Grid Computing for Bioinformatics: An Implementation of a - - PowerPoint PPT Presentation

Grid Computing for Bioinformatics:

An Implementation

• f 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

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.

Web Portal for Jobs Submission

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
• n 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.

Addition of other bioinformatics tools to the Torque

Portlet.

Deployment of the GENIUS portal to give users

access to PSciGrid and EUAsiaGrid virtual

• rganizations.

Integration of the user's x509 certificate in the Login

Portlet.

Next Steps

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