BioinfoGRID Project. Milanesi Luciano National Research Council. Milan, Italy

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1 BioinfoGRID Project Milanesi Luciano National Research Council Institute t of Biomedical Technologies, Milan, Italy luciano.milanesi@itb.cnr.it Milanesi Luciano EGEE User Forum, Clermont-Ferrand, France February, 2008

2 Networks of resources The potential of new biological and biomedical technological platforms in connection with HPC and GRID technology will be particularly useful to deal with the increasing amount, complexity, and heterogeneity of biological and biomedical data. Bioinformatics applications for ehealth have become an ideal research area where computer scientists can apply and further develop new intelligent computation methods, in both experimental and theoretical cases. Milanesi Luciano BioinfoGRID Symposium, Milan December

Bioinformatics applications for ehealth have become an ideal research area where computer scientists can apply and further develop new

3 BioinfoGRID Project web site: BioinfoGRID Project Milanesi Luciano BioinfoGRID Symposium, Milan December

4 Consortium Milanesi Luciano BioinfoGRID Symposium, Milan December

5 Objective of the BioinfoGRID project BioinfoGRID Objectives Milanesi Luciano BioinfoGRID Symposium, Milan December

6 Interaction with related projects At present the BioinfoGRID project has established co-operations with the following projects initiative: EGEE BELIEF EMBRACE EUCHINAGRID EUMEDGRID EELA DILIGENT ICEAGE LITBIO LIBI HEALTHGRID WISDOM Milanesi Luciano BioinfoGRID Symposium, Milan December

BELIEF EMBRACE EUCHINAGRID EUMEDGRID EELA DILIGENT ICEAGE LITBIO LIBI

7 BioinfoGRID Work Packages Work-package No WP1 WP2 WP3 WP4 WP5 WP6 Work Package title Genomics Applications in GRID Proteomics Applications in GRID Transcriptomics Applications in GRID Database and Functional Genomics Applications Molecular Dynamics Applications Coordination of technical aspects and relation with Grid infrastructure Projects, user training, application support and resources integration. WP7 WP8 Dissemination and Outreach. Project Management Office Milanesi Luciano BioinfoGRID Symposium, Milan December

Applications Coordination of technical aspects and relation with Grid infrastructure Projects, user training, application support and

8 WP1 Genomics Applications GCG (~130 programs) EMBOSS (~150 programs) HUSAR Program Package In-house developments - own programms - automated tasks Third-party programs DATABASES - >300 - Prompt updates (daily, weekly) SRS (Sequence Retrieval System) Milanesi Luciano BioinfoGRID Symposium, Milan December

Third-party programs DATABASES - >300 - Prompt updates (daily, weekly) SRS

9 WP1 Genomics Applications Integrating ti W3H, SoapLab and the GRID ScLinux (OS) Grid Client toolkit Grid CE SoapL ab WebService any more software?? Grid API Interface target setup preliminary setup ssh Solaris (OS) HTML pages W2H W3H analysis Grid CE ScLinux (OS) % submit_formatd b any Grid % more Client submit_blastal software toolkit?? or anywhere else % formatdb % blastall % formatdb % blastall Milanesi Luciano BioinfoGRID Symposium, Milan December

? Grid API Interface target setup preliminary setup ssh Solaris (OS) HTML pages W2H W3H analysis tasks @dkfz-heidelberg.

10 WP2 Proteomics Applications Perform functional protein analysis in GRID by using the functional protein domain annotations on large protein families using GRID and related databases. All 518 human protein kinases and 5129 proteins from non-redundant chainset of Protein DataBank were analyzed with InterProScan applications Milanesi Luciano BioinfoGRID Symposium, Milan December

All 518 human protein kinases and 5129 proteins from non-redundant chainset of Protein DataBank

11 WP2 Proteomics Applications Protein surface calculation in GRID. : the grid was used to compute the volumetric description of the proteins obtaining a precise representation of the corresponding surface. Then protein interactions could be quickly screened by the mean of surface analysis. The ProSite domains were analyzed all-against-all ATP-E against its inhibitor Collagen against integrin Milanesi Luciano BioinfoGRID Symposium, Milan December

corresponding surface. Then protein interactions could be quickly screened by the mean of surface analysis.

12 WP3 Transcriptomics applications Phylogenetics : Reconstructing ti the evolutionary history of a group of taxa is major research thrust in computational biology and a standard part of exploratory sequence analysis. An evolutionary history not only gives relationships among taxa, but also an important tool for inferring structural, physiological, and biochemical properties of sequences from other similar sequences, and reconstruction of tissue evolution. Milanesi Luciano BioinfoGRID Symposium, Milan December

An evolutionary history not only gives relationships among taxa, but also an important tool for inferring structural,

13 WP4 Databases & Genomics Applications Work Package 4: Databases and Functional Genomics Applications Testing the main biological databases in the Grid environment optimization on storage space, bandwidth, download time Testing performances and scalability of database-based applications performances/scalability testing according to various use cases and submission algorithms 1 challenge: Gene Analogous Finder 55+ years of computation on a single CPU, not feasible in a local l environment. Milanesi Luciano BioinfoGRID Symposium, Milan December 2007

applications performances/scalability testing according to various use cases and submission algorithms 1 challenge: Gene Analogous Finder

14 WP4 Databases handling GridDBManager Automatic Updater Timer based monitoring and update of Grid ported databases Adaptive replica manager Constantly adapts the number of replicas in relation to the usage of each database in the last 10 days Version Regression Keeps patches on the Grid for allowing regression of each hdatabase to an earlier version Milanesi Luciano BioinfoGRID Symposium, Milan December 2007

each database in the last 10 days Version Regression Keeps patches on the Grid for allowing regression

15 WP4 Methods - GridDBManager Milanesi Luciano BioinfoGRID Symposium, Milan December

16 WP4 Methods - DBApp Perf. Testing Testing performances and scalability of Database-Oriented Bioinformatics Applications (DBApp) in the EGEE GRID Testing Performance and Scalability Grid: too many variables (queue time, database download time, queue failures, execution failures) Submission mode: too many variables (number of jobs, rate-limiting settings, resubmission algorithm) Application too many variables: (performance of specific application, location of database) Probing of Grid performances Numeric simulation for all algorithms Milanesi Luciano BioinfoGRID Symposium, Milan December

Scalability Grid: too many variables (queue time, database download time, queue failures, execution failures) Submission mode: too many variables

17 WP4 Methods - DBApp Perf. Testing Probing Grid performances (Example) Grid queue times and reliability Sent 150 jobs in 3 groups of 50 at different times Grid queue times (normal load) % of jobs min 4-10min 30min-1h 4h-8h Time-out <1minute 2-4min 10-30min 1h-4h >8h Queue times Milanesi Luciano BioinfoGRID Symposium, Milan December

in 3 groups of 50 at different times Grid queue times (normal load) 30 25 20 % of jobs 15

18 WP5 Molecular docking The neuraminidase viruses is considered a valid target for antiviral drugs Milanesi Luciano BioinfoGRID Symposium, Milan December

19 WP5 Molecular docking Starting compound database DOCKING Starting target structure model Docking: predict how small molecules bind to a receptor of known 3D structure Predicted binding models Post-analysis Compounds for assay There are successful examples rapid, cost effective But there are limitations CPU and storage needed More specific talk by Ana Lucia Da Costa Wednesday 13 th 11:15 Room: Bordeaux Milanesi Luciano BioinfoGRID Symposium, Milan December

are successful examples rapid, cost effective But there are limitations CPU and storage needed More specific talk by

20 WP7 Dissemination The following series of events were specifically associated to or organized by the BioinfoGRID project: BioinfoGRID Symposium 2007: December 10 th -13 th 2007, Milan BioinfoGRID Session at EGEE '07: October 4 th 2007, Budapest Biomed Grid School, Varenna, Italy, May 14 th -19 th 2007 BioinfoGRID Workshop at Healthgrid 2007 Conference - Geneva, Switzerland, 24 th April 2007 NETTAB 2006 Workshop: Distributed Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics - Santa Margherita di Pula, Sardinia, Italy - July th, 2006 BioinfoGRID Initial Training Course, Bari, Italy, March 8 th -10 th 2006 In addition, the BioinfoGRID project has been represented at 58 national and international conferences and workshops. Milanesi Luciano BioinfoGRID Symposium, Milan December

NETTAB 2006 Workshop: Distributed Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics - Santa Margherita di Pula, Sardinia, Italy - July 10-13 th, 2006 BioinfoGRID Initial

21 WP7 Dissemination 24 Journal Articles written within the frame of the BioinfoGRID project: 9 - BMC Bioinformatics 4 - IEEE Transactions on Nanobioscience 3 - Studies in Health Technology and Informatics 1 - Journal of Parallel and Distributed Computing 1 - Journal of Chemical Information and Modeling 1 - Parallel Computing 1 - Int. J. of Bioinformatics Research and Applications 1 - IEEE Transactions on Systems Science and Applications 1 - Nucleic Acids Research 1 - BMC Genetics 1 - Bioinformatics Milanesi Luciano BioinfoGRID Symposium, Milan December

22 WP7 Dissemination 19 Conferences proceedings achieved within BioinfoGRID 6 NETTAB '06 2 EGEE User Forum 06/07 2 BITS '06 2 HPDC '07 1 EGEE 06/07 1 CAPI Bioinformatics of African Pathogens and Disease Vectors. Nairobi MAS-BIOMED '06 Workshop 1 CCGrid '07 Symposium 1 EvoBIO '08 1 CHEP '07 Milanesi Luciano BioinfoGRID Symposium, Milan December

23 People Acknowledgments Cristina Aiftimiei Roberta Alfieri Claudio Arlandini Roberto Barbera Endre Barta Francesco Beltrame Attila Bende Chiara Bishop Chirstophe Blanchet Ignacio Blanquer Vincent Bloch Gianpaolo Bottoni Vincent Breton Andrea Calabria Andrea Caprera Tiziana Castrignanò Federidica Chiappori Dario Corrada Paolo Cozzi Stefano Cozzini Enza D Alba Pasqualina D Ursi Ana Da Costa Paride Dagna Guilia De Sario Davide Di Pasquale Giacinto Donvito Vihang Dudhalkar Peter Ernst David Fergusson Geraldine Fettahi Sandro Fiore Riccardo Gervasoni Karl-Heinz Glatting John Hatton Ally Hume Nicolas Jacq Atul Jain Miklos Kozlovszky Giuseppe La Rocca Yannick Legré Pietro Liò Carles Loomis Mario Marchisio Hajnal Marton Rafael Mayo Garcia Mirco Mazzucato Giovanni Meloni Ivan Merelli Emanuale Merelli Luciano Milanesii Elisa Molinari Ettore Mosca Georgina Moulton Loukas Moutsianas Tibor Nagy Alessandro Negro Laszlo Oroszi Alessandro Orro Giovanni Paolella Silvano Paoli Antonio Pierro Giorgio Pietro Maggi Marco Pirola Raffaele Ponzini Ivan Porro Paolo Ramieri Paolo Romano Ermanna Rovida Erika Salvi Jean Salzemann Diego Sardaci Salvatore Scifo Martin Senger Giuliano Taffoni Livia Torterolo Gabriele Trombetti Angelica Tulipano Vania Ugè Elizabeth van der Wath Richard van der Wath Kasam Vinod Federica Viti Guy Warner Ted Wen Pierfrancesco Zuccato Milanesi Luciano BioinfoGRID Symposium, Milan December

24 Projects Acknowledgements ISSeG EUGRID Diligent A DIgital Library Infrastructure on Grid ENabled Technology Milanesi Luciano BioinfoGRID Symposium, Milan December

Applications des grilles aux sciences du vivant

Institut des Grilles du CNRS Applications des grilles aux sciences du vivant V. Breton Credit: A. Da Costa, P. De Vlieger, J. Salzemann Introduction Grid technology provides services to do science differently,