Beasiswa S2 di Ireland
MSc Fellowship: Design and implementation of a web-based microarray analysis system
MSc Fellowship: Teagasc, Animal Production Research Centre, Athenry, co. Galway
Design and implementation of a web-based microarray analysis system
Project Background
Microarrays are now widely used for gene expression profiling in many animal science-based experiments. Raw data emanating from microarray experiments, however, are very noisy and there are many sources of variation and bias. The raw data needs to be quality assessed and interactively “pre-processed” to minimise or remove this variation before statistical analysis in order to achieve any meaningful result. This requires a combination of visualisation and statistical tools which vary depending on what microarray platform or experimental design is used.
A number of stand alone tools based on the statistical software R and Bio-conductor routines are readily available for these types of analyses. However, the analysis pipeline is not always clear to the user, and the desired tools are not always available from the one source, without resorting to a command line interface, unfamiliar to most users. A user friendly interface is required to facilitate the pre-processing and analysis of microarray experiments in Teagasc addressing the most common microarray platforms and following a logical progression through an analysis pipeline that is extensible and capable of addressing current as well as future needs.
Objective
To set up a bio-informatics web server running Linux with core bio-informatics software. To design and implement a web based microarray analysis system with core and extensible functionality based on R and bio-conductor capable of addressing the current and future microarray pre-processing and analysis requirements of Teagasc research programmes.
Position
A post-graduate position is available to work on all aspects of the research project outlined above.
Requirements
Applicants should have a good primary degree (1 or 2.1) with a significant component in computing. Good quantitative data skills are essential and some knowledge of biology and bioinformatics would be a distinct advantage. It is expected that the successful candidate will register with the Mathematics Department, NUIG for a Masters degree.
Funding
The position is funded by a Teagasc Walsh Fellowship of €21,000/pa to cover postgraduate stipend and tuition fees.
Location and supervision
The student will be located, for approximately 50% of the time at the Teagasc, Animal Production Research Centre, Athenry, Co. Galway, and for the remainder at the Department of Mathematics, NUIG.
The University supervisors will be Prof John Hinde Mathematics Department and Dr Aaron Golden Information Technology and NCBES Bioinformatics Research Group, NUIG; and the Teagasc supervisor will be Dr Dermot Morris, Teagasc, Athenry.
Starting date
The project will start at the beginning of September 2007. Students will be required to register for a Masters degree at NUIG (to be completed by end of August 2009).
Application procedure
Applicants should submit curriculum vitae, detailing their qualifications and experience, together with a covering letter stating why they wish to pursue this project, by Friday, 1 June 2007. Applications should be sent by post or email to:
Prof John Hinde
Department of Mathematics
National University of Ireland Galway
Galway
john.hinde@nuigalway.ie
or
Dr Dermot Morris
Teagasc
Animal production Research Centre
Mellows Campus
Athenry
County Galway.
dermot.morris@teagasc.ie
http://www.teagasc.ie/research/postgrad/pgf20070430b.htm
MSc Fellowship: Teagasc, Animal Production Research Centre, Athenry, co. Galway
Design and implementation of a web-based microarray analysis system
Project Background
Microarrays are now widely used for gene expression profiling in many animal science-based experiments. Raw data emanating from microarray experiments, however, are very noisy and there are many sources of variation and bias. The raw data needs to be quality assessed and interactively “pre-processed” to minimise or remove this variation before statistical analysis in order to achieve any meaningful result. This requires a combination of visualisation and statistical tools which vary depending on what microarray platform or experimental design is used.
A number of stand alone tools based on the statistical software R and Bio-conductor routines are readily available for these types of analyses. However, the analysis pipeline is not always clear to the user, and the desired tools are not always available from the one source, without resorting to a command line interface, unfamiliar to most users. A user friendly interface is required to facilitate the pre-processing and analysis of microarray experiments in Teagasc addressing the most common microarray platforms and following a logical progression through an analysis pipeline that is extensible and capable of addressing current as well as future needs.
Objective
To set up a bio-informatics web server running Linux with core bio-informatics software. To design and implement a web based microarray analysis system with core and extensible functionality based on R and bio-conductor capable of addressing the current and future microarray pre-processing and analysis requirements of Teagasc research programmes.
Position
A post-graduate position is available to work on all aspects of the research project outlined above.
Requirements
Applicants should have a good primary degree (1 or 2.1) with a significant component in computing. Good quantitative data skills are essential and some knowledge of biology and bioinformatics would be a distinct advantage. It is expected that the successful candidate will register with the Mathematics Department, NUIG for a Masters degree.
Funding
The position is funded by a Teagasc Walsh Fellowship of €21,000/pa to cover postgraduate stipend and tuition fees.
Location and supervision
The student will be located, for approximately 50% of the time at the Teagasc, Animal Production Research Centre, Athenry, Co. Galway, and for the remainder at the Department of Mathematics, NUIG.
The University supervisors will be Prof John Hinde Mathematics Department and Dr Aaron Golden Information Technology and NCBES Bioinformatics Research Group, NUIG; and the Teagasc supervisor will be Dr Dermot Morris, Teagasc, Athenry.
Starting date
The project will start at the beginning of September 2007. Students will be required to register for a Masters degree at NUIG (to be completed by end of August 2009).
Application procedure
Applicants should submit curriculum vitae, detailing their qualifications and experience, together with a covering letter stating why they wish to pursue this project, by Friday, 1 June 2007. Applications should be sent by post or email to:
Prof John Hinde
Department of Mathematics
National University of Ireland Galway
Galway
john.hinde@nuigalway.ie
or
Dr Dermot Morris
Teagasc
Animal production Research Centre
Mellows Campus
Athenry
County Galway.
dermot.morris@teagasc.ie
http://www.teagasc.ie/research/postgrad/pgf20070430b.htm
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