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Virtual Laboratory Overview

Explore the distributed metacomputing Grid, secure connections, and prototype applications in the Virtual Lab environment for conducting experiments and accessing resources seamlessly. Get insights into DNA array expression, biomedical simulation, and more.

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Virtual Laboratory Overview

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  1. Virtual Laboratory Overview A collaborative analysis environment for applied experimental science • Distributed instrumentation & resource access • Remote resources transparently available • Focus on content and information • Guide the user through the experiment Virtual Lab overview

  2. Distributed Metacomputing: the Grid • Dependable, consistent and pervasive access to (high-end) resources • Guaranteed end-to-end performance • Varying resource availability • Various administrative domains • Security, policy and payment Virtual Lab overview

  3. The Grid, a layman’s view • In ye olde days (till approx 1992): • Hardly any network security • All machines in a LAN are created equal • All local users happy with remote shell, rlogin, rcp • Now: • Want to communicate globally over Gigabit WAN, but • Internet is a dangerous place full of crackers and government agencies, firewalls and barriers • The Grid: • Bring back single sign on and trust • use the WAN as the 80’s LANs: all global users happy Virtual Lab overview

  4. The fabric (machines and network) • Surfnet5/Gigaport networking • Now: 20 Gbit/s IP backbone (POS framing) • In 2003: 80 Gbit/s • Connects universities, institutes and acad. home users • Client connections now: • NIKHEF: 1 Gbit/s Surfnet,2x1 Gbit/s WTCWnet (SARA) • VU: 155 Mbit/s (soon 1Gbit/s) • Compute Resources • Farms, supercomputer, tape robot, visualization, … Virtual Lab overview

  5. Microbeam and VLAM-G network • Secure connection between microbeam and WTCW • IPsec tunnel (VPN): encryption and integrity checking SurfNet backbone VPN router VPN router ComputeFarm CampusNet Institute Network VU – counting room Virtual Lab overview

  6. The VLAM-G Applications • Three prototype applications for the VLAM-G • Materials Analysis of Complex Surfaces (MacsLab) • Microbeam, FT-IR, TOF-SIMS mass spectroscopy • Biomedical simulation and visualization (VRE) • Link patient MRI scans with blood-flow simulations in vessels • Genome expression studies using a DNA Micro Array (Expressive) • Mass-test reaction of antibodies on DNA and proteins • Applications share concept of Process Flow • Many use unique (in NL) resources or need compute power Virtual Lab overview

  7. DNA Arraygenomeexpression Bio Medicine Material Ana Application Others MRI Scanner Micro beamFTIR, ... Domains VLAM Science Portal + Workbench VLAM RTS Grid Middleware (Globus) Grid Fabric (Farms, microscope, etc.) A layered architecture Virtual Lab overview

  8. Objectives • Designing middleware:bridge gap between Grid- and application-layer • Enable VL users to define, execute, and monitor their experiments • Provide to VL users: • location independent experimentation, • familiar experimentation environment • assistance during his experiment Virtual Lab overview

  9. Information gathering Interpretation Experimentation Access todevices Access todata Access to information Grid accessible infra: apparatus, systems, network Information and process flow Virtual Lab overview

  10. VL AM Collaboration Front-end Assistant RTS Application DB Globus Toolkit A simple architecture view KernelDB Virtual Lab overview

  11. Examples: Expressive, MACS, EFC, ... MACS EFC Expressive Application Domain DB • Characteristics of typical application • Scientist(s) performing the experiment • On objects and pre-existing information & data • On which processes operate • That use apparatus with specific properties • Resulting in new data and information • A domain-specific flow of processes Virtual Lab overview

  12. VL-AM Kernel DB • Stores user support information: • experiment topology definitions • module descriptions • user information • Provides cross-links to application annotationsknows the context in which data was generated| • Extends resource directories now used in Grid Virtual Lab overview

  13. Device control • Needs a very stable and secure environment • Concurrent access: • Full control for (many) local operators • Limited control for remote end-users (laymen) • Control very device dependent (unique properties) • Use dedicated control software as user interface • DACQ output needs to be integrated in the VLAM Virtual Lab overview

  14. A microprobe experiment (Analysis) Data storage (tape robot) Local DACQ system Local or remote compute power Local Visualization Virtual Lab overview

  15. A User’s View Virtual Lab overview

  16. VLAM-G current status • Prototypes of the analysis environment exist • Distributed compute environment ready @WCW (VU soon) • Integrating the various parts of VLAM-G AM • Currently building the analysis GUI • Expect working demo in June (HPCN conference) • Analysis modules: Stefan Piet and Gert Eijkel • Secure Network to VU: now selecting equipment • Building of device interface (LabView): Q3/Q4 2001 Virtual Lab overview

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