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BTB or not to B(TB) – That’s the question BTB GRID

BTB or not to B(TB) – That’s the question BTB GRID. Marianne Heling Mark de Groot Michelle Niekoop. Bioinformatics – A. van Kampen. Overview. What is GRID? What is E-(bio)science? Introduction Project Status and future uses Goal Project Collaborators Infrastructure

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BTB or not to B(TB) – That’s the question BTB GRID

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  1. BTB or not to B(TB) – That’s the question BTB GRID Marianne Heling Mark de Groot Michelle Niekoop Bioinformatics – A. van Kampen

  2. Overview • What is GRID? • What is E-(bio)science? • Introduction Project • Status and future uses • Goal Project • Collaborators • Infrastructure • Advantages/disadvantages • Costs

  3. GRID • GRID: The Grid is a service for sharing computer power and data storage capacity over the Internet.

  4. GRID • Types: • Data GRID • Computing GRID • Knowledge GRID • Information GRID

  5. E-science VS E-bioscience • E-science: Global collaboration in key areas of science and the next generation of infrastructure that will enable it. • E-bioscience: • Data handling, preprocessing & fusion • Data integration & knowledge representation • Process modeling & dynamic simulation • Complex systems approach

  6. Cell biology Neuro sciences Ecosystems dynamics Biological research domain Biological research domain e-bioscience core domain Enabling science domain Model Data handling, preprocessing & fusion Data integration & knowledge representation Process modeling & dynamic simulation Complex systems approach Problem- driven hypothesis Data- driven hypothesis Analysis methods Generic e-Bioscience research & development core Dry-Lab Data Analysis & Integrative in-silico experiments Experiment design VL-e Wet-Lab Biological knowledge biological problem Omics Data ICT infra- structure Technology domains Exact sciences Mathematics Computer science Information technology Enabling science domains Visualization e-BioLab Biological phenomena Interpretation Biological solutions E-BioScience approach

  7. Introduction Project • Brain Tumor Bank (BTB): • Physical storage of brain tissue of patients • Databases containing all relevant patient data and lab.results. • Goal: • Research about glioblastomas in particular. • These purposes do not serve direct patient care

  8. BTB

  9. DIO • DIO (Data Integratie ten behoeve van Onderzoek): • connects different databases with each other • LIMS (Laboratory Information Management System): • manage samples, laboratory users, instruments, standards / protocols and (many) other laboratory functions.

  10. Status and Future Uses • Status: • BTB will be implemented in the AMC 2007/2008 • Future: • Why nation wide? • Storage space • Computing power • Sharing resources, data and results

  11. 6. 12. 1. 2. 3. 14. 15. 10. 7. 16. 5. 11. 13. 8. 9. 4. Collaborators

  12. Once the appropriate resources have been located, the job is executed… Security CLINICIANS RESEARCHERS Information Service Research Broker Replica Catalog DIO - AZM DIO - MZG DIO - AMC BTB AMC BTB MZG BTB AZM LIMS AMC LIMS AZM LIMS MZG Storage Media Computing Elements Resources After clearing security validation, able to talk to the Resource Broker Enter GRID using software interface that runs on your computer Resource Broker sends the results back to you Resource Broker will query the Information Service and Replica Catalog Resource Broker will find the best resources to execute your job

  13. Amsterdam: 1 Resource Broker 1 Replica Catalog 1 Computing Element 1 Storage Element Groningen: 1 Security Server 1 Storage Element Utrecht: 1 Security Server 1 Storage Element Nijmegen: 1 Storage Element Rotterdam: 1 Information Service 1 Storage Element Maastricht: 1 Computing Element 1 Storage Element Infrastructure

  14. Influence Medical Informatics ICT/ Technical Part

  15. Advantages/Disadvantages • Advantages • Closed Network • Scale Size [more data available] • Computing Technologies • More chance of major breakthroughs • Disadvantages • It takes a time to implement [approx. 5 years]

  16. Costs • UK e-science programme: • £ 213.000.000 • € 322.290.300 • Parelsnoer project: • € 35.000.000 • BTB or not to B(TB)? • € 37.500.000

  17. Conclusion • It is possible • Security has to be optimal • Economical resources are available • The technology is available • A nationwide BTB provides • Better research • More valuable data • Perform bench marking • Provide information for new research

  18. Conclusion • A nationwide BTB provides • More variety among the patient data

  19. References • http://gridcafe.web.cern.ch/gridcafe/ • http://www.minocw.nl/documenten/ocwcourant.pdf • http://www.regering.nl • UK e-Science Programme • Parelsnoer Project • Bioinformatics articles [course materials]

  20. Questions????? ? ? ? ? ? ? ? ?

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