2002 BIOi Final Project 1 A Distributed DNA Search Database System

2 Motivation Bioinformatics is an important issue in the next century. DNA sequence queries and comparisons are more and more common. Due to the long sequence of a DNA, each DNA query takes too much time.

3 Goal To accelerate the searching time, we create a stable and scalable platform for distributed computing. provide an easy and simple graphical user interface for DNA search user. dynamic joining.

4 Architecture End user Coordinator Host Coordina tor Host Coordinator

5 System Roles End user web portal Coordinator Host

6 End user’s view Submit a legal-formatted DNA query. Wait for a period of time. Receive result pages.

7 Coordinator’s view Coordinator Host

8 Coordinator’s View Accept an end-user’s request query to search in a range of database. Allocate a sub-range of database to its group hosts. Communicate with other groups’ coordinators. Return its group result to the requesting end-user.

9 Host’s View Coordinator Host

10 Host’s View Each host belongs to a group and maintain a database partition. In each query, a host accepts a group coordinator’s allocation to search in a range of DNA database.

11 Single Host’s Job 1.Search in one part of Database. 2.Share the Loading of alignment.

12 Communication Protocol 1.Coordinating Module 2.Job Communicating Module 3.Query Processing Module 4.Database Module 5.Status Communicating Module

13 Communication Protocol

14 Robustness Fault Tolerance –Fail-safe mechanism for handling failures of both coordinators and hosts. –Allow a fixed number of failed hosts. Recovery –Recover the previous state of crashed coordinators and hosts. –Job of failed hosts can be taken over by other hosts. Scalability –New hosts can join this system to enhance the computing power. –For local area networks only.

15 Implementation Pure JAVA runtime environment Web site: Apache server + JSP JAVA RMI MySQL™

16 Potential Application Mathematics. Message Encryption & Decryption. Distributed Datamining

17 Implementation Phase Database ModuleMySQL setup DNA sequence data collection Job ModuleJob assignment Query ModuleDNA comparision implementation Status ModuleHandle host failure exception Handle coordinator failure exception Coordinator ModuleGet global and group view WEBApplication module Design Web interface GUIApplication interface Realtime response insterface

18 Project participants 蔡景祥 Chin Hseung Tsai –B 資管四 徐蔚倫 Wei Lun Hsu –B 公衛四 張均合 Chun Ho Chang –R 資管所研一 羅文興 Wen Hsin Lo –R 資管所研一 劉智雄 Chi Hsiung Liu –R 資管所研一

19 Question?

20 ThanQ