FP6−2004−Infrastructures−6-SSA E-infrastructure shared between Europe and Latin America EELA Demo: Blast in Grids Ignacio Blanquer Espert Damià Segrelles Quilis Universidad Politécnica de Valencia
E-infrastructure shared between Europe and Latin America FP6−2004−Infrastructures−6-SSA Madrid, First Annual EELA Review, BiG Demo Test Input data –Sequence PfEMP1. Protein of the membrane of Plasmodium Falciparum. MAAQSSGGGGGCGEEDKDAKYMFDRIGKEVHDE…FNEPYYYD MYDDDIYYDVNDDNDTSTVDSNNMDVPSKVQIEMDVNTKLVKEK YPISDVWDI. Sequence of 2241 Amino acids. Expected results –10 Sequences from the swissprot database have similarities with this protein (potential targets). EBA1_PLAFC ▪ PVDB_PLAKN PVDR_PLAVS ▪ PVDA_PLAKN PVDG_PLAKN ▪ DDR48_YEAST MSP1_PLAFC ▪ MSP1_PLAFP WDR7_MOUSE ▪ POLS_BFV
E-infrastructure shared between Europe and Latin America FP6−2004−Infrastructures−6-SSA Madrid, First Annual EELA Review, BiG: BLAST in Grid is a Grid-enabled BLAST Interface (Input Sequence) MAAQSSGGGGGCGEE DKDAKYMFDRIGKEVH DE…DDNDTSTVDSNN MDVPSKVQIEMDVNTKL VKEKYPISDVWDI (Input Sequence) MAAQSSGGGGGCGEE DKDAKYMFDRIGKEVH DE…DDNDTSTVDSNN MDVPSKVQIEMDVNTKL VKEKYPISDVWDI Execution Parameters Execution Parameters Protein Database (swiss- prot e.g.)
E-infrastructure shared between Europe and Latin America FP6−2004−Infrastructures−6-SSA Madrid, First Annual EELA Review, BiG: BLAST in Grid is a Grid-enabled BLAST Interface A sequence will be submitted through the portal. (Input Sequence) MAAQSSGGGGGCGEE DKDAKYMFDRIGKEVH DE…DDNDTSTVDSNN MDVPSKVQIEMDVNTKL VKEKYPISDVWDI (Input Sequence) MAAQSSGGGGGCGEE DKDAKYMFDRIGKEVH DE…DDNDTSTVDSNN MDVPSKVQIEMDVNTKL VKEKYPISDVWDI Execution Parameters Execution Parameters Protein Database (swiss- prot e.g.)
E-infrastructure shared between Europe and Latin America FP6−2004−Infrastructures−6-SSA Madrid, First Annual EELA Review, BiG: BLAST in Grid is a Grid-enabled BLAST Interface A sequence will be submitted through the portal. The portal will create and submit the job to the EELA Grid. (Input Sequence MAAQSSGGGGGCGEE DKDAKYMFDRIGKEVH DE…DDNDTSTVDSNN MDVPSKVQIEMDVNTKL VKEKYPISDVWDI (Input Sequence MAAQSSGGGGGCGEE DKDAKYMFDRIGKEVH DE…DDNDTSTVDSNN MDVPSKVQIEMDVNTKL VKEKYPISDVWDI Execution Parameters Execution Parameters Protein Database (swiss- prot e.g.)
E-infrastructure shared between Europe and Latin America FP6−2004−Infrastructures−6-SSA Madrid, First Annual EELA Review, BiG: BLAST in Grid is a Grid-enabled BLAST Interface A sequence will be submitted through the portal. The portal will create and submit the job to the EELA grid. After the processing, results are return to the portal. (Input Sequence) MAAQSSGGGGGCGEE DKDAKYMFDRIGKEVH DE…DDNDTSTVDSNN MDVPSKVQIEMDVNTKL VKEKYPISDVWDI (Input Sequence) MAAQSSGGGGGCGEE DKDAKYMFDRIGKEVH DE…DDNDTSTVDSNN MDVPSKVQIEMDVNTKL VKEKYPISDVWDI Execution Parameters Execution Parameters Protein Database (swiss- prot e.g.) Output Matches Xxxxx x x x x x xxx xx xxx x Output Matches Xxxxx x x x x x xxx xx xxx x
E-infrastructure shared between Europe and Latin America FP6−2004−Infrastructures−6-SSA Madrid, First Annual EELA Review, Portal Authentication Users access the system through bio.ula.ve. bio.ula.ve The BiG users do not need an EELA grid certificate. A “portal” Grid certificate is obtained from a MyProxy server under the name of the operator of the portal. User operation is however registered for further auditing.
E-infrastructure shared between Europe and Latin America FP6−2004−Infrastructures−6-SSA Madrid, First Annual EELA Review, Submitting Jobs Each BLAST is one session (one or more MPI Jobs of 20-CPUs).
E-infrastructure shared between Europe and Latin America FP6−2004−Infrastructures−6-SSA Madrid, First Annual EELA Review, Introducing Input Data The portal calls the Grid Service in the UPV, which constructs the JDLs and the necessary data and submits the parallel Grid job through the RB to the appropriate resource. target databases have been previously registered in the Grid data space by the portal operator.
E-infrastructure shared between Europe and Latin America FP6−2004−Infrastructures−6-SSA Madrid, First Annual EELA Review, Monitoring Jobs The status of the job can be easily seen from the portal, which contacts the Grid service. Once the job reaches the “Done” stage, data from the RB is downloaded and stored in the Grid Service, which makes it available to the portal.
E-infrastructure shared between Europe and Latin America FP6−2004−Infrastructures−6-SSA Madrid, First Annual EELA Review, Getting the Output The result is an XML file with the codes of the sequences that fulfil the alignment criteria. These 10 sequences are shown along with the result of the matching.
E-infrastructure shared between Europe and Latin America FP6−2004−Infrastructures−6-SSA Madrid, First Annual EELA Review, Why the Grid? In the demo we have shown a short time-bounded example of the possibilities of BLAST. BiG is intended for processing big sets of sequences, although it works efficiently even with short sequences. A complete genome screening implies tens of thousands of sequences and could take more than 30 hours in a conventional computer. This is done periodically to check the new versions of the target databases.