Imperial College London

Ms Jacintha Mack Smith

Faculty of MedicineDepartment of Metabolism, Digestion and Reproduction

Data Science Engineer - Bioinformatics
 
 
 
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Contact

 

j.mack-smith

 
 
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Location

 

126Sir Alexander Fleming BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
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2 results found

Mack Smith J, 2008, Adding Standards Based Job Submission to a Commodity Grid Broker, eScience, 2008. eScience '08. IEEE Fourth International Conference

Journal article

Barton G, Abbott J, Chiba N, Huang DW, Huang Y, Krznaric M, Mack Smith J, Saleem A, Sherman BT, Tiwari B, Tomlinson CD, Aitman T, Darlington J, Game L, Sternberg MJE, Butcher Set al., 2008, EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management, BMC Bioinformatics, Vol: 9, ISSN: 1471-2105

BackgroundMicroarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management.ResultsEMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms.ConclusionEMAAS enables users to track and perform microarray data management and analysis tasks through

Journal article

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