Tag Archives: tree of life

Recap and State of the Project, Week 11

Before I get started: As part of my masters’ degree, my program requires that I do a write-up of my internship experience. You can see the complete product here, but here’s an excerpt and a YouTube video demo-ing what Phylet looks like right now:

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State of the Project, Week 7


  • Got a working Neo4j flare visualization (big intermediate step on the way to getting a tree viz instead of a network!) See my bitbucket page for the code, and a copy of flare.db.
  • Got a working tree visualization of the taxonomy from the bird database. Also exciting, though using taxonomy removes the most difficult part of getting the full tree – having multiple parents and a more web-like structure with conflicts, etc. This is what (part of) the tree currently looks like:


I rotated the visualization to be vertical rather than horizontal, though I haven’t decided which one is more readable. I also added tiers, so all the nodes can fit – and this is still only part of the dataset. Two options would be to either continue adding tiers to fit everything (“life” seems to be an outlier in the number of children it has), or to have another node for “more” that would load the next set of nodes.

Currently, the only major issue left is that when you click on a node, say “Frogmouths,” the viz redraws with Frogmouths as the root node (see below). This is because of the way data gets served to the viz. It works okay for the taxonomy, but needs to be solved before the more complicated phylogeny will work.


  • Began work on the two biggest problems: 1) cutting down on the number of layers of data the viz needs to run, to improve speed, and 2) get the viz to build, rather than to just switch root nodes.
  • Did sketches of alternate viz styles (circular, etc.), and sketches of the bird.db data structure.
  • Uploaded a number of scripts I wrote to my personal bitbucket page. Did clean-up/debugging of all code uploaded; wrote draft of how-to for uploading to bitbucket (which as always, is a little different on Windows. I’ve had the most luck with Tortoise HG).

To do:

  • Solve the two problems listed above
  • Add caching back into the script – only way that building nested jsons (a possible solution for building the viz) will be at all workable. Too much lagging and refetching is going on anyway.
  • Add toggle for common/latin name labels
  • Implement a few alternate viz styles, once problems are fixed
  • Aesthetics of viz (colors for conflicts, resolved/unresolved nodes, etc.)

Visualization research brain-dump

As progress advances in Phylet, I’ve moved into the experimentation phase—looking for alternate visualization styles of the tree of life. The way Phylet is visualized now does a good job of visualizing conflicts—indications that one or more of the source taxonomies do not agree on how nodes relate.  However, its readability is seriously restricted by its unordered format, which dissolves the structure of the tree and leaves a pretty but chaotic visualization. Continue reading