1. Integration of the Biological Databases into Grid-Portal Environments Michal Kosiedowski, Michal Malecki, Cezary Mazurek, Pawel Spychala, Marcin Wolski

2. Agenda Introduction PROGRESS Grid-Portal Environment Data Management System Enabling SRS resources within DMS Case study Conclusions

3. 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

4. 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

5. PROGRESS (2) The PROGRESS project produced a set of open source tools for use by: –Grid constructors –Computational applications developers –Computing portals operators

6. 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

8. 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

9. PROGRESS

10. Web Services and PROGRESS PORTLETS GRID SERVICE PROVIDER DATA MANAGEMENT GRID RESOURCE BROKER WS

11. 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

12. 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)

13. 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

14. DMS Architecture

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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

21. 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)

22. SRS Installation - Schema storage 02 SRS srs.man.poznan.pl offline online indexing offindex flatfiles storage 01 flatfilesindex viola.man.poznan.pl bellis-e.man.poznan.pl

23. 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

24. Portal Interface – databanks list

25. Portal Interface – databank content

26. Portal Interface - searching

27. Portal Interface – search results

28. Portal Interface – copying entries

29. Portal Interface – file properties

30. 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

31. 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

32. AminSim portlet (1)

33. AminSim portlet (2)

34. AminSim portlet (3)

35. AminSim portlet (4)

36. 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

37. 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