1. DNA Awesomeness! Theodore D. Hellmann Christina L. Murphy CPSC 410 Fall ‘07

2. 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

3. 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.

4. 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

5. 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.

6. 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

7. Operating System Elements Semaphores Multi-threading File Management

8. Operating System Elements: Significant Points Semaphores Control partitioner and reader access Multi-threading Fully utilize the available processor capability. File Management Partition large data files into multiple files.

9. 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.

10. 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!

11. 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=Bla stFAQs#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/

12. 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=46 8852&messageID=2167964

13. The GUI

14. GUI Features: Tooltips

15. GUI Features: File Chooser

16. GUI Features: File Menu

17. GUI Features: Run Menu

18. GUI Features: Help Menu

19. GUI Features: Results Area

20. Boredom Fighting Pong!