1. INFSO-RI-508833 Enabling Grids for E-sciencE www.eu-egee.org Activities of the UPV in NA4- Biomed Ignacio Blanquer Vicente Hernández Universidad Politécnica de Valencia

2. Enabling Grids for E-sciencE INFSO-RI-508833 Contents The GRyCAP. Applications –Pharmacokinetics. –Clinical Decision Support. Other Issues Related with Grids and Biomedicine –EELA. –TRENCADIS.

3. Enabling Grids for E-sciencE INFSO-RI-508833 The Research Group of Advanced Computing and Networking The GRyCAP Started 20 Years Ago in the Field of Parallel Computing, and it is Currently Formed by 30 Researchers. It has Participated in 17 European Project, Being Prof. V. Hernández the Project Manager in 10 of Them. It has Large Experience in the Research of Development of HPC and Grid and the Application to Different Areas. The Biomed Area is Active Since 7 Years Ago. The GRyCAP is Integrated in the Institute for the Implementation of Advanced Info. and Communication Tech. (ITACA) and the Network Centre of Biomedical Engineering. European National Private Total 2002 2003 2004 0 50 100 150 200 250 300 350 400 450 Funding (in Keuro) Source of the Funds www.grycap.upv.es

4. Enabling Grids for E-sciencE INFSO-RI-508833 EGEE Applications Pharmacokinetics Application Clinical Decision Support

5. Enabling Grids for E-sciencE INFSO-RI-508833 Pharmacokinetics Application Objective: The Analysis of the Angiogenesis in Hepatic Lesions for the Estimation of Tumour Aggressiveness and Response to Therapy Using Medical Images. Stages –Image Acquisition and Pre-processing. –Time Series Co-Registration. –Time Series Reordering. –Estimation of the Pharmacokinetic Model. Needs: Computational Intensive. Recent Dissemination –Demo on the 2nd Review of EGEE. –Presented in the NA4 User Forum and in the ECR’06. –Paper Accepted in HealthGrid’06.

6. Enabling Grids for E-sciencE INFSO-RI-508833 Pharmacokinetics Application Image Acquisition and Pre-processing –Images Obtained in DICOM.  Previously to the Injection of the Contrast Bolus (Called Reference).  3D Volumes at Different (Non-Uniform) Time Stamps (Called Dynamics). –Anonymised and Converted into Analyze. –Blank Areas Cropped. Time Series Co-Registration –Deformable Co-Registration of the Dynamics with Respect to the Reference Image. –Computing Intensive. –Implemented on the Grid. Time Series Reordering –The Images are Reordered into Files with One Slice per Each Dynamic. Estimation of the Perfusion Model –This Implies Solving an Over-Determined System Of Equations for Each Voxel in each Slice.

7. Enabling Grids for E-sciencE INFSO-RI-508833 Pharmacokinetics Application Time Series Co-Registration Advances –Tested on gLite PPS and on Gilda. –Changes on the Authentication System  Certificates are Preloaded on the UI.  Available VOs are also Listed from a Configuration File.  Proxyes are Created From the Web Service Using the Private Key Provided on the Login.  Concurrent Users are Supported Through Different Subdirectories and Proxies.  It Includes a “White List” of Nodes and Supports Several RBs (Through the WMS).

8. Enabling Grids for E-sciencE INFSO-RI-508833 Clinical Decision Support Objective: Extraction of Medically Relevant Knowledge from a Large Set of Information with the Objective of Guiding the Practitioners in their Clinical Practice. Stages –Corpus Pre-Processing. –Classifier Training [Computational Intensive]. –Publication of Classifiers. –Production [Short Jobs]. Other Issues –Paper Accepted for the VECPAR’06.

9. Enabling Grids for E-sciencE INFSO-RI-508833 Clinical Decision Support Development of a Classification Engine Training Module –Trains and Classifies a Large Database using the K-Nearest Neighbours Engine, SVM in Process. –The Application Developed Uses Three Levels of Parallelism:  The Grid for Searching the Best Value for ‘k’, Launching one Complete Execution in Each Resource.  MPI Parallel Computing for Each Resource, to Divide the Database into Blocks.  POSIX Threads Inside Each Parallel Process For the Fine-Grain Parallelism. –Outstanding Speed-ups are Being Obtained (>150), Reducing the Process to a Nightly Run. –Support for Site Exclusion (‘Black List’), e-Mail Notification, Selection of CEs from the Best SEs, Application-Controlled Resubmission.

10. Enabling Grids for E-sciencE INFSO-RI-508833 Clinical Decision Support Publication of Classifiers –Once Trained, Classifiers are Installed on CEs and WNs. –Authorized Users can Access Them Through the CDSS Application. Production [Short Jobs] –The CDSS Application Enables Launching Individual Runs or Larger Blocks or Runs. –It is Penalized by the Efficiency of Short Jobs. –A Short Jobs Queue has Been Created in the UPV Following the Recommendations of the SDJ-WG (Open to biomed VO)  ramses.dsic.upv.es:2119/jobmanager-pbs-sdj

11. Enabling Grids for E-sciencE INFSO-RI-508833 Other Issues Related to Grids EELA: “E-Infraestructure shared between Europe and Latin America” –Deployment of Grid Applications in Latinoamerica in three Areas: Biomed, Physics and Other (Climate and eLearning). –UPV is on Charge of the Task for Biomedical Applications –Applications Selected  Mature: GATE, WISDOM.  New Applications: Processing Services for the Biocomputing Portal of the ULA: BLAST and Phylogenesis. –The GRyCAP is Developing a Grid Service for Higher Productivity  Using MPI-Blast for Parallelising Individual Searches.  Using Grid for Parallelising Blocks of Sequences and Different Databases.

12. Enabling Grids for E-sciencE INFSO-RI-508833 Other Issues Related to Grids TRENCADIS: Towards a Grid Environment for Processing and Sharing DICOM Objects –Middleware for Federating Existing Resources in a Virtual DICOM Storage. –Indexed by a Semantic Structure Based on the Metadata and Structured Reports. –Explicit Encryption and Decryption and Key Sharing. –Link to Image Pos-Processing Services. –Progressive Transmission. Currently Being Developed to Link 5 Hospitals of Valencia Region.

13. Enabling Grids for E-sciencE INFSO-RI-508833 Contacto Vicente Hernández / Ignacio Blanquer Universidad Politécnica de Valencia Camino de Vera s/n 46022 Valencia, Spain Tel: +34-963879743 Fax. +34-963877274 E-mail:vhernand@dsic.upv.esvhernand@dsic.upv.es iblanque@dsic.upv.es