Monthly Archives: June 2013

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 website would lead one to believe. This, of course, may have something to do with the fact that I am both on a Windows computer and am still a relative coding/data newbie.

In the interest of lessening frustration all-around, I’ve made two tutorials for how to get Neo4j both installed (the easy part) and actually running (the hard part). The short version is immediately below; try the walkthrough a little farther down if the command line still stresses you out a bit.

There’s also a troubleshooting section at the end of the post, so check that out if you’ve already gotten to the banging-head-against-keyboard stage. Continue reading


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 repository here and my project plan here. See Phylet’s main code repository here.

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 (I’ll be working on Phylet, a visualization of the tree of life being built by the Open Tree of Life project). After a few weeks of oscillating between looking forward to an exciting summer, and fussing about not being good enough to pull it off, I’m ready to actually get started and hopefully put my doubts to rest. As a graduate student who intended to study behavioral economics and ended up studying data visualization, after spending several years in a soybean pathology research lab armed with nothing but a bachelor’s degree in English literature, I have a permanent case of impostor’s syndrome. Though the internet has probably beaten all of the humor out of it by now, the popular macro of the dog-scientist so perfectly encapsulates how I have felt for the past few years that I will include it anyway.


This one.

That golden retriever has been my mental mascot when my PI sat me down in front of a hood and told me to do pathogen transfers for the first time, pretty much every time I sit down to write a new Python script, and now, when I am setting out on a summer full of visualizing the immensely complex tree of life.

I have never been so excited.

Because the flip side of impostor syndrome is that I get to feel challenged every day and get the immense satisfaction of proving the doubting voice in my head wrong on a regular basis. So tomorrow, it starts! I’ll be easing into the coding – first order of business is to write an installation guide for the Phylet visualization, which is powered by the graph database Neo4j. After that, the first big coding thing I’m hoping to tackle is finding a way to make the visualization ordered (look more like a tree and less like a free-form web). Stick around for updates as I get my project plan and git repository up and running (also on the agenda for tomorrow). See you on the other side!