In partial fulfillment of the Requirements for the Degree
of
Master of Science
Qing Mi
will defend her thesis
A DISTRIBUTED BIOINFORMATICS SOFTWARE with CROSS-LANGUAGE
CALLS AND HETEROGENOUS DATABASE CONNECTION
Abstract
The recent flood of data from genome sequences and functional
genomics has given rise to a new field, bioinformatics, which
combines elements of biology and computer science. Perl
(Practical Extraction and Report Language) programming language
plays a very important role in Bioinformatics because of its
flexibility and power in text file and text string processing. In
Cancer Genomic Core Lab of M.D. Anderson Cancer Center, a lot of
Perl application programs are developed to do data analysis,
database management, or even PCR primer design. How to share
these Perl application programs from different computer
workstations becomes a critical issue.
This paper reports a method to enable multiple programming
languages invoking and heterogeneous databases’ connection
across different operating systems. It uses a TCP/IP server
written in Perl to handle multiple requests from users. A client
interface written in Java lets users issue program-invoking
request and receive responses from the remote Perl server. XML
message exchanging are what we adopt to solve problems which
multiple operating systems and different programming languages
bring to us. Either Perl DBD::Proxy server and Openlink Software
Development Kit can connect to any database management systems
(DBMS) on any remote hosts via ODBC interfaces.
Date: Friday, March 29, 2002
Time: 2:00 PM
Place: 550-PGH
Faculty, students, and the general public are invited.
Thesis Advisor: Dr. Stephen Huang