Grid Computing for Bioinformatics: An Implementation of a User-Friendly Web Portal for ASTI's In Silico Laboratory

Transcription

1 Grid Computing for Bioinformatics: An Implementation of a User-Friendly Web Portal for ASTI's In Silico Laboratory R. Babilonia, M. Rey, E. Aldea, U. Sarte gridapps@asti.dost.gov.ph

2 Outline! Introduction: Who are we and what we do! The Philippine e-science Grid (PSciGrid): The National e-science Grid Initiative! What we have developed: web portal for jobs submission! Conclusion

3 The Advanced Science & Technology Institute (ASTI)! A research and dev t institute under the Philippine Government's Department of Science and Technology (DOST)! Our mandate! Conduct R&D in the advanced fields of ICT and Electronics! Bioinformatics, being a priority area of the DOST, has been one of ASTI's focus areas

4 The Advanced Science & Technology Institute (ASTI)! Since 2003, ASTI has been actively involved in a national initiative for bioinformatics development! Objective: To initiate the formation of a bioinformatics community Network for Integrative Multidisciplinary Bioinformatics Utilization Strategies or NIMBUS! ASTI's activities on bioinformatics include: site mirroring (BioMirror, S-Star); set-up of APBioBox & SunBioBox; the Philippine e-science Grid (PSciGrid) initiative

5 PSciGrid: The national e-science Grid initiative! Response to the emerging need of the Filipino scientific community for a national highperformance computing facility! ASTI has set up a high-performance computing (HPC) facility with installed applications for bioinformatics, seismology, and meteorology

6 The ASTI HPC Facility Currently has 45 computing nodes. Each node has a 2 x 2 Intel Xeon processor 360 cores, ~ 2.88 teraflops processing power Storage capacity: - 6tb for raw data (1tb of modis aqua satellite images); - 4tb for DNA and protein sequences (Bio-Mirror); 4tb for software mirror Operating System: ROCKS with bundled Grid and cluster middleware - Middleware: glite, which enables seamless communication between different computers/clusters in different locations

7 PSciGrid: The national e-science Grid initiative! One of the projects being implemented under this program is Boosting Social and Technological Capabilities for Bioinformatics Research! Objectives:! To enhance availability of bioinformatics locally! To provide rapid access to major biological sequences & structures! To provide web-hosting services for bioinformatics software

8 Web Portal for Jobs Submission! What is this tool we have developed?! a web portal (with multiple applications or portlets) designed to provide a flexible and usable web environment for defining and running bioinformatics application.

9

10 ! Why did we develop this web portal?! The web portal is easy to install and comes with many portlets and functionalities.! Because of the increasing need for...! greater computing power! updated bioinformatics! diverse bioinformatics tools! Who are our intended users?! Local bioinformatics researchers

11 ! Overview of the web tool! Implemented using the OGCE Portal! - OGCE Portal or Open Grid Computing Environments Portal is an open source project that comprises several portlets aimed to be used in web portals for science purposes.! A Java implementation of SSH2! - Used to log in and access the applications installed on the Banyuhay cluster, where the Bioboost & BioRoll are installed.

12 Bioinformatics Software/Applications currently installed in the Banyuhay cluster ClustalW; FASTA; GMAP; HMMER; MrBayes; PHYLIP; EMBOSS; Glimmer; GROMACS; mpiblast; NCBI; T_Coffee Hardware-accelerated HMMER; hardware-accelerated multiple sequence alignment (ClustalW); hardwareaccelerated pairwise sequence alignment (Smith- Waterman)

13 ! What are the features?! User account management! Profile management! Theme and layout management! The (3) portlets that will run together with the default portlets:! - GenBankERS Portlet! - Torque Portlet! - Grid Portlet

14 1. GenBank Entry Retrieval System (GenBankERS) Portlet! Allows bioinformaticians to view and download DNA sequences in GenBank and FASTA format;!

15 Fig.2 GenBankERS Portlet

16 1. 2. Grid Jobs Submission Portlet! Enables users to submit batch jobs to remote resources via Globus Resource Allocation Manager.! It allows user to specify job parameters, submit the job and view the job status information.!

17 Fig.3 Grid Job Submission Portlet

18 3. Torque Jobs Submission Portlet! Allows users to submit inputs of predefined bioinformatics tools and run to the Banyuhay cluster.! Operational bioinformatics tools:! - ClustalW, Glimmer, Hardware-Accelerated PSA and Custom Application! Bioinformatics tools with working prototype:! - FASTA, GMAP, HMMER, MPIBlast, MrBayes, MSA, NCBI BLAST, Phylip, T-Coffee

19 Fig.4 Torque Job Submission Portlet

20 ! Default Portlets! Proxy Manager Portlet! File Manager Portlet! Condor Jobs Submission Portlet!

21 ! How to use or access the Web Portal 1) Request for an account from the Grid Applications team 2) Request for a user certificate fromregistration Authority (gridgc@asti.dost.gov.ph) which you must install on your user interface account. 3) Go to 4) Customize the layout and check the portals that you will use.

22 Next Steps! Addition of other bioinformatics tools to the Torque Portlet.! Deployment of the GENIUS portal to give users access to PSciGrid and EUAsiaGrid virtual organizations.! Integration of the user's x509 certificate in the Login Portlet.

23 Conclusion! We successfully integrated custom JSR 168 portlets into the OGCE portal.! Particularly helpful for the local bioinformatics researchers to be able to use bioinformatics tools through a Web-based user interface.! Rapid access to popular bioinformatics softwares and databases which run on the Grid.! Contact us: gridapps@asti.dost.gov.ph

24