Clik here to view.
Countdown to official start…
June 17 is almost here! Less than two hours away, technically, but I suppose I will have to wait until tomorrow morning to ring in the official start. I’m excited to finally start my GNOME project...
View ArticleClik here to view.
Code repository and project plan
I’ve hosted both my code repository and project plan on bitbucket (I have a simmering hatred of GitHub that I cannot fully explain). Both will be updated as the summer progresses. See my code...
View ArticleClik here to view.
Neo4j installation guide
Neo4j installation guide After spending some good quality time banging my head against the keyboard, I finally got Neo4j running on my machine – it was quite a bit more of an adventure than the Neo4j...
View ArticleClik here to view.
State of the Project (Week 4)
Did: (With assistance,) finally determined the cause of the problems I had been having with my local Phylet (the visualization space was empty). Turned out that the Python package py2neo had gotten a...
View ArticleClik here to view.
State of the Project (Week 5)
Did: Fixed the problem illustrated in the previous State of the Project post, with the child_count and parent_count properties not being picked up properly. Turns out the database we’ve been using does...
View ArticleClik here to view.
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...
View ArticleClik here to view.
State of the Project, Week 6
Did: Function map draft of service.py Proofread service.py, gol.js, and index.html Created stripped-down versions of service.py, gol.js, and index.html, to prepare for switching out for different...
View ArticleClik here to view.
State of the Project, Week 7
Did: 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...
View ArticleClik here to view.
State of the Project, Week 9
Did: Visualization currently looks like what you can see above. Things I did to get there: Tree can now build, instead of just switching root nodes – this is done by storing the original json in...
View ArticleClik here to view.
State of the Project, Week 10
The Dids and the To-Dos are the same this week: continue to work on developing the “backwards tree,” and the “breadcrumb tree.” Backwards tree: On right-click, reload a separate viz in a splitscreen...
View ArticleClik here to view.
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...
View ArticleClik here to view.
State of the Project, Week 12
This week’s theme: clean-up and organization! Did: Cleaned up my code and re-integrated it into the original Phylet framework – I’d cut out a lot of the toggle-button functionality, etc. when I first...
View ArticleClik here to view.
State of the Project, Week 13
Did: Finished the “breadcrumb” visualization – it is accessed by right-clicking on the node (which I will have to change later, as this is not Mac-friendly). This collapses the visualization down to...
View ArticleClik here to view.
State of the Project, Last week!!
Everything that needs to be done by the end of the project, in various stages of completion: Coding: Integrate the breadcrumb and backwards tree viz-es into the full visualization (status: debugging)...
View ArticleClik here to view.
Phylet wrap-up
Documentation on how to set up Neo4j and Phylet is here. All code will be uploaded to bitbucket here by September 23, 11:59 p.m. EST:...
View Article
