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Distributed Computing in Life Science Research

Distributed Computing in Life Science Research. - Presenter: Yijian Yang 4-28-2003. Motivation. Huge computational task in life science research Heterogeneous, distributed computing environment. Problem. Unix. Windows. Linux. CORBA. What is CORBA?.

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Distributed Computing in Life Science Research

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  1. Distributed Computing in Life Science Research -Presenter: Yijian Yang 4-28-2003

  2. Motivation • Huge computational task in life science research • Heterogeneous, distributed computing environment

  3. Problem Unix Windows Linux

  4. CORBA • What is CORBA? Common Object Request Broker Architecture.

  5. CORBA (cont.) It can be simply conceptualized as a communication bus for client-server object. Invoke function Run() on Z Z Run() IDL IDL Object Request

  6. CORBA (cont.)

  7. How to develop CORBA applications • Module XXX{ • interface YYY{ • Method1(); • Method2(); • }; • }; 1. Define interface 2. Write the .idl file 3. Compile it with an idl compiler 4. Use the output to build the server and the client

  8. Server .idl specification file Compilation A package of empty source code for server skeleton Implement the object Create and register the object to CORBA server Ready for client request

  9. Client Start locator service Bind to CORBA server Invoke remote method

  10. Example • European Bioinformatics Institute: corba.ebi.ac.uk • For example: http://corba.ebi.ac.uk/idl/doc/nsdb.Embl.html • To get the access number of a sequence, the corresponding function: • getEmblSeq • EmblSeq getEmblSeq(in string bio_seq_id) raises(type::NoResult, Superceded);

  11. Example (cont.) In client program, if we want to use remote object Emblin EBI EMBL CORBA server, we should do: • org.omg.CORBA.ORB orb = org.omg.CORBA.ORB.init(); • Embl sample = EmblHelper.bind(orb, “Embl”) ; //bind to server orb • sample.start(); • sample.getEmblSeq(arg[0]);

  12. Example (cont.)

  13. Other Method • Microsoft’s DCOM (Distributed Component Object Model) • Java RMI (Remote Method Invocation)

  14. Conclusion • CORBA is a promising technology for distributed object computing in life science research and has provided pointers to further information.

  15. Reference • http://bioinformer.ebi.ac.uk/newsletter/archives/3/lead_article.html • http://www.corba.org/ • http://www.omg.org • http://corba.ebi.ac.uk/

  16. Thanks

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