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RapidSeis: Enabling User-Defined Seismological Waveform Data Processing over the Grid

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talk

The objective of this JISC-funded pilot project was to remove perceived barriers to uptake of an application that performs analysis of seismic waveform data. The aim was to provide the seismological community with a simplified system that overcame important barriers such as installation and understanding of the analysis package, location and transfer of large amounts of input data and visualisation of results.

Date and time: 
Tuesday, 4 May, 2010 - 10:30
Location: 
European Geosciences Union, General Assembly 2010, Vienna, Austria
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Rapid featured in the newsletter of the Network of Research Infrastructures for European Seismology

RapidSeis: a NERIES spin-off pilot

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.

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RapidSeis: Rapid Portals for Seismological Waveform Data

Final project report for JISC, with links to all individually created deliverables and progress posts. RapidSeis has produced a scientific gateway via a web portal that allows seismologist to pick up data from Orfeus—the central repository for earthquake data in Europe—and then run several analyses on these data. Advanced users can also create new analyses and share these with all the other users.

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RapidSeis workflow explained

RapidSeis consists of two porlets that run within the NERIES portal. Both assume the user logged in has already filled his/her cart with seismological data.

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Screencast: Rapid Portals for Seismological Waveform Data

Welcome to the RapidSeis demo. This portal was created using Rapid and enables the use of Seismic Data eXplorer within the web portal of the Network of Research Infrastructures for European Seismology.

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Tutorial for Rapid

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.

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RapidSeis Workshop

At the meeting we will present the result of the RapidSeis project, a collaboration between ORFEUS, the UK National e-Science Centre and the University of Liverpool. Over the past six months, this project has created a system that facilitates running waveform analysis on data from ORFEUS where the computation is performed on remote compute resources provided by the University of Liverpool.

Location: 
Department of Earth & Ocean Sciences, University of Liverpool, UK
Dates: 
12 Nov 2009 to 13 Nov 2009
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Rapid portals improve teaching in practical sessions

Written by Nick Funnel (2nd year PhD in the School of Chemistry).

The lab has been much easier to teach this year.

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Apache's Virtual File system is part of Rapid's architecture

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).

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Unit-testing code is especially important in code-generating projects

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.

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Apache's Maven for management of code structure?

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.

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Rapid prevents a disaster in the classroom

For the first time, chemists at the University of Edinburgh are using a portal developed with Rapid to teach 140 undergraduates computational chemistry.

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Rapid Tutorial at Advanced Distributed Services Summer School

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tutorial

Tutorial on how to create a basic portlet with Rapid, which includes:

  • installation of required software
  • authentication to data and compute resources through username and password
  • transportation of data before and results after computation
  • use of rich user interface elements, such as a file browser and job monitoring
  • submitting the job to another computer
Date and time: 
Thursday, 10 September, 2009 - 09:00
Location: 
Advanced Distributed Services Summer School 2009, Coseners House, near Oxford
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Happy end user of Rapid gives praise

"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.

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Next Generation Embryology

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talk

We introduce the Next Generation Embryology project: Next Generation in two ways. First, because its aim is to revolutionise the way the next generation of developmental biologists are educated. Where instead of relying on plastic models and diagrams in books, the idea is to use a digital library that is indexed using virtual 3D models of mouse and human embryos.

Date and time: 
Wednesday, 8 July, 2009 - 09:00
Location: 
JISC Information Environment and Virtual Research Environment projects start-up meeting, Leicester, UK
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