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HP-SEE project and the HPC Bioinformatics Life Science g ateway

HP-SEE project and the HPC Bioinformatics Life Science g ateway. M. KOZLOVSZKY Obuda University. Overview. The HP-SEE project HP-SEE Life Sciences Virtual Community HP-SEE Bioinformatics Life Science gateway Sequence alignment a pplications  workflow based online bioinformatics services

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HP-SEE project and the HPC Bioinformatics Life Science g ateway

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  1. HP-SEE project and the HPC Bioinformatics Life Science gateway M. KOZLOVSZKY Obuda University The HP-SEE initiative is co-funded by the European Commission under the FP7 Research Infrastructures contract no. 261499

  2. Overview The HP-SEE project HP-SEE Life Sciences Virtual Community HP-SEE Bioinformatics Life Science gateway Sequence alignment applicationsworkflow based online bioinformatics services Working with workflows/gUSE Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.20122

  3. Pan-European e-Infrastructures vision e-Science Collaborations • The Research Network infrastructure provides fast interconnection and advanced services among Research and Education institutes of different countries • The Research Distributed Computing Infrastructure (Grid, HPC) provides a distributed environment for sharing computing power, storage, instruments and databases through the appropriate software (middleware) in order to solve complex application problems • This integrated environment is called electronic infrastructure (eInfrastructure) allowing new methods of global collaborative research - often referred to as electronic science (eScience) • The creation of the eInfrastructure is one of the key objectives to facilitate building of the European Research Area DCI Infrastructure Network Infrastructure Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.20123

  4. Context: the Model -Converged Communication & Service Infrastructure for South-East Europe Seismology, Meteorology, Environment Comp physics, Comp chem, Life sciences User / Knowledge layer HP-SEE SEE-GRID & EGI SEE-LIGHT & GEANT Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.20124

  5. Context: Timeline and funding Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.20125

  6. HP-SEE: Project • Contract : RI-261499 • Project type: CP & CSA • Call: INFRA-2010-1.2.3: VRCs • Start date: 01/09/2010 • Duration: 24 + 9 months • Total budget: 3 885 196 € • Funding from the EC: 2 100 000 € • Total funded effort, PMs: 539.5 • Web site: www.hp-see.eu Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.20126

  7. HP-SEE: Partnership Contractors (14) Third Party / JRU mechanism used associate universities / research centres Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.20127

  8. HP-SEE: Project Objectives • Objective 1 – Empowering multi-disciplinary virtual research communities • Objective 2 – Deploying integrated infrastructure for virtual research communities • Including a GEANT link to Southern Caucasus • Objective 3 – Policy development and stimulating regional inclusion in pan-European HPC trends • Objective 4 – Strengthening the regional and national human network Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.20128

  9. The HP-SEE Life Science VRC and its objectives Main goal: Utilize the combined HPC resources with regional needs coming from the life/bioscience communities, fostering the research process in the field within the region with the help of the large-scale high availability infrastructure, and facilitate the cooperation between the sparsely distributed life science research centres. Data and limitations The Life Sciences domain has been revolutionized by advances in both computer hardware andsoftware algorithms. Assembling the Human Genome Gene-expression chips to understand cellular processes Exponential growth in the amount ofpublicly available genomic data. GeneBank Traditional database approachesare no longer sufficient for rapidly performing life science queries involving the fusion of datatypes. Existing computational tools were created by experimentalists dealing with data sets that were miniscule in comparison to those available today. As a result, software that was once perfectly adequate now performs slowly or is incapable of successful analysis on traditional computational platforms. Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.20129

  10. Accessible infrastructure • HP-SEE Supercomputing infrastructure • SEE-GRID-SCI Grid infrastructure Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.201210

  11. HP-SEE’s LS Applications 7 applications from 5 countries Greece: Searching for novel miRNA genes and their targets(miRs) Network models of short and long term memory (CMSLTM) Montenegro: DNA Multi-core Analysis (DNAMA) Hungary: Deep sequencing for short fragment alignment (DeepAligner) - gUSE & workflow based In-silico Disease Gene Mapper (DiseaseGene) - gUSE & workflow based Georgia: Modeling of some biochemical processes with the purpose of realization of their thin and purposeful synthesis (MSBP) Armenia: Molecular Dynamics Study of Complex systems(MDSCS) Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.201211

  12. Why gUSE/WS-PGRADE • Infrastructure • HP-SEE infrastructure • Based on gLite and Arc as middleware • Authentication procedures are painfull (as usual) • Interoperabilty with grids is a plus • Application • Workflow like process with embedded (legacy) applications • Restricted input parameter sets for the algorithms • Service like operation • Portal features for a community • Knowledge,licensing & support • Open source software environment needed • Knowledge transfer required for the application specific modules Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.201212

  13. HP-SEE Bioinformatics eScience Gateway • HP-SEE Bioinformatics eScience Gateway hosted at Obuda University, operated by MTA SZTAKI. • gUSE+WS-PGRADE (v3.3.2) - Liferay based • SEE region’s supercomputing & grid infrastructure used • Accessible at: http://ls-hpsee.nik.uni-obuda.hu:8080/liferay-portal-6.0.5 Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.201213

  14. Architecture and application porting steps Unified porting steps of the applications: Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.201214

  15. DeepAligner-Deep sequencing for short fragment alignment • Description& Objectives Mapping short fragment reads to open-access eukaryotic genomes is solvable by a group of algorithms (BLAST, BWA, PatternHunter, and other sequence alignment tools – BLAST /mpiblast or scalablast/ is one of the most frequently used tool in bioinformatics and the others are relative new fast light-weighted tools that aligns short sequences. Local installations of these algorithms are typically not able to handle such problem size therefore the procedure runs slowly, while web based implementations cannot accept high number of queries. The HP-SEE infrastructure allows accessing massively parallel architectures and the sequence alignment code isdistributed free for academia. • Result Online workflow based short sequence alignment service • Impact Freely available service/code for large scale short sequence alignment • Collaborations • Hungarian Bioinformatics Association, Semmelweis University • HP-SEE infrastructure used: Hungarian HPC, NIIF’s supercomputing sites Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.201215

  16. DeepAligner-Deep sequencing for short fragment alignment (contd.) Small scale launch (Home cluster): PBS/Linux Cluster, at the Obuda University – John von Neumann Faculty of Informatics. Activity and technical assistance in pre-production stage: Technical assistance was provided by MTA SZTAKI and NIIF. Porting: Application was ported using(Perl/C). Workflow and GUI was created for the application by Obuda University. Benchmarking Scaled from 32 cores to 96 cores (MPI). DeepAligner Status The online service is using two from NIIF’s supercomputing infrastructure (Budapest site and Szeged site). Foreseen activities: Parameter assignments optimization of the GUI, more scientific publications about short sequence alignment. Further scaling is planned with performance analysis. More information: http://hpseewiki.ipb.ac.rs/index.php/DeepAligner Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.201216

  17. Development & working on gUSE/WS-PGRADE • Pros • Close collaboration and useful support (pros) • ARC middleware connector was developed from scratch by MTA SZTAKI on request • ASM and ARC submitter related bugs have been found and reported • Helpful and skilled support & development team • Cons • ARC middleware problems (internal) hard to find Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.201217

  18. Future plans • Additional plug-in like online bioinformatics services • More sequence alignment workflows • More sequence multiple alignment workflows • Sequence database quality measurement workflows • Open up the gateway for users outside SEE region Thank you for you attention! Questions? Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.201218

  19. gUSE/WS-PGRADE architecture DeepAligner DiseaseGene ASM Application specific Module WS-PGRADE Summer School on Workflows and Gateways for Grids and Clouds 2012– Budapest ,Hungary 2-6.07.201219

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