Posts tagged 'science'


Tips on designing, writing and debugging individual based simulations

This post was originally written in 2012, and was slightly updated in 2017.

When I first started writing stochastic, individual-based computer simulations in 2005, I thought it would be a pretty straightforward job. Although I’m technically a biologist, I already had quite some (self-taught) experience in C-programming and knew ...


Useful tricks with spatial data

For my research on Avian Influenza in waterbirds, I recently needed data on lakes and marsh-areas in Europe. I ended up compiling a spatial dataset from a number of different sources, including the EU Corine Land Cover database (CLC2000v13), the lake depth dataset compiled by Ekaterina Kourzeneva for the FLake ...


Scientific Software Favourites

Here’s a little list of software I regularly use for science-related work.

Zotero A highly useful reference manager implemented as a Firefox plugin (although there’s now also a Standalone-version, which works with Chrome, Safari and, well, stand-alone ;-). Especially useful are its features to retrieve citations and PDFs while ...


Fun With Shapefiles

Shapefiles are a format developed by ESRI (the makers of ArcGIS) to store and share geospatial data. Many interesting datasets are freely available in shapefile format. Shapefiles can be viewed with a number of freely available applications, such as ArcGIS Explorer (which requires the .NET framework or Silverlight) or ArcReader ...


Changing the evolutionary dynamics of Influenza?

An interesting news-article appeared today, claiming a possible breakthrough in the development of a universal influenza vaccine. It describes the development of a new influenza vaccine at the Jenner Institute. Traditional influenza vaccines prime the adaptive immune system against the hemagglutinin (HA) and neuraminidase (NA) proteins (the H and N ...


PDL, The Perl Data Language

PDL is an extension of Perl for numeric/scientific data processing. It was originally developed by astrophysicists as a free alternative to packages like IDL and Matlab. It’s quite fast and memory-efficient, and very powerful. I’ve found it to be most useful in cases where you have to ...


Data Clustering

I’ve written a fast perl/PDL implementation of UPGMA data clustering for very large datasets. The problem is that existing clustering packages have difficulty handling datasets with more than a few thousand data points. Especially the distance matrices tend to become a problem. For example, clustering the outcome of ...


Ubuntu Repository


The original repository was getting a bit outdated. It was trailing a few Ubuntu-releases behind and only had i386-builds. You can still use it for Hardy or manually download packages (see below) for installation on newer releases, but I’m no longer going to maintain the old ...