Distributed Computing in Life Science Research

-Presenter: Yijian Yang4-28-2003

Motivation

Huge computational task in life science research

Heterogeneous, distributed computing environment

Problem

Unix

Linux

Windows

CORBA

What is CORBA?

Common Object Request Broker Architecture.

CORBA (cont.)

It can be simply conceptualized as a communication bus for client-server object.

Object Request

Invoke function Run() on Z

ZRun()

IDL IDL

CORBA (cont.)

How to develop CORBA applications

1. Define interface

2. Write the .idl file

Module XXX{interface YYY{Method1();Method2();};};

3. Compile it with an idl compiler

4. Use the output to build the server and the client

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

Client

Start locator service

Bind to CORBA server

Invoke remote method

Example

European Bioinformatics Institute: corba.ebi.ac.uk

For example: http://corba.ebi.ac.uk/idl/doc/nsdb.Embl.htmlTo get the access number of a sequence, the

corresponding function:getEmblSeq

EmblSeq getEmblSeq(in string bio_seq_id) raises(type::NoResult, Superceded);

Example (cont.)

In client program, if we want to use remote object Embl in EBI EMBL CORBA server, we should do:

1. org.omg.CORBA.ORB orb = org.omg.CORBA.ORB.init(); 2. Embl sample = EmblHelper.bind(orb, “Embl”) ; //bind to server orb3. sample.start(); 4. sample.getEmblSeq(arg[0]);

Example (cont.)

Other Method

Microsoft’s DCOM (Distributed Component Object Model)

Java RMI (Remote Method Invocation)

Conclusion

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

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/

Thanks