6/26 - 7/6

Tasks accomplished:

• Applet can now read and write graphs in XGMML.
• GUI is more interactive - loading graphs and analyzing for dimension can now be done dynamically
• I got data for the metabolic network of E. coli and the protein interaction network (PIN) for yeast  from http://www-levich.engr.ccny.cuny.edu/~hmakse/soft_data.html and analyzed them, getting very close to the same results as others (3.4 for E. coli and 1.9 for the yeast).  My results for E. coli are often a little high, but perhaps I'm not using the identical data (it seems there are several versions of these data - everywhere I look gives a slightly different number of nodes).
• Minor improvements to the data displays

Some screenshots of results:

E. coli.  The horizontal axis (ignore all coordinate labels for now; this was before I fixed them) represents box-size (maximum path length between any two nodes in a "box", or sub-net), and the vertical axis is the number of boxes needed to cover the network.  For a fractal network the graph when scaled logarithmically (like here) should approximate a straight line.  Notice the "D: 3.40..."  Never before have I been so excited to see that number.

Same chart for the PIN of yeast.  D = 1.91 - yay!

Yeast again; this time the vertical axis represents calculated dimension at each stage of the algorithm.  As mentioned in my previous post, the values should end up very close to a single value for a fractal network, and here they do.

Things to focus on now:

• Further improve gui - draw networks themselves, make the charts more readable and customizable
• Look into more applications - find interesting networks to test (if anybody has any ideas, let me know!)