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

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Presentation on theme: "BTB or not to B(TB) – That’s the question BTB GRID Marianne Heling Mark de Groot Michelle Niekoop Bioinformatics – A. van Kampen."— Presentation transcript:

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

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

8 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

9 BTB

10 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.

11 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

12 Collaborators

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

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

15 Influence Medical Informatics ICT/ Technical Part

16 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]

17 Costs UK e-science programme:  £  € Parelsnoer project:  € BTB or not to B(TB)?  €

18 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

19 Conclusion A nationwide BTB provides  More variety among the patient data

20 References courant.pdf courant.pdf UK e-Science Programme Parelsnoer Project Bioinformatics articles [course materials]

21 Questions?????


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