year IMCS has started project on
upgrading Cloud Computing facilities with 1.5 Peta Byte data storage and
High Performance Computing (HPC) (~ 40 Tera Flops).


-eScience functional application of e-infrastructure:
       CLARIN-http://www.clarin.eu,
       ELIXIR- http://www.elixir-europe.org ,
       radio astronomy data streaming facility from Irbene radiotelescope,
   The resources we can provide
IMCS

Development of biomedical information software. During the course of several
EU projects (MolPAGE, ENGAGE, CAGEKID) a SIMBioMS software suite has been
developed providing facilities for phenotype and experiment (genotyping,
microarray, high throughput sequencing) data storage, exchange, analysis and
transfer to permanent repositories.

Hosting of bioinformatics and/or biomedical databases and web services (the
resources developed within specific EU projects, an experimental semantic-web
technologies based integrated Latvian Disease Registry etc).

Providing computational resources (GRID network, “cloud computing”) for data
analysis.
10 Gbps (operational today 2.5 Gbps)




                GÉANT IP
                     Computing resources
                     (after upgrade)



GRID 3 clusters            CLOUD           HPC:
EGEE sertificed            1.5 PTB         LINUX, PMI
                                           40 Tera Flops
                                           INVIDIA TESLA GPU




                  Up to 10 Gbps
                              SAN today
Highly scalable disk storage solution with cluster file system
                                                                                  aproximetly 500 NFS/CIFS clients



                                                                              ...... Virtual server with storage
                                                      LAN



                                  Cluster file management system (parallel)
                                                                                       8 servers x 8 cores = 64 cores
                      FIBRE CHANNEL
 Included in tender




                                 SAN switch                      SAN switch


                      FIBRE CHANNEL




                            Min 400 TB - total physical, SATA disks
                            Min 4 TB - total physical, FC disks
                            ===========================
                            Min 404 TB - TOTAL

								
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