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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.

The goal of your project is to outline the analysis processes, then wrap the individual steps and tools as web services. Finally, you will use a workflow tool, such as Taverna, to run those processes by calling the appropriate web services. Currently, one analysis takes the researchers two weeks; it is your goal to reduce this time considerably. If time permits, you will design, and perhaps implement a portal interface to the individual workflows.

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: