Current need/availability: 1-2 projects, starting whenever possible.
Are you interested in doing a master thesis somewhere between engineering and research? It would officially be under KI, the Department of Bioscience & Nutrition (leading medical university in northern Europe!). We're involved in cutting-edge research in
As we are doing research, you should have in mind that anything we do will be state-of-the-art and hence rather demanding (or impossible!). While I have "safe" work with little theory and just programming, I will not list it here and anyone who wants this kind of work should explicitly ask for it.
Choice of language and libraries is semi-flexible. Producing quality code fast is however better than producing buggy fast code. Portability is a hard requirement. Normally we release under the newer BSD license. Recommended prerequisites:
Also check Nationella Exjobb-poolen, this list might be out of date.
There is a need for a good package for computational geometri written in
a modern programming language. Plenty of code exists, in Fortran, C,
C++ etc but usually not functional, with a useless license or we have trouble
using it in our code.
The aim is to implement state-of-the-art algorithms in a Java library, with a copyleft license, and make it available to the community. It is possible to publish an article on the work to receive technical citations.
You will learn java, searching & reading scientific articles, how to deal with the issues of floating point and basic computational geometry (voronoi, delaunay, complex hull etc).
Bioinformatics today tend to be a cut'n'paste experience deluxe. Data is taken from some sites and submitted to other sites via various web forms. Large
scale bioinformatics tend to mean more of the same thing. Some use perl to automatically submit data. Notepad and excel are used for databasing. If this
sounds horrible then this project is for you.
The aim is to make a new database that fits the need of biology. Much headache comes from SQL and relational databases which are unsuitable in the current form. Someone with ideas on what can be done is very wanted but I have some already; adding CVS semantics, sandboxing for remote execution and some OO semantics will improve the situation greatly.
The next thing is to design an open source replacement for Filemaker/Access but allow much larger customizations to add things like genome browsers, microarray views etc. In the end, biologists need be able to use it.
We wish to detect C.e nuclei from DIC images. If it worked out it would greatly improve the situation in the field but it is rather hard. If you are into image analysis then you have a challenge. Mail me to get up to date example images.
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