Integration of the Biological Databases into Grid-Portal

Environments

Michal Kosiedowski, Michal Malecki, Cezary Mazurek, Pawel Spychala, Marcin

Wolski

Agenda

• Introduction• PROGRESS Grid-Portal

Environment• Data Management System• Enabling SRS resources within DMS• Case study• Conclusions

R&D Center

• PSNC was established in 1993 and is an R&D Center in:– New Generation Networks

• POZMAN and PIONIER networks• 6-NET, ATRIUM, Muppet,

– HPC and Grids• GRIDLAB, CROSSGRID, VLAB,

PROGRESS, Clusterix, HPCEuropa

– Portals and Content Management Tools• Polish Educational Portal "Interkl@sa",

Multimedia City Guide, Digital Library Framework,Interactive TV

PROGRESS (1)

• Project Partners– PSNC IBCh Poznan– SUN Microsystems Poland– Cyfronet AMM, Krakow– Technical University Lodz

• Co-funded by The State Committee for Scientific Research (KBN) and SUN Microsystems Poland

PROGRESS (2)

• The PROGRESS project produced a set of open source tools for use by:– Grid constructors– Computational applications

developers– Computing portals operators

PROGRESS (3)

• Cluster of 80 processors

• Networked Storage of 1,3 TB

• Software: ORACLE, HPC Cluster Tools, Sun ONE, Sun Grid Engine, Globus

Wrocław

Gdańsk

Data Management Issues

• Hide the data management complexity from the end users

• Use new standards defined by grid organizations• Co-operate with different kinds of client

applications• Provide seamless access to data and information

for grid computing• Enable intuitive and efficient methods for resource

exploration• Providing friendly interface to data management

for administrators and scientists

PROGRESS

Web Services and PROGRESS

PORTLETSPORTLETS GRID SERVICEGRID SERVICEPROVIDERPROVIDER

DATADATAMANAGEMENTMANAGEMENT

GRID GRID RESOURCERESOURCE

BROKERBROKER

WSWS

Data Management System

• A distributed system enabling the management of grid data files

• Stores files in distributed storage modules of various types: generic filesystems, archivers, relational databases

• Uses metadata to describe files• Allows access to data banks like a mirror

of Sequence Retrieval System• Exposes its functionality within the Data

Broker Service

DMS Functionality

• Virtual file system keeping the data organized in a tree structure– Metadirectories – hierarchize other

objects– Metafiles - represent a logical view of

computational data regardless of their physical location

• DMS provides its services in a form of Web Services API (Data Broker Service)

DMS Functionality

• Web Services interface: storing, access, describing and delivery of data– directory mgmt.: e.g. add, remove and rename

directories, retrieve root and current path, change path,

– file mgmt.: e.g. add, remove and rename files, add, remove and retrieve physical file location,

– metadata mgmt.: e.g. retrieve list of schemes and attributes, assign schemes to files and edit values

– external datasource mgmt.: e.g. databanks content retrieving, entry resolving, databanks exploring

DMS Architecture

Data Broker

• Serves as an interface (Web Services) for external clients, such as the HPC Portal and the grid resource broker

• Mediates in the flow of all requests directed to the DMS

• Authorizes the client that submitted the request

Metadata Repository

• Central and single point of metadata management

• Responsible for all metadata operations and their storage and maintenance

• It stores the following sorts of information:– metadata about resources: data files, its physical

localization and possible way to access them,– metadata about rights: all information related to the

rights – users, their groups, access rights.– metadata describing the standards for file description,

e.g. Dublin Core (DC)– metadata about services: data brokers, data containers

Data Container

• Enables access to physical data• Data can be stored on various media types • Data can be organized as files on generic

filesystems, BLOBs in databases or files on data tapes

• All Containers possess a uniform interface regardless of the media types they manage

• Container does not perform file transfers - it uses external services like ftp, https, gass, gridftp

Proxy (SRS Container)

• Enables access to external scientific databases• Includes both Repository (listing entries,

retrieving attached metadata, building queries) and Data Container (downloading files) functionality

• DMS treats the Proxy as a separate, independent module, that manages read-only data

• The PROGRESS grid-portal environment: the Proxy (named SRS Container) enables access to SRS resources

Administrative Portal

• Web application allowing users to handle grid data management with the use of a web browser

• An intuitive interface allowing to execute superset of DMS services

• An effective way to explore huge SRS resources

• On-line help

SRS Resources in PSNC

• Genbank Release (about 32 mln entries)Updates (about 2 mln entries)

• EMBL - European Molecular Biology Laboratory Release (about 42 mln entries)Updates (about 2 mln entries)

• PDB – Protein Data Bank• Swissprot

Swissprot Release, Swissprot New, SPTREMBL, REMTREMBL

SRS Installation

• Installation uses multiple storage resources• Data access interface delivered via a

common portal (srs.man.poznan.pl)• Administrative tasks (retrieval and data

preparation) splitted onto multiple machines• Parallel data retrieving from remote

resources• Offline data indexing and packing on a

computational machine (0.5Tb storage)• Compressed online data (2*250Gb storage)

SRS Installation - Schema

storage 02

SRSsrs.man.poznan.pl

offlineonline

indexing offindex flatfiles

storage 01

flatfilesindex

viola.man.poznan.pl

bellis-e.man.poznan.pl

SRS Container• Using shell-based access to the SRS

– SRS operations are sent via a shell command

• Access interface based on Web Services– Internal functionality delivered using SOAP

communication

• Data access - ftp, gsiftp, gass protocols– Data are accessed using external file servers

integrated with SRS module

• Advanced caching system– Databanks and entries are cached and reused in the

following user requests

Portal Interface – databanks list

Portal Interface – databank content

Portal Interface - searching

Portal Interface – search results

Portal Interface – copying entries

Portal Interface – file properties

DMS Installation Requirements

• Java virtual machine: recommended Java(TM) 2 Runtime Environment, Standard Edition 1.4.1 or higher.

• Database server: DMS is ready to cooperate with Oracle and PostgreSQL engine:– Oracle - Oracle8i or higher recommended– PostgreSQL - version 7.3 or higher is required with

the additional extentions:• chkpass and tablefunc

from contrib package• plpqsql support

Usage scenario: PROGRESS HPC Portal

• SRS resources can be used as input for grid jobs created, configured and submitted for execution in the grid with the use of the PROGRESS HPC Portal

• An example application is AminSim –aminoacid sequences similarity – developed by Prof. Jacek Blazewicz group at the Institute of Computing Science, Poznan University of Technology

AminSim portlet (1)

AminSim portlet (2)

AminSim portlet (3)

AminSim portlet (4)

Conclusions

• SRS resources have been integrated with the distributed file structure of DMS and enabled for use within a grid-portal environment (PROGRESS HPC Portal)

• A web interface (DMS Portal) enhances the efficiency of the SRS resources exploration:– fast copying interesting entries directly to the users’ home

directory– merging files– saving files in various formats (e.g. Fasta)

• The universal access layer to the to the scientific databases may by successfully used to connect other data sources to the Data Management System

Contact info

• Check http://dms.progress.psnc.pl for more information about DMS

• Check http://dms.progress.psnc.pl/docs/demo.htm for the DMS Portal demo

• Check http://progress.psnc.pl for more information about PROGRESS

• Download it now: http://progress.psnc.pl• Mail DMS team: szd@man.poznan.pl• Mail PROGRESS team: progress@man.poznan.pl