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Student projects

Below follows a list of project descriptions for students. Some of the projects are finished, some are in progress, and some are still available to students that want to do a UG4, MSc or a PhD projects.

If you want to do an MSc or PhD with us then you need to go through the application procedures set by the School of Informatics. Make sure you discuss your research proposal first with Malcolm Atkinson or David Robertson. Important to note: you need to apply under Intelligent Systems & their Applications.

List of projects

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: 

GridDrive: Using sshfs to access the Grid

Student: 
Ciaran Hearne
Grade: 
first

To patch sshfs to make it work with Grid certificates, then install it on a Linux machine and mount a directory on a machine that is part of the National Grid Service.

Project status: 
Finished
Degree level: 
UG4
Background: 
You must like hacking Linux kernels and understand the idea behind ssh authentication, and be a proficient C programmer.
Supervisors @ NeSC: 
Subject areas: 
Computer Architecture
Distributed Systems
Other
Software Engineering
Student project type: 
References: 
SSHFS & FUSE http://fuse.sourceforge.net/sshfs.html National Grid Service http://www.grid-support.ac.uk/ x509 proxy certificates http://www.ietf.org/rfc/rfc3820.txt x509 patch for SSH http://roumenpetrov.info/openssh/

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