1. 1 P2P Workshop for Automatic Synchronization and Distribution of Biological Databases and Software over Low-Bandwidth Networks Unitsa Sangket, Amornrat Phongdara, Wilaiwan Chotigeat, Darran Nathan, Woo-Yeon Kim, Tin Wee Tan, Jong Bhak, Chumpol Ngamphiw, Sissades Tongsima, Asif M. Khan and Honghuang Lin By

2. 2/17 Outline  Background  Objectives  Methods  Results  Setup of the P2P node

3. 3/17 Background  Bioinformatics and the need for network bandwidth Bioinformatics involves the collection, organization and analysis of large amounts of biological data. normally update database by a file transfer over FTP Network bandwidth within developing countries  still very low  the low reliability of connections means breaks / aborts in downloads are common

4. 4/17 Background  the revolution in file sharing technology Peer-to-Peer (P2P) file exchange  1 st generation  Napster  exchanging files among client through server  2 nd generation  FastTrack/Kazza  continued to evolve and improve, no server  3 rd generation  Azureus  advance over previous P2P protocols with BitTorrent  a large file will be broken up into smaller fragments and reassemble

5. 5/17 Background  the revolution in file sharing technology source: http://no.wikipedia.org/wiki/BitTorrent traditional client/server distribution of files P2P distribution of files using BitTorrent protocol

6. 6/17 Background  3 rd generation P2P technology solve Low international bandwidth  provide additional bandwidth, speed up the overall download rate Unreliable connections  download automatic from the best connections

7. 7/17 Background  applied in three areas – the distribution of biological software (size of files ~ < 1GB) courseware (size of files ~ 1GB – 10GB) databases (size of files ~ 10GB - 100GB)

8. 8/17 Objectives  To extend a P2P client application base on 3 rd generation P2P protocol for use in the distribution of biological software, courseware, and databases.  To set up and test the performance with nodes in countries in the Asia-Pacific region.

9. 9/17 Methods  The Azureus P2P (http://azureus.sourceforge.net/) suite was selected because open-source runs on Java well documented plugin interface

10. 10/17 Methods  A RSSFeed Scanner Plugin was used to trigger automatic synchronization of data at regular intervals

11. 11/17 Methods  Four trial nodes have been setup Prince of Songkla University (PSU, Thailand) Korean Bioinformation Center (KOBIC, Korea) National University of Singapore (NUS, Singapore) National Center for Genetic Engineering and Biotechnology (BIOTEC, Thailand). NodeTracker url PSUhttp://biotracker.psu.ac.th:6969 KOBIChttp://ftp.kobic.re.kr:6969 BIOTEChttp://protcluster.biotec.or.th:6969

12. 12/17 Results Fig. Total data size downloaded

13. 13/17 Acknowledgements  the International Development Research Centre (IDRC) Canada  the Asia-Pacific Bioinformatics Network (APBioNet)  MOST and KADO of MIC in Korea.

14. 14/17 P2PWiki  http://everest.bic.nus.edu.sg/p2p/index.php /Main_Page

15. 15/17 Setup of the P2P node 1. Install Azureus and Java 2. Set up Azureus Set up client of Azureus  To download and upload data Set up server of Azureus  To create the.torrent files and publish them 3. Install and set up RSSFeed Scanner Plugin To synchronize data automatically 4. Install and set up Advanced Statistics Plugin To test performance

16. 16/17 1. Install Azureus and Java  ftp://192.168.1.2  http://azureus.sourceforge.net/download.php

17. 17/17