Edinburgh Data-Intensive Research

ISBN:

978-0-7695-4039-9

Abstract:

Proteomics, the study of all the proteins contained in a particular sample, e.g., a cell, is a key technology in current biomedical research. The complexity and volume of proteomics data sets produced by mass spectrometric methods clearly suggests the use of grid-based high-performance computing for analysis. TOPP and OpenMS are open-source packages for proteomics data analysis; however, they do not provide support for Grid computing. In this work we present a portal interface for high-throughput data analysis with TOPP. The portal is based on Rapid, a tool for efficiently generating standardized portlets for a wide range of applications. The web-based interface allows the creation and editing of user-defined pipelines and their execution and monitoring on a Grid infrastructure. The portal also supports several file transfer protocols for data staging. It thus provides a simple and complete solution to high-throughput proteomics data analysis for inexperienced users through a convenient portal interface.

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The inherent limits to the predictability of brittle failure events such as earthquakes and volcanic eruptions are important, unknown, and much debated. We will establish techniques to determine what this limit is in the ideal case of controlled laboratory tests, for the first time in real-time, prospective mode, meaning before failure has occurred.

Develop domain-specific web portals for submitting and managing corresponding compute jobs on the HECToR National Supercomputing Facility (http://www.hector.ac.uk/) in order to reduce the current failure rates and lower the barrier of uptake to new user groups.

Not every user knows how to submit a compute job by a remote login or to adapt to different job- submission systems when switching between facilities. In recognition, a recent trend is to provide web portals as an interface, which come in two types, each with its own major drawback.

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.

To work on producing a combination of Rapid and Taverna that will enable delivery of Taverna workflows with customised portal interfaces.

Josep is a postgraduate student at the Computer Science Department. He is visiting our group as part of the HPC-EUROPA2 programme where he will use our expertise on web portals and parallel computing for the Parallel-TCoffee sequence alignment software.

Principal goal: to extend Rapid, a tool for developing web portals for scientific computing, to operate with jclouds.

This is project is part of the Google Summer of Code 2010 (see http://www.omii.ac.uk/wiki/RapidJclouds)

Principal goal: to extend Rapid, a tool for developing web portals for scientific computing, to operate with Apache Hadoop.

This is project is part of the Google Summer of Code 2010 (see http://www.omii.ac.uk/wiki/RapidHadoop)

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.