BioHive: Bioinformatics blast from the past

July 7, 2016 at 10:30 am (Computer Science, Processing, Programming) (, , , , , , , )

Lately, I’ve been combing through some of my old projects so I can index and archive them. Among these old projects was my BioHive code; a bioinformatics visualization tool I wrote years ago. It was an attempt at exploring genome comparison data sets. It was actually the first non-trivial Processing (P5) app I wrote.

Different genomes would get organized into layers (indexed using colour) and nodes would be joined together based on similarity strength. Thickness of the lines would indicate connection strength, and filters could be applied to reduce clutter. Selecting a node in a layer would show information on the genome it represented as well as the top similar genomes.

These are a few screenshots of the app. In this example, Syphilis is the point of interest and they are just different views of filtered results.


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Nov 17, 2014: Activity Log

November 17, 2014 at 10:59 am (Rant, Thinking) (, , , , , , , , )

I thought I’d write a quick post about what I’ve been up to recently (mostly for myself). I can’t talk about some of the neat side projects I have going on at work, but I’m using Entity Framework, MVC, Web API, and the D3 web visualization library and it’s fun stuff.

I spent some time on the weekend watching some more videos for some Coursera courses I’m taking. It got me playing around with R, the statistics software. This is a pretty nifty system; in my opinion much better than my MatLab experiences (although still similar in some ways). It’s worth checking out if you do anything with numbers. The best part is that it’s free! You have no reason NOT to check it out!

Also, I spent a short while playing with WebGL. I wrote some quick app stuff to get it going and see what was required. My initial reaction is that it’s pretty low level, code-wise. You have to have a pretty good grasp of OpenGL, and a very good grasp of shader programs. Still, it looks pretty nice for what it is; definitely worth playing around more.

I’ve also been reading a book on criminal profiling (for fun). There’s some interesting stuff there, and it’s rekindled my interest in psychology as well. I’m trying to find a decent (and inexpensive) Kindle book on Amazon that covers a good overview of psychology. I picked one out and it ended up not being supported on the version of Kindle that I have. Sad days.

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Project updates from 2010

May 5, 2010 at 1:46 pm (Computer Science, Graphics) (, , , , , , , , , , )

So I’ve been fairly busy with finishing off the coursework required for my Masters degree lately. I’m in the process of tying up some loose ends right now before I start putting all my attention towards my thesis research.

One of the projects I’m finishing up is a software for visualizing genome comparison data. I’ve named it BioHive due to it reminding me of a bee hive because of the layered approach I used. I might post some screenshots at a later point in time once I finish fixing it up and use it a bit.

Another interesting project is a Russian propaganda poster generator. I call it Red Art and it turns photographs of people into traditional propaganda posters from the 1930’s. It was a little irritating to work on due to the difficulties with consistent automatic image segmentation, but overall I had fun making the software. I’ll post images of the results later as well, but I’m currently trying a new approach to this idea to try and improve it. We’ll see how far I get with it.

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