Visual Pathway Diff: First Screenshots

As the mid-term evaluation is underway, I reached a major milestone: My program can now output the difference set in SVG format, meaning that it is possible to compare Biological Pathways visually.

Here are two examples (click on the thumbnails to see a larger image)

Pathway Comparison A

In this screen shot you see two versions of the Acetyl Choline Pathway (very important for transmitting electrical signals between neurons). As you can see I’ve straightened out a few arrows in the new version (on the right). The yellow color indicates things that have changed, the text balloons in the middle explain in more detail which attributes of those things have changed.

Pathway Comparison B

This pathway represents the Alcohol Dehydrogenase reaction (activated when you have a hangover 😀 ). In the image you can see I’ve added a few missing reaction compounds (in green) as well as set the label for the other compounds (in yellow).

SVG output is only one of the possible output formats of GpmlDiff. Another option is to write to an XML-type format that I dubbed DGPML. DGPML is designed in such a way that it should be possible to write a patch utility that takes a GPML Pathway and then applies a DGPML difference set to it.

In the context of wikipathways, I think there are a couple of interesting use cases for a patch utility. I didn’t think about this when I wrote my GSOC proposal, but I think this would be very useful. So useful in fact that I’m going to ask my supervisor Alex Pico if he thinks I should put it in my plan for the second half of the summer.

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2 Responses to “Visual Pathway Diff: First Screenshots”

  1. Tim Ansell says:

    This looks really cool. Where is your code published? Some of the methods described here would be useful in visualising the differences in some stuff Thousand Parsec – uses.

  2. The svn repo is here:, in particular At the moment it’s svn only, we’re not doing source code drops yet.