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Posts tagged ‘git’

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…)

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. (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

Software Carpentry

I really enjoy the environment of the DTC. We have recently started a weekly event called “Coffee, Cake and Science Talk”. Its main purpose is to get DTC students together and have a chat about their work (or unrelated things…) while enjoying some nice cake.

Last time we entered a really fruitful and encouraging discussion about making you research truly reproducible and coding practices. One website that got mentioned is Software Carpentry, which is exactly about writing code to make your research reproducible. I found this website particularly useful, since recently I had to go on a parameter goose chase for a model that I needed to reimplement.

The website mostly talks about things that actually are (or should be) common sense, but setting up repositories for your code or keeping exact track of software versions you use is a bit annoying. So at least I find it quite useful to be reminded of all these things. After looking at the website I set up a Git repository on Bitbucket, which gives you unlimited private repositories. Normally I would always be on the open source side, but if you’re working on a project that involves unpublished stuff, you might rather choose to not entirely open it to the public straight away.