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A High Throughput Bioinformatics Distributed Computing Platform
 

A High Throughput Bioinformatics Distributed Computing Platform

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A Research Paper review presentation on "A High throughput bioinformatics distribute computing platform", presented by Md. Habibur Rahman, BIT0216, Institute of Information Technology University of ...

A Research Paper review presentation on "A High throughput bioinformatics distribute computing platform", presented by Md. Habibur Rahman, BIT0216, Institute of Information Technology University of Dhaka.

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    A High Throughput Bioinformatics Distributed Computing Platform A High Throughput Bioinformatics Distributed Computing Platform Presentation Transcript

    • INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA A High-Throughput Bioinformatics Distributed Computing Platform19-09-2012 1 A high-throughput bioinformatics distributed computing platform
    • INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA Presented by- Md. Habibur Rahman BIT 0216 Institute of Information Technology University of Dhaka Bangladesh19-09-2012 2 A high-throughput bioinformatics distributed computing platform
    • The contributors of the paper INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA Thomas M. Keane, Andrew J. Page, James O. McInerney, and Thomas J. Naughton Bioinformatics and Pharmacogenomics Laboratory, National University of Ireland, Maynooth, Co. Kildare, Ireland Department of Computer Science, National University of Ireland, Maynooth, Co. Kildare, Ireland Homepage: http://www.cs.nuim.ie/distibuted19-09-2012 3 A high-throughput bioinformatics distributed computing platform
    • INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA Publications18th IEEE Symposium on Computer- Based Medical System (CBMS’05)19-09-2012 4 A high-throughput bioinformatics distributed computing platform
    • Suitability of Bioinformatics to INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA Distributed Computing A Class of Algorithmic Parallelism referred to as coarse-grained parallelism.  High compute-to-data ratio.19-09-2012 5 A high-throughput bioinformatics distributed computing platform
    • Topic and Problem Overview INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA  Demand for high performance computing has increased dramatically in the area of bioinformatics due to rapid increase in the size of genomic databases.  Traditional database search algorithm was not feasible to perform full search of a large database in a reasonable time.  Feasibility of heuristic algorithm but reduction of sensitivity of search.  Evolutionary biology, phylogenetic tree and greedy heuristic algorithm.19-09-2012 6 A high-throughput bioinformatics distributed computing platform
    • INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA Proposed solutiono According to the writers of the paper--- “We present a general- purpose programmable distributed computing platform suitable for deployment in a typical university environment where many semi-idle desktop PC’s are connected via a network” The system is fully cross-platform. Two distributed bioinformatics applications: i) DSEARCH ii) DPRml19-09-2012 7 A high-throughput bioinformatics distributed computing platform
    • Proposed solution(cont.) INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA o Java Distributed Computing platform - Client Server model - Server controls the resources (database, algorithm or computer hardware) - The model is divided into three separate pieces of software: server, client and remote interface.19-09-2012 8 A high-throughput bioinformatics distributed computing platform
    • Proposed solution(cont.) INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA Fig: Diagram of the complete system19-09-2012 9 A high-throughput bioinformatics distributed computing platform
    • Proposed solution(cont.) INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA Installation and Deployment- Consists of three executable JAR files corresponding to the server, client and remote interface.- Run the client as a low priority background service.- Hardware specification: At least Pentium IV processor- OS compatibility: Windows, Sun Solaris, Mac OSX and Linux.19-09-2012 10 A high-throughput bioinformatics distributed computing platform
    • INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA DPRml - Distributed Phylogeny Reconstruction by maximum likelihood Previous situation: Maximum likelihood evolution is one the most accurate techniques for reconstructing phylogenies. Developed parallel ML programs for reconstructing large and accurate phylogenetic trees. Implemented in platform specific language19-09-2012 11 A high-throughput bioinformatics distributed computing platform
    • INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA DPRml (cont.) - Distributed Phylogeny Reconstruction by maximum likelihood After the development of distributed computing platform: One of the most general and powerful likelihood-based phylogenetic tree building program. Used proven tree building algorithm and phylogenetic Analysis Library Possibility of multiple phylogenetic computation. Platform independent ML program.19-09-2012 12 A high-throughput bioinformatics distributed computing platform
    • DPRml (cont.) INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA - Distributed Phylogeny Reconstruction by maximum likelihood Speed up Testing: Fig. Speedup achieved by running 6 simultaneous DPRml problems using between 1-40 semi-idle processors.19-09-2012 13 A high-throughput bioinformatics distributed computing platform
    • DSEARCH INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA  Fully cross-platform parallel database search program.  Operates in a master slave environment.  Splitting the database into fixed sized units that are subsequently searched on the donor machines.,19-09-2012 14 A high-throughput bioinformatics distributed computing platform
    • DSEARCH (cont.) INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA Speed up Testing: Using- - FASTA database file, - A FASTA query sequence file. - A searching scheme - A configuration file. Fig. Speedup achieved by DSEARCH running on between 1-80 semi-idle processors.19-09-2012 15 A high-throughput bioinformatics distributed computing platform
    • My criticism and future work to do INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA  No detail description about how the applications works on the distributed computing platform.  If we don’t get the spare clock cycle of the semi-idle pc then the system will not give us the best result.  Failure of interconnected network of the desktop-pc’s will reduce the performance.  To improve and expand the range of bioinformatics applications for the system.19-09-2012 16 A high-throughput bioinformatics distributed computing platform
    • Conclusion INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA “There should not have any conclusion of research work, It is a continual process and it will be continued for the betterment of the human being.”19-09-2012 17 A high-throughput bioinformatics distributed computing platform
    • INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA ANY QUESTION?19-09-2012 18 A high-throughput bioinformatics distributed computing platform
    • INSTITUTE OF INFORMATION TECHNOLOGY (IIT), UNIVERSITY OF DHAKA19-09-2012 19 A high-throughput bioinformatics distributed computing platform