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Archive for the ‘Research’ Category

Research Update

The last month I’ve spent working hard on my summer project, which is the last hurdle on my way to the “official” research part of my PhD Programme. Now, I finally had some time to tend to my website again and realised that I could do a much better job describing my research, which I have done now. I have also finally managed to fully resolve my supervisory team, which is made up of a whopping three people from engineering, mathematics and medicine. I feel truly interdisciplinary.

A Workflow for Reproducible Research

All research should be reproducible. This fact gets engraved into the brains of all potential researchers and that is for a very good reason. Reproducible research means it can be tested or improved by people in a different lab maybe at the other end of the world and it can also reveal mistakes that have been carried out during the research, which may have changed the results of the study altogether. I’d like to say that with peer reviews there is, in theory, a very efficient mechanism in place to ensure all published research is reproducible. On the other hand though, as the Retraction Watch blog shows us time and time again, it doesn’t always work and there are some bogus papers out there (and some researchers seem to be running some sort of a retraction leaderboard). (more…)

Phosphorus Dynamics & Lake Eutrophication

One of the projects I carried out as part of my PhD decision process is nearly finished now. Or let’s say it is finished, but I am still writing it up. I have published my Matlab code on my Git repository, so feel free to have a look.

I have reimplemented a model on lake eutrophication developed by Carpenter (2005). It is a very neat mathematical model that can predict eutrophication and algal blooms. However, this model does not take into account the role of the biota explicitly. I attempted to fill this gap, but had to discover that essential data to take out this model extension in a justifiable way is missing. Therefore my report will be a position paper that points out gaps in knowledge and gives suggestions on how to fill these gaps with the sampling of further lake data.

Carpenter S R: Eutrophication of aquatic ecosystems: bistability and soil phosphorus. Proceedings of the National Academy of Sciences of the United States of America 102 (29): 10002-10005, 2005

Research Update

My Research page still claimed that I am quite indecisive for what I want to do with that PhD position of mine. That has actually been untrue since January, because then I had finally decided that I will leave bioinformatics behind me and engage in more physical fluid dynamics simulations for medical research and Alzheimer’s Disease (AD) in particular. I am still quite unsure of what “field” that now leaves me with. Medical physics Simulation? With a big question mark attached to this I think I can deservedly claim to be in complex systems simulation.

Because I have trouble naming my research in less than 10 words I have finally got round to updating my research page. That also means that it is getting serious now. Soon I will have finished the first taught year in the DTC and in the remaining three years after that I will hopefully manage to answer at least a few of the many unresolved questions surrounding AD resulting in a doctorate degree.

Litmus Science & Poetry Event

Have you ever wondered what happens when scientists and poets work together? Register for the Litmus Science & Poetry Event on 18/03 during Multidisciplinary Week to find out!

Making science available for a broad audience is something that is very important to me. I’ve worked together with Gosport based writer Mark Iles and he has created a brilliant poem on eutrophication that will be exhibited in the Gallery above the Hartley Library until 22/03. After that it will go into Building 16, where I am working.

Litmus: Poetry & Science Event

Litmus: Poetry & Science Event

PhD Complex Systems Simulation

One month ago I have finally started my PhD in Complex Systems Simulation at the ICSS at the University of Southampton, UK. The first year will be a mostly taught MSc, followed by a three year PhD. This first year will give me the opportunity to explore different fields of research that interest me and could potentially make up the topic for my thesis. At the moment I am exploring ecological modelling to develop early-warning systems for ecosystems and modelling of the blood flow in human blood vessels. Although seemingly very different fields, they are joined by the tools to create appropriate models and the complexity of both systems.

SCCS 2012

I will be attending this year’s Student Conference on Complexity Science, which is held annually by the Complexity Science DTCs in Southampton, Bristol and Warwick.