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JCSG Technical Resources

JCSG Technical Resources. jcsg-jet 32 processor Linux cluster 2 Sun servers( E420 4 CPUs ) jcsg-dwarf small, auxilliary Linux cluster Oracle 8i Data Base ---------------------------------------- Access to Meteor Cluster Access to Blue Horizon. JCSG Data Base.

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JCSG Technical Resources

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  1. JCSG Technical Resources • jcsg-jet32 processor Linux cluster • 2 Sun servers( E420 4 CPUs ) • jcsg-dwarfsmall, auxilliary Linux cluster • Oracle 8i Data Base---------------------------------------- • Access to Meteor Cluster • Access to Blue Horizon

  2. JCSG Data Base • Self-updating annotation tables for target selection and bioinformatics research: • storing genomic and protein sequences and subsequences (>90,000 protein sequences so far) • Storing results: • FFAS • HMMer suite • Blast suite • SAM HMM suite • Secondary structure prediction • other • Tracking Tables: • Crystal Production • Structure Determination • Ready for high throughput

  3. Self-updating Process World and External Data Bases Cluster (Linux) Control (Linux) 1. Check for new releases of sequences and tools Solaris 2. Update sequences in the DB JCSG 3. Prepare incremental run for tools and send to the cluster Oracle DB (Solaris) 4. Compute 5. Update results in the DB

  4. Savings on Incremental Updates s = 95,000 sequences ds = 1,500 Example for hmmer tools have: 95,000 sequences3,000 HMM models rate 760 queries / h or 2.28e+4 pairs(seq,model) / h adding 1,500 sequences 50 HMM models Time needed for incremental update~ 4 h Time needed for full recalculation ~ 129 h ( 5.4 d ) Necessary condition for incremental updates: the Data Base for storing sequences, models and results m = 3,000models dm = 50 New pairs (sequence,model) np = ( s + ds ) * dm + m * ds np = 23,800,00 time needed for update tu = np / rate = 4 h time needed for full recalculation tf = ( s + ds ) * ( m + dm ) / rate = 129 h

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