EMBRACE An example of Grid Integration (I): The EMBRACE project Jean SALZEMANN CNRS/IN2P3

Introduction EMBRACE is a EU-sponsored Network of Excellence aimed at enabling bioinformatics research through better operability of databases, servers, and services.

Example You want to predict phosphorylation sites just outside transmembrane helices in 1329 membrane proteins. Yesterday: 1) Obtain software to predict transmembrane helices; 2) Obtain software to predict phosphorylation sites; 3) Install both programs; 4) Write software that calls both programs; 5) Write software that combines outputs and presents results. Tomorrow: 1) Import APIs for the two services; 2) Write software that combines outputs and presents results.

The Goal Of EMBRACE Embrace aims at building a « knowledge grid » allowing integrated exploitation of data: –collection, curation and provision of biomolecular information –Availability of most of the popular databases and software products –tools and programming interfaces to exploit that information –taking away the need for maintaining local copies of databases and software

Data EMBRACE includes nearly all European bioinformaticians with longstanding track-records in terms of providing databases, servers, and services. Data types that they will make available: DNA sequences, protein sequences, macromolecular structures, SNPs, expression information, alignments, untranslated regions, structure domains, protein families, literature, electron micrographs, orthologs, ORFs, genome annotation, proteomics patterns, GPCRs, protein interactions, nucleotid

Software EMBRACE includes nearly all large European bioinformatics centers that all will make their servers, services, and computational tools available using the EMBRACE-GRID. Computational facilities that all European bioinformaticians will get at their finger tips include: DNA sequence analysis, genome annotation, homology searches at sequence and structure level, structure analysis, visualization, protein sequence analysis, phylogeny, protein domain mapping, pattern matching, HMM, neural nets, micro-arrays, workflow management, text-mining, systems biology, database techno

Education The EMBRACE portal ( lists the courses that EMBRACE has presented and will present: July 2005 France Grid technology October 2005 EnglandData modeling and integration February 2006 England Portal tools October 2006 FinlandTools for grid usage February 2007 DenmarkBioinformatics of immunology April 2007 SwedenRegulatory sequence motifs (10 more courses not listed) July 2009 SpainDatabases and gene annotation

The EMBRACE Challenge Applied bioinformatics need various computer resources The amount and size of databases and tools are growing rapidly Systems Biology is predicted to become more important A lot of existing tools and data sources to integrate

Technology Recommendation Use Web Services, especially WS-I profile Use of XML-schema to describe DataTypes Give standard definition to DataTypes Use Standardized Databases Interfaces (make workflows with the EMBRACE services)

Web Services advantages Replace local resources with remote resources Web Services provide a standardized access method Web Services are widely adopted in the BioInformatics community They are evolving constantly with new specifications

The EMBRACE VO on EGEE Infrastructure to deploy cpu-intensive and data-intensive applications Testbed to validate the technology recommendation 400 CPUs and 3 TB of Data Storage

Statistics on EGEE

SiteCity, countryNumber of nodesRelated Embrace partner CSCEspoo, Finland124 National Supercomputer CenterLinköping, Sweden97- Umea UniversityUmea, Sweden94- Center for Parallel Computers (PDC)Stockholm, Sweden82- Centro Extremeño de Tecnologías Avanzadas, CIEMAT Trujillo, Spain40- Life sciences Institut Universitaire de Technologie Aurillac, France387 (CNRS) Institute of Biomedical TechnologyBari, Italy222 (CNR-ITB Bari) Center for Molecular and BIomolecular Informatics Nijmegen, NL17CMBI Centro National de BiotecnologiaMadrid,Spain169 (CNB) Sites of EMBRACE VO

An Example of Application: PDB Database Refinement Recomputation of protein structures in 3 steps, using the WISDOM Environment. Deployment on EGEE (Spring 2007): –673 CPUs used –70000 jobs submitted –17 CPU years –500 GB of data produced

Application example: WISDOM Type of computations: docking with proteins and ligands databases. Web service interface to submit jobs. Users can use the interface to send docking jobs without specific knowledge of the grid, and embed dockings into their workflows

Application example: Automatic update of databases Service that automatically replicate and update biological databases (file databases) Web service interface to deploy new databases or retrieve status of a deployment. Service can be used also in workflow to make an update before experiment Hide the datamanagement for non grid expert users

Contacts EMBRACE is coordinated by Graham Cameron and Kerstin Nyberg at the EBI. Peter Rice coordinates the content integration Alan Bleasby coordinates the tools integration Vincent Breton coordinates technology recommendation Erik Bongcam Rudloff coordinates the test cases Gert Vriend coordinates outreach and education

Acknowledgements The EMBRACE project is funded by the European Commission within its FP6 Programme, under the thematic area "Life sciences, genomics and biotechnology for health,"contract number LHSG- CT