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MSc student project

A project suitable for an MSc project of three months.

Analysing Spatio-Temporal Gene-Expression Data

Student: 
Lihao Liang
Grade: 
first

In modern scientific researches, a lot of computer programs have been developed for scientists to do different computation or analysis on their data. And database technologies are commonly used in e-Science community to store massive mount of scientific data. But the challenge still exists.

Project status: 
Finished
Degree level: 
MSc
Supervisors @ NeSC: 
Other supervisors: 
Richard Baldock (Human Genetics Unit, MRC)
Subject areas: 
Bioinformatics
Distributed Systems
Other
Software Engineering
Student project type: 

Wrapping Tools to Automate Workflows for Gene Therapy in Cystic Fibrosis

Student: 
Rob Kitchen
Grade: 
first

The cystic fibrosis group in the Molecular Medicine Centre (MMC) at the Western General are developing gene gene therapies to treat cystic fibrosis, a life-threatening hereditary disease. To understand which genes are responsible for the disease, and which genes may have diagnostic or prognostic value, they go through a long process of laboratory experiments and analysis, involving microarray experiments and several types of statistical tests. Many of the laboratory experiments are currently automated, but all of the analysis and data handling steps require human interaction.

Project status: 
Finished
Degree level: 
MSc
Background: 
This requires someone with versatile skills. You must be able to communicate well and work closely with the users of your system at the MMC. Moreover, you should expect messy text files and existing software, and while we expect you to program clean web services to hide all the mess for future generations of e-Science students.
Supervisors @ NeSC: 
Other supervisors: 
Varrie Ogilvie (Molecular Medicine Centre, University of Edinburgh)
Subject areas: 
Bioinformatics
Databases
Other
Software Engineering
References: 
What is cystic fibrosis? http://en.wikipedia.org/wiki/Cystic_fibrosis The group you will work in: http://www.genetics.med.ed.ac.uk/ Tavera, a workflow tool: http://taverna.sourceforge.net/
Student project type: 

Building Gene Homologs Web Services

Student: 
Ian Archibald

An important way of understanding genetic diseases in humans is to perform research on animal models, such as mice. Unfortunately, mapping genes from one species to another is not straightforward. Some data are available to map genes from one species to another, but where these data do not exist, other approaches are required. This could involve running so called blast queries to determine the most likely candidates.

Project status: 
Finished
Degree level: 
MSc
Background: 
This requires a person that is willing to search for information on its own and is willing to communicate with domain experts (i.e., bioinformaticians and biologists). You will need to program the web services and deploy these in Tomcat. Moreover, you will need to call other web services to perform the more advanced methods of linking.
Supervisors @ NeSC: 
Other supervisors: 
Richard Baldock (Human Genetics Unit, MRC)
Subject areas: 
Bioinformatics
Databases
Other
Software Engineering
References: 
The Edinburgh Mouse Atlas (EMAGE) http://genex.hgu.mrc.ac.uk/ The human equivalent of EMAGE, the Electronic Atlas of the Developing Human Brain: http://www.ncl.ac.uk/ihg/EADHB/ What does homology means in the context of genes: http://en.wikipedia.org/wiki/Homology_%28biology%29#Homology_of_sequences_in_genetics An example of a web page to search for homolog genes http://bioinfo.cnio.es/cgi-bin/db/homologene
Student project type: 

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