DNA Search Algorithm Optimization using Operating System Principles, Slides of Computer Science

Download DNA Search Algorithm Optimization using Operating System Principles and more Slides Computer Science in PDF only on Docsity! DNA Awesomeness! Docsity.com 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 Docsity.com 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. Docsity.com 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 Docsity.com Operating System Elements o Semaphores o Multi-threading o File Management Docsity.com 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! Docsity.com 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/ Docsity.com 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 Docsity.com e GUI Features: File Chooser Look In: | Local Disk (C:) Gal] Ct] |] |e] ga -/) o— CE) atl (J e758a0dd9c6e1d8c5b8989F3c 12513 [1 Course Technology 4 i386 4 cyawin [4] New Folder CJ dell CJ plan [J Documents and Settings (J Program Files EJ drivers [A robocode 4] FileName: — | Files of Type: |All Files Docsity.com GUI Features: File Menu DNA Awesomeness! Exit ence to Search For... Select file with sequence to search for... OQ Choose file! <...10 file selected... > Enter sequence to search for... Oo [e fo string entered... = File to search through... Choose file! = ...n0 file selected... = -Search Bounds (2 Time Limit ‘© Number of hits ®@ No Limits |g seconds [0] hits rResults Application loaded normally rlimers Time Elapsed 0:00:00 Estimated Time [over 9000] Start Pause/Resume Pong Stop /Log Docsity.com GUI Features: Run Menu DNA Awesomeness! Pause Resume earch For... h sequence to search for... Stop joose file! PONG B selected... > Enter sequence to search for... Oo [e fo string entered... = File to search through... Choose file! = ...n0 file selected... = -Search Bounds (2 Time Limit ‘© Number of hits ®@ No Limits |g seconds [0] hits rResults Application loaded normally rlimers Time Elapsed 0:00:00 Estimated Time [over 9000] Start Pause/Resume Pong Stop /Log Docsity.com