Theobio features

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Currently, most work on theobio is done using a handful of programs:

  • latex is a typesetting program
  • gcc is a compiler for the low-level programming language C.
  • perl is a flexible scripting language
  • python is a generally agreed to be better than perl, but we haven't mostly switched yet
  • maxima is a symbolic algebra language
    • Theobio has some simple rules to help you use maxima
  • Octave is a free, matlab-like program.
  • We are also thinking of adding some bioinformatics functionality.
    • We have started mucking around with PAML
  • Gnuplot is a flexible plotting program
    • We are developing rules for gnuplot on a project here

Stuff in the default makefiles

Most of this is not documented, or documented but not easy to find. I'm trying to catch up.

R rules

Our R machinery is very general, and a little bit complicated. I have the idea of making a parallel track ((R step)) where each script is designed to only make one target (although it can still contribute to multiple targets, via having its final environment read in).


The target ls lists the working directory. passes arguments to ls.


The < target can be a useful failsafe when debugging.

MediaWiki customizations

There are some customizations we make to skins, extensions and other components of our MediaWiki installs.

Other projects

We have a hacky but working Refs project that can be used to make links and bibtex files (to be used with latex) from Pubmed IDs or links.

Many projects on theobio use "dumb markup" ( dmu), basically random assortments of rules for source files that are supposed to be human-friendly. We eventually hope to regularize and document this.


The main settings file is /usr/local/mediawiki/wwfarm-1.21/template/extensions/enable-ww.php