About me

Currently I am a Ph.D. student at the Bioinformatics Research Center at Aarhus University in Aarhus, Denmark, though my background is in Computer Sicence. I expect to finish my study in the Summer of 2011.

The university maintains an official publications list.

I can be reached by e-mail at jn@cs.au.dk, or you can call me at my work phone (+45)89423187.

Software

During my study I have written a fair amount of software, most of it research related:

c2flib

c2flib is a C++ library for coarse-to-fine k-best viterbi. Along with the C++ code comes a set of command line tools that may be enough for many purposes. The library has been developed and testet using Linux, OS X and Windows 7, with MSYS and MinGW. Use CMake to build the project. c2flib has no other dependencies.

c2flib 1.0.0 source may be downloaded here. See the included README file for installation and usage instructions.

parredhmmlib

parredhmmlib is a C++ library for parallelization of Hidden Markov Models with a small state space. Details here.

Inverted indices and LINGOs

Software for computing LINGO scores, based on the inverted indices datastructure. Found here.

TanimotoQuery

By storing chemical fingerprints in trees one can quickly find molecules similar to a given query-molecule. Download here.

SNPFile

Back, when I was a student programmer I worked on a C++ library and file format for efficient storage of SNP data called SNPFile.

HPCanvas

Slightly unrelated I also experimented with using the HTML5 canvas tag and javascript to make a score counter and visualizer for HP folding. Find it here. All of it is contained in one singl HTML file, with no dependencies on images or external scripts.

TCCal

Not related to research at all, but I hacked together an iGoogle gadget for showing the next upcomming TopCoder events.