status of biomed applications (task 3.1)

Santiago de Chile, 1st EELA Conference, 4-5/9/06 1FP6−2004−Infrastructures−6-SSA-026409

E-infrastructure shared between Europe and Latin America

Status of Biomed Applications(Task 3.1)

Vicente Hernández

Universidad Politécnica de Valencia (Spain)

1st EELA ConferenceSantiago de Chile, 4-5 September 2006



• 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.

Contents



• 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 Future Plans

in the Frame of T3.1.

Objectives



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



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)



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 Simulation of Particle Physics Emission in the Medical Field.1. Simulation of gamma-cameras and PET-scanners.2. Simulation of dosimetry on radiotherapy

treatments in oncology • The Interest of the LA Community is

Leaded 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)



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.


E-infrastructure shared between Europe and Latin AmericaStatus 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 Family of Proteins Produced by a Protozoan Parasite (Plasmodium Falciparum ) that Causes Malaria.

• However is Being Applied to Other Diseases, such as H5N1 (Avian Flu).


E-infrastructure shared between Europe and Latin AmericaStatus 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 New Targets in New Data Challenges.



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 Sequences in Protein and DNA Databases.

• BLAST can be Applied, Among Other Uses, to Annotate the Estimated Function of Unknown Sequences.

• BLAST is Computationally Intensive.



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.

WEB Environment EELA Grid InfrastructureSE aker.dsic.upv.es

WNs

CE ramses.dsic.upv.es

Bioinformatics Portal

Gate-to-Grid



BiG Security

• Technologies – Changes on the Security Schema are Being

Implemented Instead of Storing a Portal Certificate Private Key or

Transferring User Private Keys (Even securely), a myProxy Certificate 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.



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 Bioinformatics Portal is Completed.



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.



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.



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

o 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 ActionsPresentation 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) o “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)

o 16 partners (11 LA, 5 Spain and Portugal).• Discussions on Biomed Collaboration

o Director of the Centre for Bioinformatics and Genome Biology within the Life Science Foundation of Chile.



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.



Contact

Vicente Hernández

Universidad Politécnica de Valencia

Camino de Vera s/n

46022 Valencia, Spain

Tel: +34-963879743

Fax. +34-963877274

E-mail: [email protected]

[email protected]

status of biomed applications (task 3.1)

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