## Personal Website.

### 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). Read the rest of this entry »

### Photos on Flickr

I’ve got myself an account on Flickr a while ago and after an amazing holiday in Alaska I finally uploaded some pictures into it. I’ve also got myself a new camera, a used Canon EOS 5D, which had its first outing at the F1 Young Drivers’ Test in Silverstone last week. I think I got quite good results there. And I will pass on the advice that if you’re thinking about getting an SLR, consider buying a used professional full-frame camera instead of a new crop. The original Canon EOS 5D is only about 350£ on eBay since the Mark III has come out.

### LaTeX Template for Dissertations

The summer project that marks the end of year 1 of my PhD and the beginning of my actual research is going to start very soon. On that occasion I thought it would be a good idea to recycle my old dissertation template for $\LaTeX$ and make it publicly available. It is based on a template that was available from one of the computer science groups at my old university and I’ve modified it to fit the requirements of our summer project module. The main idea behind it is to have every chapter of the dissertation in a different file, which makes the handling of large documents, such as a dissertation, a lot easier. Read the rest of this entry »

### One Hour on Procrastination

Procrastination – we all do it (admittedly or not admittedly) and we presumably all hate that we’re doing it. I’m doing it right now. Tuesday evening we Southamptoners were lucky enough to enjoy a talk by Jorge Cham, the creative mind of PhD comics. His presentation was called “The Power of Procrastination” and like the comics just hits the nail on its head. Very often I find myself thinking or saying to someone “Oh my god, I could be and should be doing work right now and I won’t even have any time to sleep anymore” and find myself browsing the internet five minutes later. But Jorge’s talk gave me a new viewpoint on the whole topic and can probably help keeping many PhD students sane. Read the rest of this entry »

### 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.