I've been meaning to post my slides from my dissertation presentation for awhile. In general, I'm committing myself to practicing more "science in the open" (meaning my presentations/posters/code), so here is the embed link. Better late than never I always say.

I gave this presentation at Northwestern University on June 4, 2013 in order to attain the degree of Doctor of Philosophy in Biological Sciences. It goes along with the publication "Use of a global metabolic network to curate organismal metabolic networks". It also goes along with the MetExplore application that I've detailed in the projects tab.

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I've been working with my friend for awhile now and for the entire length of our project we've struggled to name it. Over the last week we finally bit the bullet and decided that we would finally name it so other people could start using it.

It was a struggle.

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I really dislike boilerplate code, it drives me a little bit crazy. Starting database connections falls squarely into that realm. So in the vein of "sharing is caring" here is what I'm currently using with pymongo. It's pretty simple, but why code it twice right?

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I read an article in the last month that really rubbed me raw, it was this one:

Why you should never use MongoDB

Why does it bother me so much? Mostly because it’s bullshit, but I also feel that NoSQL solutions (and MongoDB specifically) are getting an undue bad reputation due to “MongoDB/NoSQL is bad” articles making great link-bait. Even more than that, people present themselves as experts when in reality they just make extremely broad claims about a lack of suitability without properly defining what their REAL needs are that make a technology so poor.

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I'm developing an node.js application with a friend and after a few weeks of actual coding we decided to change the name of one of the models from "Organization" to "Board". Pretty simple change actually, the design of the app had changed slightly enough that the rewording would make more mental sense for us.

So as I'm on the call I change the initial model details in the file and then change it in the router file where I know it's been used so far. Before I add the changes and commit though, I just run a quick check to make sure that it doesn't appear anywhere else like so:

$ grep -R organization .

...and then I got this fun little surprise.

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Well, at least they make great structural support.

So, you're working with windows, either by choice (wait. what?) or force (gah, somebody else making computer purchase decisions), and you're a programmer. Not just any programmer, a terminal acolyte that's chosen sides on the great vi/emacs holy war. I'll be blunt, that first sign-on is painful. But hey, the world keeps turning and it's best to stay on top of technology. Here's how I've adjusted, with the all the steps (minus getting vim happy) coming from my Windows trailblazing amigo Dan McClary.

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Some backstory. I think I first started talking about MongoDB in earnest maybe five months ago in my research lab. After having one person convert with a big project and some successful presentations (which weren't even done by me!) research has finally peaked. Now that everyone is converting, people are going through the same growing pains I had when I first started. Instead of forgetting these nuggets of information again I wanted to put them done in text.

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In Scientific Reports. Just glad to have it published finally. I gave a more complete write up of what this work means on the Amaral Lab website.