Short courses in 'Practical High Throughput Bioinformatics'

Lead Research Organisation: Imperial College London
Department Name: Biological Sciences

Abstract

Bioinformatics in essence, is the use of computers for the analysis and management of biological data. As biological research embraces new techniques and new technologies, the data being generated increases continually both in terms of the absolute volume and in the speed of its creation. In order to understand the biological meaning of these data we need to be able to efficiently analyse them, and to do this we use bioinformatics. The necessary analyses are also increasing in size and complexity as our knowledge and data increase, and also as new methods of analysis are discovered. Larger data sets and more complex analyses are using ever-increasing computer resources and recently e-science reseach has produced new methods to spread the computing load across a community of computers, perhaps on different sites, rather than relying on individual ones. We aim to produce a training course which will assist bioinformaticians, particularly those starting out on their career to learn the use of some of these new methods in order to improve their research and ability to handle the ever increasing volumes of data efficiently.

Technical Summary

This project aims to produce a new set of training materials suitable for production of a one week intensive training course on 'practical high throughput methodologies for bioinformatics'. The proposed course is aimed primarily at bioinformaticians (particularly young ones) who need a rapid focussed practical introduction to the application of some of the newer methodologies coming out of the high throughput and e-science arenas into the bioinformatics arena - such as job scheduling and management using grid engine, GLOBUS and CONDOR, web services, Distributed annotation systems (DAS) and AccessGrid. The course will be carefully tailored using examples specfically drawn from common bioinformatics tasks and scenarios and will be developed and taught jointly by a group comprising computer scientists who develop, deliver and maintain the technologies in question and bioinformaticians who use and support them in current bioinformatics research applications

Publications

10 25 50
 
Description The grant was an award to develop and deliver a training course. The main development was the production of a full set of high quality lecture and practical tutorial course materials which together comprise a one week duration self-contained course on 'High throughput computing for bioinformatics'. In addition to developing the course materials themselves, the course 'High throughput computing for Bioinformatics' was delivered on 3 separate occasions, to a total of 50 participants of whom 22 were BBSRC-funded researchers/students. Participants were drawn from 22 different institutions, with a number sending participants on all 3 courses.
Exploitation Route The course notes were used in aspects of delivery of other training courses. Inter-disciplinary expertise and collaborations honed during the project have been maintained and have formed the basis of other successful joint research funding in the area of cloud-based computing and workflows.
Sectors Agriculture, Food and Drink,Education,Healthcare

 
Description The successful delivery of this course on 3 separate occasions, to a total of 50 participants of whom 22 were BBSRC-funded researchers/students. Participants were drawn from 22 different institutions, with a number sending participants on all 3 courses. Furthermore,62% students rated the course overall as good/very good in meeting its objectives and a further 33% rated it excellent (15% questionnaires were not returned/ non-responders) and 92% said they would recommend it to colleagues (remainder were non-responders)
First Year Of Impact 2008
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description EPSRC responsive mode
Amount £116,322 (GBP)
Funding ID EP/K038877/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start 07/2013 
End 06/2015
 
Description EPSRC/JISC cloud pilot
Amount £14,909 (GBP)
Funding ID EP/I034246/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start