New free eBook: The Fourth Paradigm

October 16th, 2009

The UK e-Science programme always recognised the importance of data. The Fourth Paradigm recognises that data-intensive science is dramatically changing the way research is performed, and is an excellent compendium of progress with this new approach. It is also dedicated to the memory of Jim Gray, who christened data-intensive research “The New Paradigm”, who shaped the transactional model of databases we all depend on, who led Microsoft into supporting the Sloan Digital Sky Survey and into developing new database technology to support data-intensive research. Sadly, Jim was mysteriously lost at sea in January 2007.

The book has several connections with UK e-Science since the prime mover and first editor is Tony Hey. OMII-UK PIs, Carole Goble and Dave De Roure, have both written chapters in the book and are attending the book launch at the Microsoft e-Science conference in Pittsburgh today.

The book will be available for free download from the website (at 9.00am East Coast time and 2.00pm UK time):

In addition, the New York times also had a highly relevant article this week:

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Software Sustainability: Looking Past the Myths

October 12th, 2009

Neil Chue Hong, the Director of OMII-UK, will be presenting a public lecture ‘Software Sustainability: Looking Past the Myths’, at the e-Science Institute, Edinburgh on 29 October 2009 at 4.00pm UK time (GMT+1).

Further information can be found on the lecture web page .

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Setting up OGSA-DAI 3.2 and playing with DQP

October 2nd, 2009

I was keen to play with DQP so I decided to test it by pulling data from two databases. I have found the documentation descriptive enough but I will write the procedure I followed. Hopefully, it will be helpful to some.

I want to deploy OGSA-DAI Axis on Tomcat. I have a MySQL database on my machine and a Postgres database on another machine. My plan is to use DQP (which is bundled in OGSA-DAI 3.2) to do a join across these databases. I will deploy OGSA-DAI on my machine. I will then deploy two data resources, one for each database, and a DQP resource that includes these two resources. Finally, I will run some queries.

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OGSA-DAI 3.2 released

October 1st, 2009

The OGSA-DAI project, a partner in OMII-UK, have released version 3.2 of their database access and integration software.

OGSA-DAI is an extensible framework for the access and management of distributed heterogeneous data resources – whether these be databases, files or other types of data – via web services. OGSA-DAI provides a workflow engine for the execution of workflows implementing data access, update, transformation, federation and delivery scenarios.

 The main features of OGSA-DAI 3.2 are as follows:

OGSA-DAI 3.2 now includes Distributed Query Processing (DQP).

  • DQP allows the tables from multiple distributed relational databases to be queried, using SQL, as if there were multiple tables in a single database. These databases are exposed via OGSA-DAI servers.
  • DQP was originally designed and developed by at the University of Manchester and the University of Newcastle upon Tyne. Previous versions of DQP were released as a separate product – OGSA-DQP.
  • DQP has now been rewritten and is now simply an extension to OGSA-DAI. DQP’s functionality is now exposed as OGSA-DAI resources and activities and accessed via OGSA-DAI’s standard services. This greatly simplifies deployment and enables extensibility within a single framework.

Non-blocking data sinks that allow data pushed to OGSA-DAI from a client to be cached until it’s ready to be processed.

A new monitoring framework which tracks the data blocks produced and consumed by each activity in a workflow.

Support for relational database-specific meta-data extractors and mappers from JDBC column types to OGSA-DAI tuple types.

New security activities for passing client credentials through workflows and retrieving credentials from a Globus Delegation Service.

More efficient GridFTP activities.

A number of bugs have been fixed, components made more efficient or robust.

Unlike previous versions of OGSA-DAI, OGSA-DAI 3.2 only compiles under Java 1.5 and not Java 1.4. Apart from this, OGSA-DAI 3.2 is designed to be backwards compatible with OGSA-DAI 3.1 without the need for recompilation – data resource, activity and presentation layer APIs and service WSDLs remain the same.

OGSA-DAI is a free, open source, 100% Java product and is released under the Apache 2.0 licence. Downloads compatible with Apache Axis 1.4, Globus 4.0.8 and Globus 4.2.0, are available

To download OGSA-DAI 3.2 visit: http://sourceforge.net/projects/ogsa-dai/files/

OGSA-DAI 3.2’s user doc is at

http://sourceforge.net/apps/trac/ogsa-dai/wiki/UserDocumentation/ogsadai3.2

and the release notes at:

http://ogsa-dai.sourceforge.net/documentation/ogsadai3.2/ogsadai3.2-axis/Release.html

http://ogsa-dai.sourceforge.net/documentation/ogsadai3.2/ogsadai3.2-gt/Release.html

To find out more about OGSA-DAI visit our project WWW site at

http://www.ogsadai.org.uk

and our open source project site at

http://sourceforge.net/projects/ogsa-dai

The OGSA-DAI project – which involves both EPCC and NeSC – is funded by EPSRC through OMII-UK. For further information about OMII-UK visit

http://www.omii.ac.uk.

Cheers, mike

On behalf of the OGSA-DAI team.

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OGSA-DAI source code on SourceForge

October 1st, 2009

OMII-UK’s OGSA-DAI project is currently in the process of transforming itself from being an open source product to an open source project, encouraging an open development model so that the OGSA-DAI community can become more involved in future development of OGSA-DAI. As part of this process we are migrating our source code to reside in an open source project site hosted by SourceForge.

The initial upload of our new Subversion repository can now be browsed online at:

http://ogsa-dai.svn.sourceforge.net/viewvc/ogsa-dai/

or can be anonymously checked out using an SVN client:

http://sourceforge.net/scm/?type=svn&group_id=261620

Please see our SourceForge SVN pages for full information on how to check out the code using an SVN client, the repository structure, how to build it and how to run unit and system tests within your own environment:

http://sourceforge.net/apps/trac/ogsa-dai/wiki/OGSADAISubversion

If you would like to get involved please see our governanace model at:

http://sourceforge.net/apps/trac/ogsa-dai/wiki/GovernanceModel

There is also an e-mail list – ogsa-dai-svn-commits@lists.sourceforge.net - that you can subscribe to if you want to be notified of source code commits, see:

http://sourceforge.net/mail/?group_id=261620

Over the next month we will be migrating additional code into this repository to bring it into alignment with our OGSA-DAI 3.2 release. This includes adding DQP which is now an integral part of the OGSA-DAI product.

Cheers,

mike

On behalf of the OGSA-DAI project team.

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OMII-UK e-Research survey

September 29th, 2009

OMII-UK is carrying out a survey to find out what you know about e-Research? Let OMII-UK know, and you could win a £20 Amazon voucher.

OMII-UK are looking for volunteers to fill in a ten-minute survey.

Completing the survey not gives you the chance to win an Amazon voucher, it also means that you will be directly contributing to development of the software and support that is needed by the research community.

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September OMII-UK Newsletter Out Now

September 11th, 2009

This issue of the OMII-UK newsletter talks to some of the big names in e-Research. Anne Trefethen from OeRC talks about e-Research South: a new consortium that will embed e-Research technologies in the research community, and Ross Gardler from OSS Watch talks about why he thinks that open development is the key to sustainability.

You may obtain copies of the newsletter in the following formats:

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Secure Deployment of OGSA-DAI on to GT4.2

August 19th, 2009

In order to do a secure deployment of OGSA-DAI on to GT4.2 I found that there were a number of changes to what is described in our documentation (mainly pertaining to the security descriptors). Thus in:

http://ogsa-dai.sourceforge.net/documentation/ogsadai3.1/ogsadai3.1-gt/AdminSecurityGT42.html#AdminSecurityGT42MethodsAndLevels

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OMII-UK CSP Funding

July 13th, 2009

Call for Proposals in Data and Information Management

OMII-UK identifies gaps in the provision of e-Research software and commissions developers to produce software accordingly through its Commissioned Software Programme (CSP).

At this time, OMII-UK invites organisations to submit funding proposals for software development projects which address the changing needs of the research community in its ability to deal with data and information.

Some of the drivers for this include: increased access to machine-readable public data sets; use of in-silico experimentation; emergence of storage clouds; lack of integration between different data storage mechanisms and data analysis frameworks and tools; and additional requirements for data curation, integrity and provenance.

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ADS Summer School 2009

July 3rd, 2009

There are still places left for the Advanced Distributed Services Summer School (ADSSS) 2009. The aim of this summer school is to help develop the skills of those involved in providing computational support for research in a wide range of disciplines. ADSSS will be taking place at Coseners House in Oxfordshire in the UK from the 7th-11th of September. More details are available from their web site: http://www.iceage-eu.org/adsss09/index.cfm

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