Kreft Lab: University of Birmingham

Postdoctoral Positions

There are currently no postdoctoral positions being advertised for our group

PhD Students

Please go to Find a PhD to view PhD opportunities in the Kreft group.

Undergraduate and Masters Student Summer Projects

University of Birmingham Computer Science Final Year Undergraduate / Masters Student Project
To be undertaken between June and September 2013

Final year undergraduates / masters project students have the opportunity to contribute towards the development of eGUT this summer. This short project will provide you with a good grounding in the use of computational tools to further our understanding of biological systems.

We have been awarded funding to create individual-based computational tools to reduce or replace the need for animal experimentation required to understand how the gut affects human health. For a full background on our project, you can read the grant proposal here.

You will work with our research fellow, Kieran Alden, and investigators within the Kreft lab to develop our simulation further. You will be tasked with adding some extra biological features (such as a cell type) to our simulation. Initially, you will need to do some reading to understand the role this new biological feature plays in the gut. You will then create a specification of how this behaviour can be encoded in our simulation. Once this is agreed with our collaborating microbiologists, you will be tasked with coding this behaviour in Java. Should there be time remaining, we will then run some simulations and attempt to understand how this new feature affects the formation of biofilms in the gut.

We are however open to suggestions and can tailor the project based on your experience and ambitions.

Project Requirements:

The simulation has been developed in Java, and you will need a good understanding of how to program in this language.
Previous experience of R, MATLAB, and/or Python would be advantageous for analysing results.
An interest in using computational tools to further understand biological systems
A willingness to learn a little microbiology (but not too much!)
Experience of using Eclipse and Github would be beneficial but we can introduce this to you

Some Background Reading:

iDynomics – the simulator on which the work will be based (Lardon et al)
Background to computational models and how these are specified / designed (Alden et al)

More Information - contact Dr Kieran Alden to discuss in person on campus or via email (k.j.alden@bham.ac.uk)