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The Next Generation Embryology project is funded by JISC (Joint Information Systems Committee), a sponsor that supports education and research by promoting innovation in new technologies. The attached PDF flyer provides a brief introduction to the main aims of the project.
The objective of this six-month pilot project was to provide a simplified system to perform analysis of seismic waveform data through a web browser. The specific aims were that no data or application be download to the user’s computer, for the user to create algorithms to customise the analysis and to allow sharing of algorithms within the seismological community.
Henceforth we will call ourselves the Data-Intensive Research Group. Where data-intensive refers to huge volumes of data, complex patterns of data integration and analysis and intricate interactions between data and users.
As a young researcher, I was intrigued by Lance Fortnow's explanation (Aug. 2009) of why the CS community is dominated by conference proceedings. However, I was less excited by his proposed solution, that "...leaders of major conferences must make the first move, holding their conferences less frequently and accepting every reasonable paper for presentation without proceedings." I fear such a move would not have the intended effect of a more journal-focused community.
This brief tutorial covers the installation of Rapid and the components it depends on. It explains how to get a simple portlet running and then increases the complexity of this portlet to include more functionality by exploiting Rapid's features.
Apache's Virtual File system helped us to access different file systems transparently. The Rapid project implemented a new 'GSIFTP' (Grid Security Infrastructure File Transfer Protocol) module, which adds Grid connectivity to the set of supported file systems. This sub-project of Rapid, spawned the commons-vfs-grid module (http://sourceforge.net/projects/commonsvfsgrid/) which now supports GSIFTP, SRB (Storage Resource Broker) and iRods (https://www.irods.org).
The use of testing frameworks, such as Junit is extremely valuable. It takes quite a bit of discipline to write new unit tests for each new piece of 'real' code that is written, but the benefits in the end in terms of stability, confidence and debugging make the extra overhead more than worth it. This is especially useful in a project such as Rapid, where code is being generated. Testing in the 'traditional' way, by examining or running generated code is extremely difficult and by using testing frameworks we can actually determine correctness of Rapid, before running any generated code.
Apache's Maven project management tool (http://www.apache.org) helped the Rapid team structure code modules in a 'standardised' way. It helps managing dependencies and facilitates distributing the final product as dependencies are automatically downloaded and do not need to be packaged separately. However, the learning curve is rather steep and even now we sometimes have to go back to ANT (http://ant.apache.org/) to accomplish certain tasks.
The research group of the National e-Science Centre in Edinburgh has moved to the Informatics Forum to become more integrated with the Informatics research culture. Our new address:
School of Informatics
Informatics Forum
10 Crichton Street
EH8 9AB Edinburgh
United Kingdom
"Just wanted to say that the Jython plugin tag in the new Rapid version is really useful. I have just started playing with it and have managed to create a portlet that gets the batch job lists back from various hosts and also now enables you to select a job using a radio button and then delete it or view it in more detail - no hack scripts required! I can also dynamically set the batch system commands so I can handle hosts that use SGE, PBS ot LoadLeveller with no external input required.
Portlets make inaccessible technology accessible, because they run from within a browser – a familiar interface for even the most technophobic researcher. To encourage the use of portlets, it is necessary for them to be easy to develop. This led OMII-UK to fund Rapid, an easy-to-use portlet development tool. Chemists from the Universities of Edinburgh and St. Andrews (EaStCHEM) have recently used the software to create portlets that have allowed access to computational-chemistry software by over 140 students.
Download the flyer for Rapid, which explains in brief and non-technical terms how it works.
