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IGER Affiliation to the National Grid Service

IGER Affiliation to the National Grid Service. Peter Oliver, Jonathan Churchill e-Science Centre, CCLRC-RAL July 2006. Agenda. “ Bioinformatics Support on the NGS” NGS Bioinformatics resources. IGER / BITS Status ? NGS Affiliation Overview. “ Bioinformatics support on the NGS ”.

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IGER Affiliation to the National Grid Service

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  1. IGER Affiliation to the National Grid Service Peter Oliver, Jonathan Churchill e-Science Centre, CCLRC-RAL July 2006

  2. Agenda • “Bioinformatics Support on the NGS” • NGS Bioinformatics resources. • IGER / BITS Status ? • NGS Affiliation Overview.

  3. “Bioinformatics support on the NGS” • October 2005: • Setup project team. • Start consultation phases with BRIDGES and MyGrid projects. • February 2006: • Software and databases installed on at least one core NGS site for BRIDGES and MyGrid. • June 2006: • IGER passes the requirements to become an NGS affiliate. • September 2006: • Expand software & databases req’d for BRIDGES and MyGrid to the rest of NGS core nodes. • 2006/7: Setup and run NESC Bio-informatics specific training courses; • 2006/7: Expand NGS affiliation to other BBSRC institutes using the IGER model.

  4. NGS Bioinformatics Resources • BBSRC grid support website http://www.ngs.ac.uk/sites/ral/applications/bioinformatics/ ( http://hpcsg.esc.rl.ac.uk/bbsrc-grid-support/bbsrc-grid-supportFrontPage.html ) • BBSRC applications grid-support email bbsrc-support@grid-support.rl.ac.uk • A range of bio-informatics software has been installed on the NGS: version NAMD 2.5 NCBI BLAST 2.2.6 NCBI BLAST 2.2.10 MPIBLAST 1.1.1 MPIBLAST 1.2.1 MPIBLAST 1.3.0 GROMACS 3.2.1 GROMACS 3.3 EMBOSS 2.8.0 EMBOSS 3.0.0 FASTA 3.4 Siesta 1.3 • The EBI Nucleotide Sequence Database Release 86 March, 2006 is on the NGS. • R87 (June 2006) this week. • Outreach: Stand on BBSRC Bioinformatics and e-Science Grant Holder’s Workshop, 18 - 19 October 2005. BBSRC Strand e-Science All Hands Meeting September 2006.

  5. IGER/ BITS Status ? • Computers to be part of the NGS affiliation ? • NGS (and IGER) capabilities, users would like to access when linked to the NGS ? • Status of the GRID cluster demonstration ? • Mark Roberts IGER_A / BITS.

  6. NGS Affiliation Affiliates commit to: • running NGS-compatible middleware • as defined in NGS Minimum Software Stack • this means users of affiliate’s resources can access these using same client tools they use to access NGS • a well-defined level of service and problem referral mechanisms • SLD approved by GOSC Board and published on NGS web-site • providing technical, administrative, and security contacts • providing an account and mapping for daily compliance tests • accepting UK e-Science certificates • maintaining baseline of logs to assist problem resolution

  7. Minimum Software Stack

  8. Minimum Software Stack

  9. References • http://www.ngs.ac.uk/guide/index.html • http://www.ngs.ac.uk/man/documents/NGS_Joining_Quickstart.pdf • http://www.ngs.ac.uk/man/documents/NGS_Minimum_software_stack_1.0.pdf • http://www.ngs.ac.uk/guide/NGS-Partners-AHM05-Young.ppt • http://www.ngs.ac.uk/guide/NGS-Partners-AHM05-Pickles.ppt j.f.churchill@rl.ac.uk p.m.Oliver@rl.ac.uk

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