1. N. Jacq – Bio informatics Tests WP6-10 - 0701 - n° 1 WP6-WP7-WP10 Biology applications on testbed 0 jacq@clermont.in2p3.fr Laboratoire de Biologie des Protistes

2. N. Jacq – Bio informatics Tests WP6-10 - 0701 - n° 2 Goals u Test Globus functionalities u Start using remote sites on testbed0 u Bio-informatics algorithms well fitted for tests n Both simple & complex algorithms n Scalable size of input and output files n Immediately available

3. N. Jacq – Bio informatics Tests WP6-10 - 0701 - n° 3 12345 Binary initially on LDLDL Input files & Execution LDDDD Output fileLDDLL Result+++++ There were unsuccessful tests. For instance when entry files and algorithms are on two different machines L : Local machine D : Distant machine Successful tests

4. N. Jacq – Bio informatics Tests WP6-10 - 0701 - n° 4 Comparison of two genomes Genome 1 Homologies Séquence Genome 2 Alignment Search Tool Parser.out.ace.out

5. N. Jacq – Bio informatics Tests WP6-10 - 0701 - n° 5 A first attempt to « gridify » an algorithm u BLAST : Similitude search between a list of sequences and a database of sequences n Goal : compare the proteins of a given organism to classify them according to their patterns n Example : 155’ on one CPU to compare yeast proteins (5MB) against themselves. Output file : 40MB u Trivial parallelisation : n Input file made of a list of sequences. Divide the input file by the number of CPU’s available. Run in parallel and concatenate. n Test in June 01 with 2 CPU’s in Clermont, 1 in Marseille : 60’ instead of 155’

6. N. Jacq – Bio informatics Tests WP6-10 - 0701 - n° 6 WP6-WP7-WP10 common tests : SwissProt vs SwissProt with GridBLAST Swissprot : public bank of Proteins 40MOx40MO input, 10GO output (F. Bonnassieux – WP7)