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
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
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
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
PSciGrid: The national e-science Grid initiative � Response to the emerging need of the Filipino scientific community for a national high- performance computing facility � ASTI has set up a high-performance computing (HPC) facility with installed applications for bioinformatics , seismology, and meteorology
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 5.2.2 with bundled Grid and cluster middleware Middleware: gLite, which enables seamless communication between different computers/clusters in different locations
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
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.
� 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
� 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.
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); hardware- accelerated pairwise sequence alignment (Smith- Waterman)
� 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
1. GenBank Entry Retrieval System (GenBankERS) Portlet � Allows bioinformaticians to view and download DNA sequences in GenBank and FASTA format; � http://wiki.pscigrid.gov.ph/index.php/GenBankERS
Fig.2 GenBankERS Portlet
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. � http://wiki.pscigrid.gov.ph/index.php/Batch_Job_Submission
Fig.3 Grid Job Submission Portlet
3. Torque Jobs Submission Portlet � Allows users to submit inputs of predefined bioinformatics tools and run to the Banyuhay cluster. � http://wiki.pscigrid.gov.ph/index.php/Torque � 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
Fig.4 Torque Job Submission Portlet
� Default Portlets � Proxy Manager Portlet � http://wiki.pscigrid.gov.ph/index.php/Proxy_Manager � File Manager Portlet � http://wiki.pscigrid.gov.ph/index.php/File_Manager � Condor Jobs Submission Portlet � http://wiki.pscigrid.gov.ph/index.php/Condor
� How to use or access the Web Portal 1) Request for an account from the Grid Applications team (gridapps@asti.dost.gov.ph) 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 http://portal.pscigrid.gov.ph:8080/gridsphere 4) Customize the layout and check the portals that you will use.
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.
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
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