1. A Massively Parallel Architecture for Bioinformatics Presented by Md Jamiul Jahid

2. Introduction Bioinformatics algorithms are demanding in scientific computing In general most of the bioinformatics algorithms are fairly simple Dealing with huge amount of data The size of DNA sequence database doubles every year

3. Introduction A typical DNA contains 3.4 billion base pairs Maximum algorithms use only simple operations with input data like – Arithmetic operation – String matching – String comparison

4. Introduction Standard CPUs are designed for providing a good instruction mix for almost all commonly used algorithm For a target class of algorithm they are not effective Results – High runtime – Energy – Money

5. Contribution Present a massively parallel architecture Using low cost FPGA(Field Programmable Gate Array) They called it COPACOBANA 5000 – Meaning Cost-Optimized Parallel Code Braker ANd Analyzer

6. COPACOBANA 1000 This machine is for cryptanalysis: fast code breaking 120 low cost FPGAs 20 subunits Each has Xilinx Spartan -3 XC3S1000 FPGAs

7. COPACOBANA 1000 Assumptions – Programs are parallelizable – Demand of data transfer is low – All node needed very little local memory which can be served from on-chip RAM of FPGAs

8. COPACOBANA 5000 Bus Concepts – Point to point connection two neighboring FPGA- cards – Point to point connection contain 8 pairs of wire – Each 250MHz, total 2Gbit/s

10. COPACOBANA 5000 Controller – Root entity of control is running on a remote host computer – Connected to COPACOBANA5000 by LAN – Two scenario Data on remote host Data on COPACOBANA5000

11. COPACOBANA 5000 FPGA-Card – Xilinx Spartan-3 5000 is used – Contains 8 FPGAs – All FPGAs are globally clocked

12. Performance Estimation Between – PC – COPACOBANA1000 – COPACOBANA5000

13. Performance Estimation

14. Conclusion In this paper a new hardware for running bioinformatics algorithm is proposed The hardware are – Cheap – Low power consumption – Efficient

15. Questions ?

16. Thank You

17. Reference Gerd Pfeiffer, Stefan Baumgart, Jan Schröder, and Manfred Schimmler, A Massively Parallel Architecture for Bioinformatics, 9th International Conference on Computational Science (ICCS 2009).A Massively Parallel Architecture for Bioinformatics