sstucki / pa-ode-gen

The Preferential Attachment ODE GENerator

The Preferential Attachment ODE Generator

pa-ode-gen, the Preferential Attachment ODE Generator, is a small, proof-of-concept tool for generating ODEs describing the time evolution of arbitrary moments of star-counting functions in preferential attachment networks.

How to get started

1. pa-ode-gen is written in Scala, which runs on the JVM. So for starters, you'll need an up-to-date JRE/JDK. If you're on a Debian/Ubuntu system, this should do the trick:

   $ sudo apt-get install openjdk-7-jre
   

2. Get an up-to-date Scala distribution.

3. Clone the GitHub repository:

   $ git clone https://github.com/sstucki/pa-ode-gen.git
   

4. Run ./ode-gen -h to build the ODE generator and get basic instructions on how to run it.

How to run it

pa-ode-gen has various output formatting options so one can

1. generate code to solve the ODEs in Matlab or GNU/Octave,
2. generate pretty pictures of various graph motifs using Graphviz,
3. generate TeX for the ODEs.

For example, running

$ ./ode-gen 3 2 odes.m

will generate a Matlab/Octave file called odes.m containing the necessary function for computing the time evolution of the 2nd-order moment of a 3-star, as well as some instructions on how to perform the computation (i.e. specify rates, time steps, etc).

Similarly, to generate the ODEs in TeX, just run

$ ./ode-gen 3 1 gluings.tex

You can also generate a DOT file for visualizing a all the graph motifs necessary to compute the mean evolution of the 3-star by running

$ ./ode-gen 3 1 gluings.dot

This will generate a single DOT file named gluings.dot with four graph definitions (one per gluing) that you can process with Graphviz to generate a PDF like so:

$ dot gluings.dot | gvpack -array_6 | neato -Tpdf -n2 -o gluings.pdf

If you just want to visualize the motifs, you can use e.g.

$ ./ode-gen -d 3 1 | dot | gvpack | neato -Tx11

Here the -d flag tells the generator to produce DOT output directly to standard out (there's no file name so it can't infer the format).

For a summary of all format options, run

$./ode-gen -h

More documentation

We're working on it...

Source code

Visit pa-ode-gen on GitHub.