Be Involved with the Development of eGUT - Project Ideas

Here are three potential projects that we need help with over the summer. If these are of interest, send us an email ( But if there is something else you want to contribute why not get in touch and ask about that too.

1. User Interface for eGUT/iDynoMiCS

eGUT is being built upon a previously published simulator called iDynoMiCS. This has a fairly large number of users, and is also is constant development in the Kreft Lab. At the moment, users specify their simulation choices in XML tags in a text file. Although this works well, we feel that more people may use the software if it had a nice graphic interface that helps them build their simulation. We're not looking for anything very complicated: just a few screens that help the user make choices on how their simulation runs. We're open to ideas on how this is built: could be in Java, Python, PHP, and maybe others

2. Code Profiling and Checking

eGUT will be an agent-based simulator. What this means is that each 'cell' is its own object: it has its own behaviour, state and variables. For some simulations where there are a large number of species, a lot of memory is required and the simulation can run quite slow. So we are interested in knowing what parts of the simulation take the most time, and whether these could be improved. To do this, we intend to run the simulator and use a profiler to examine the behaviour of the code, and then examine the parts that take a while to run. This could be an interesting project if you are interested in code performance. If we can improve parts of our code that run slowly, we may then be able to run more complex biological simulations

3. Materials for Public Engagement

Letting other researchers and the general public know what we are doing is an important part of research here at Birmingham. We would be interested in hearing from anyone who has an interest in making media material that could help us here. This could include videos that demonstrate the current software or state what we are trying to do, maybe sound clips such as podcasts, or printed material. If this interests you we can discuss these ideas further.

University of Birmingham | Centre for Systems Biology | Institute of Microbiology and Infection | School of Biosciences | Find The Lab