DNA Awesomeness!

Theodore D. Hellmann

Christina L. Murphy

CPSC 410

Fall ‘07

Overview

Executive Summary System Selection System Analysis System Design Operating System Elements Operating System Elements: Significant Points Methodology and Technology for the Solution References Screen Shots

GUI Features

Demonstration

Executive Summary

Bioinformaticists derive knowledge from computer analysis of biological data. In an effort to try to find specific segments of DNA in the human genome, bioinformaticists wrote a program that would search for a particular segment of DNA in a file. While their program may work, it is very inaccurate and inefficient. Our project uses semaphores, multi-threading, and file management to provide a quick and accurate means of accomplishing this type of search.

System Selection

The current system produces inaccurate results

There were many areas that could be improved by the incorporation of OS principles, policies, techniques and architecture

System Analysis

Searching the entire human genome is daunting. The current method uses shortcuts to overcome this problem, producing inaccurate results:Approximate matches are returned.Only regions with the highest

probability of finding a match are searched.

System Design

A user-friendly GUI has been designed. Tool tips Search timer Search results Search bounds Controls

• GUI buttons• Menu items

String to search for• Entered by typing• Entered by indicating a file containing the string

Pong

Operating System Elements

Semaphores Multi-threading File Management

Operating System Elements:

Significant Points Semaphores

Control partitioner and reader access Multi-threading

Fully utilize the available processor capability.

File ManagementPartition large data files into multiple

files.

Solutions for significant points

Supplier/Consumer use of semaphores.

Utilize multiple processors through multi-threading.

Decrease search time by breaking large files down into many smaller files.

Methodology and technology for the solution

Create GUI Add code to make GUI functional Create Reader class Create Partitioner class Create SearchControl class Create ResultsPair class Create custom Timer class Incorporate Pong!

References

Addison-Wesley (2002), The Java Developers Almanac 1.4. Retrieved 12/01/07, from http://www. exampledepot.com/egs/java.io/CreateDir.html

Basic Local Alignment Search Tool (BLAST) FAQ. Retrieved 9/15/07, from http://www.ncbi.nlm.nih. gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastFAQs#LCR

Java™ Platform, Standard Edition 6 API Specification. Retrieved multiple times 9/15/07 through 12/6/07, from http://java.sun.com/javase/

6/docs/api/

References (cont.)

Stallings, W. (2005). Operating Systems: Internals and Design Principles. Upper Saddle River, New Jersey: Pearson Prentice Hall.

Sun Developer Network (SDN): Developer Forums 12/1/03. Retrieved 12/1/07 from http://forum.java.sun.com/thread.jspa?threadID=468852&messageID=2167964

The GUI

GUI Features: Tooltips

GUI Features: File Chooser

GUI Features: File Menu

GUI Features: Run Menu

GUI Features: Help Menu

GUI Features: Results Area

Boredom Fighting Pong!