Web Portal Access to Bioinformatics Resources on the NGS. Jonathan Churchill STFC eScience – RAL / NGS High Performance Computing Services Group

Demo Outline NGS Computing Resources. (Free !!) NGS Bioinformatics S/W and Databases. NGS Web portal –Portal to both NGS and local resources. –‘Templates’ available for all NGS installed sw –Build and share ‘templates’ for local site sw –Ease of use. How do I get started ?

NGS Compute Resources Phase I Core Sites : –336 3GHz, 32 bit, Intel Xeon CPUs –44 Tbytes Storage (Local SAN and via SRB) Phase II Core Sites : –> GHz, 64 bit, AMD Opteron CPUs –~200 Tbytes Storage (Local SAN and via SRB) Partner Sites: –Cardiff, Bristol, Westminster, Lancaster,… –Includes: WinXP, SGI Irix, etc resources All Free !!

NGS Bioinformatics Available databases: –EBI EMBL Database Quarterly release and daily updates (fasta, blast, mpiblast formats). –EBI PEPTIDE DB (Swissprot, Trembl, Uniprot ) Daily updates (fasta, blast and mpiblast formats) –EBI PRINTS DB –PROSITE motif DB mirror from expasy.org (updated every two weeks) –REBASE restriction enzyme DB mirror from neb.com (updated monthly) Software: –NCBI-BLAST, MPI-BLAST, BLAST-TOOLBOX, EMBOSS, FASTA, EXONERATE, Gromacs, NAMD, Siesta, Weka –Requested s/w.

DEMO

Getting Started Users: –Browse the portal No NGS a/c or certificate required. –Apply for NGS access Apply for UK eScience Certificate “Apply for Access” Sites: –NGS Affiliation / Partner Status Ensures NGS compatible s/w stack NGS ‘Buddy’ And/or BITS help (for BBSRC funded Institutes only).

Thanks Mark Roberts, Andrew Cowley, Colin Edwards, Doug Maxwell –BBSRC Bioscience IT Services (BITS) Harpenden (BITS Development Cluster) Mina Maniopoulou –STFC/RAL (NGS Bioinformatics DB & SW support) Dave Meredith –STFC/NGS (NGS Portal) Kevin Haines, Duncan Tooke –STFC RAL (RAL-NGS2 cluster, STFC SCARF Cluster)