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Status of Biomed Applications (Task 3.1)

Status of Biomed Applications (Task 3.1). Vicente Hernández Universidad Politécnica de Valencia (Spain) 1 st EELA Conference Santiago de Chile, 4-5 September 2006. Contents. Objectives of the Presentation. Introduction to the Biomed Applications in EELA.

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Status of Biomed Applications (Task 3.1)

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  1. Status of Biomed Applications(Task 3.1) • Vicente Hernández • Universidad Politécnicade Valencia (Spain) • 1st EELA Conference • Santiago de Chile, 4-5 September 2006 Santiago de Chile, 1st EELA Conference, 4-5/9/06

  2. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Contents • Objectives of the Presentation. • Introduction to the Biomed Applications in EELA. • Status of the Biomed Applications • GATE. • WISDOM. • BiG Processing Service. • Phylogenetics • Summary and Conclusions.

  3. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Objectives • To Describe the Applications that Have Been Selected for Being Deployed in EELA in the Biomedical Area . • To Present the Current Status of the Biomed Applications. • To give an overview of the FuturePlans • in the Frame of T3.1.

  4. Santiago de Chile, 1st EELA Conference, 4-5/9/06 T3.1 Biomedical Applications • Participants: UPV (Task Leader), CUBAENERGIA, UFRJ, ULA. • Work in the Task • A3.1 - Identification and selection of applications and tools. [COMPLETED] • A3.2 - Customization of grid applications and tools. [IN PROGRESS] • A3.3 - Evaluation of the impact on dissemination of the select applications and tools. [STARTED] • Deliverables and Milestones (Biomed) • D3.1.1 - Selection report, M2 [DONE] • D3.2.1 - Application and tools customized, M6 [DONE], M18 (Revised). • D3.3.1 - Impact on dissemination report, M9, M23 (Revised). • M3.1 - Successful use of the selected applications and tools, M9

  5. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Identification of Applications in EELA • EELA Biomedical Applications Fall into Three Categories • Bioinformatics Applications • BLAST in Grids. • Phylogeny. • Computational Biochemical Processes • Wide in-Silico Docking on Malaria (WISDOM). • Biomedical Models • GEANT4 Application for Tomographic Emission (GATE)

  6. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Status of Mature Applications: GATE • Geant4 Application to Tomographic Emission (GATE) OpenGate Collaboration (http://www-lphe.epfl.ch/GATE -GATE is an Environment for the Monte-Carlo Simulationof Particle Physics Emission in the Medical Field. • Simulation of gamma-cameras and PET-scanners. • Simulation of dosimetry on radiotherapy treatments in oncology • The Interest of the LA Community isLeaded by CUBAENERGÍA • It is Focused Towards Two Main Oncological Problems: • Thyroid Cancer. • Treatment of Metastasis with P32. • 9 centers in Cuba are Interested (5 Hospitals and 4 Oncological Centers and Institutions)

  7. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Status of Mature Applications: GATE • Resources Available • UPV (ramses.dsic.upv.es; GATE-1.0.2-3) • CIEMAT (ce-eela.ciemat.es; GATE-2.1.0) • INFN CATANIA (grid012.ct.infn.it; GATE-1.0.0-3) • UFF (ce-eela.ic.uff.br; GATE-1.0.0-3) • UFRJ (ce01.eela.if.ufrj.br; GATE-1.0.0-3) • User Communities • Cuban Centres have Problems with Bandwidth • A Local Deployment is Being Developed. • Other Users have Been Contacted • University of Santiago of Chile.

  8. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Status of Mature Applications: WISDOM • WISDOM (Wide In-Silico Docking Of Malaria) is a Deployment of a High-Throughput Virtual Screening Platform in the Perspective of In-Silico Drug Discovery for Neglected Diseases. • The In-Silico Docking is Faster and Much Cheaper than the Experimental Docking, Which is Restricted to the Most Successful Ligands Obtained After the Simulation Process. • The Initial Objective of WISDOM is the Proposition of New Inhibitors for a Familyof Proteins Produced by a Protozoan Parasite (Plasmodium Falciparum ) that Causes Malaria. • However is Being Applied to Other Diseases, such as H5N1 (Avian Flu).

  9. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Status of Mature Applications: WISDOM • WISDOM has been installed in the UPV and can be executed on the whole EELA Grid infrastructure. • UPV already participated as Docking Operator in the previous data challenge on Malaria. • An Experiment is Being Prepared Jointly by UPV and ULA. • Raul Isea will Come to the UPV on Next Week. • Initial Tests have Been Prepared. • Next Steps will be: • Set ULA as Docking Operator and CIEMAT as Donor of Resources in the Docking Data Challenge. • Inclusion of NewTargetsin New Data Challenges.

  10. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Status of New Applications: BiG • BLAST in Grid (BiG) is a Grid-enabled BLAST Interface. • BLAST (Basic Local Alignment Search Tool) is a Bioinformatics Procedure Applied to Identify Compatible Protein and Nucleotide Sequencesin Protein and DNA Databases. • BLAST can be Applied, Among Other Uses, to Annotate the EstimatedFunction of UnknownSequences. • BLAST is ComputationallyIntensive.

  11. Santiago de Chile, 1st EELA Conference, 4-5/9/06 BiG Architecture • Users Access the Service Through a Web Portal. • Access to the EELA Grid is Performed Through the Gate-to-Grid. • Gate-to-Grid is an EELA Grid Node Which Provides a WSRF-Based Web Interface.

  12. Santiago de Chile, 1st EELA Conference, 4-5/9/06 BiG Security • Technologies • Changes on the Security Schema are Being Implemented • Instead ofStoring a Portal Certificate Private Key orTransferringUser Private Keys (Even securely), a myProxyCertificate Server will be Used. • Certificates in the MyProxy Server will be Manually and Temporally Renewed (Planned Weekly) and Short-Time Certificates will be Retrieved by the UI when Required. • This model Enhances the Security and Does not Expose Credentials, Even in Secure Environments.

  13. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Current BiG Tests on EELA • BiG Application has Been Installed on ULA Computers. • Tests Have Been Performed Successfully on a Dataset of Around 3000 Sequences of the Plasmodium Falciparum. • Integration in the BioinformaticsPortal is Completed.

  14. Santiago de Chile, 1st EELA Conference, 4-5/9/06 New Applications: Phylogeny • A Phylogeny is a Reconstruction of the Evolutionary History of a Group of Organisms. • The Inference of Phylogenies with Computational Methods is Widely Used in Medical and Biological Research and has Many Important Applications, Such as Gene Function Prediction, Drug Discovery and Conservation Biology. • Most Approaches Depend Upon a Mathematical Model Describing the Evolution of Characters Observed in the Species Included, and are Usually Used for Molecular Phylogeny Where the Characters are Aligned Nucleotide or Amino Acid Sequences. • Interest of the LA Community • ULA is Leading the Interest in the LA. • A Grid Service Will be Developed to Run a Parallel Version of MrBayes from the Bioinformatics Portal. • Analisys of the Application has Started.

  15. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Summary and Conclusions • Deployment of Mature Applications • GATE • Installed on five EELA sites. • At Least 62 Computing Resources have GATE Available. • New User Communities have been Contacted. • WISDOM • Available at the UPV to be Launched on EELA Infrastructure. • A Testing Experiment is Being Planned . • UPV and ULA will act as Docking Experiment Operators and CIEMAT as Donor of resources in Next Data Challenge. • Development of New Applications • BiG • First Prototype Available and Being Updated. • New Security Model in Progress. • Integration in the Portal is Finished. • Phylogenetics • Analysis of the MrBayes Application has Started. • Migration is Expected to Start After the Deployment of BiG.

  16. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Dissemination in the Frame of WP3 - Several Actions Already Performed. • Reported in 2nd Workshop • Mérida and Itacuruça EELA Workshops: An Outline of the EELA Biomed Applications and the Technical Details of BiG. • HealthGrid 2006 Conference (7-9 June, Valencia, Spain) • Participation in the WISDOM and SHARE Workshop. • Poster with All the EELA Biomed Applications. • Talk about Technical Details of BiG. • Stand of the UPV with a Demo on BiG and a Poster and Shared Flyer. • Discussions on Biomed Collaboration • International Relationships Coordinator of the Latin American Bioinformatics Network. • ICT for BIO-Medical Sciences 2006 Meeting (29-30 June, Brussels, Belgium)–Talk • Concertation Meeting on HealthGrid - Health Information Infrastructure and Applications. • NETTAB-Network Tools and Applications in Biology 2006 Conference (10-13 July, Sardinia, Italy)- Invited Talk. - New Actions Presentation of the Main Goals of EGEE and EELA projects and discussion on EGEE and EELA Biomed Applications: • XXXII Conferencia Latinoamericana de Informática - CLEI 2006 (20-25 August, Santiago, Chile) • “HealthGrids: Challenges and Opportunities” – Invited Plenary Talk. • Coordination Meeting of CYTEDGRID Project: Grid Technologies as an Engine for the Regional Development (22-26 August, Santiago, Chile) • 16 partners (11 LA, 5 Spain and Portugal). • Discussions on Biomed Collaboration • Director of the Centre for Bioinformatics and Genome Biology within the Life Science Foundation of Chile.

  17. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Issues in Progress • Actions Performed Since Last Meeting • Contacts have been Made to Increase the Size of the EELA Biomed User Communities. • Security Model of BiG is being Updated According to the Suggestions Raised in the Previous Meeting. • WISDOM Experiments are Being Planned. • Biomed Part of Deliverable D3.2.1 - Application and tools customized – was Prepared. • New Dissemination Actions in Latin America.

  18. Santiago de Chile, 1st EELA Conference, 4-5/9/06 Contact Vicente Hernández Universidad Politécnica de Valencia Camino de Vera s/n 46022 Valencia, Spain Tel: +34-963879743 Fax. +34-963877274 E-mail: vhernand@dsic.upv.es iblanque@dsic.upv.es

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