libXmu.so.6 and libgthread-2.0.so.0 error, or getting Wolfram CDF Player working on Ubuntu

Recently a colleague sent me some information on his model and a bunch of Mathematica .nb files. I don’t use Mathematica (if I felt the need for that kind of thing I’d go for Sage) and I don’t have access to it, so I started looking around for a way to export the notebook, say to pdf. I found an online nb to pdf converter … Continue reading libXmu.so.6 and libgthread-2.0.so.0 error, or getting Wolfram CDF Player working on Ubuntu

Basic mercurial commands

I’ve started using the Mercurial version control system. I like that it doesn’t leave a whole heap of files around, just one .hg directory. The commands to get started are fairly straightforward: hg init . hg status: Look at what is included or not. hg add *: Add everything in the directory. hg commit: Here you can enter some initial comment about the repository hg … Continue reading Basic mercurial commands

Installing Sphinx

Many times I have found someone’s log of an installation of some new software incredibly useful, so here’s my log from installing Sphinx a while ago. First I followed the instructions in the Sphinx tutorial here, namely: Installed using sphinx-quickstart sphinx-build -b html sourcedir builddir make html This gave me a basic html page with no content I Created a python program with some rst … Continue reading Installing Sphinx

Pretty food web graphs

When analysing output from the Webworld food web assembly algorithm (Drossel et al. 2001, J. Theor. Biol.), I often need a good way to quickly summarise the key properties of a web. In a recent project, I created a version of Webworld in which species could invade from outside the web (randomly generated species traits, as opposed to traits derived through mutation of a native … Continue reading Pretty food web graphs

An example linear programming problem in Octave

Tools for solving linear programming problems are useful to me because the necessary condition for permanence in a Lotka-Volterra system can be reduced to a linear programming problem (Jansen 1987, J. Math. Biol.; Law & Morton 1996, Ecology). Below, I’ve adapted an example from Tommi Sotinen’s ORMS 1020 lecture notes (p. 24-38) to demonstrate how to solve a linear programming problem in Octave. —– Giapetto’s … Continue reading An example linear programming problem in Octave