Generating plots and correlation coefficients with PostgreSQL and R

The major task of today was to generate some correlation coefficients showing that our approach to inferring data was consistent with established results. One of my colleagues generated a plot a few months (years?) ago that showed a respectable correlation of 0.86. Unfortunately, there are only 11 points on the plot, where there should be closer to 500 000. In the many presentations I’ve seen on this topic, that correlation slide is always questioned.

Fortunately, all of this data is available in our PostgreSQL database. Unfortunately, it was an adventure in several languages and programs that I tend to avoid: Perl, vi, and especially R.
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Avoiding spam using mouseOver

All saavy website designers come across the problem sooner or later: how to make my email address easily accessible to the world, but not to the spam bots who creep through the internet looking for unsuspecting @ signs. Googling for an answer to the problem returns widespread cynicism. Many people have invested quite a lot of their time into making email addresses ‘bot-resistant, hoping that they won’t alienate their users  while at the same time keeping spam-free.
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HTML love and my new website

I have known how to write HTML code for over half of my life. How many people can say that? I learned to write it twelve years ago. I signed up for GeoCities and Tripod and built half a dozen websites. Although they’ve all been long retired, I can still remember the joy I derived from tweaking the code, a little here and a little there, to make something that the world could see.

Several years later, my first work website was also coded by hand, with amazing CSS drop-down menus and PHP include statements that made website maintenance simple, provided you could actually sort out the layers within layers. I think that website was the first time I realized that it was possible for code to be beautiful.

That website is now offline too (though available on the Wayback Machine! Aw, look how cute it is!). I’ve pondered what kind of new site to create. By pondered, I mean procrastinated. Finally, after going to the Cytoscape Retreat and seeing how woefully backward I am without my own webspace, I finally gave in and spent a day of my free time crafting a new home for my details. And fell in love all over again with HTML and associated technologies.

I could probably spend a week tweaking and modifying my website so it is perfect. However, since I have a life these days and also more work to do than I have available time, I’ll have to satisfy myself with a few tweaks here and there.

Some places that really helped in my search:

  • Open source web design: lots of great free and easily tweakable templates. And open source!
  • COLOURlovers: For those of us who aren’t art majors, finding more than two colors that go together is challenging. COLOURlovers have over a million pre-conceived palettes with fanciful and fun names like Pluck Off and Wasabi Suicide. They also provide hex and RGB codes for each color.
  • Cytoscape: Cytoscape didn’t exactly help me with the details of the website, but thanks to it, I finally have some of my work that pretty enough to be made into a website banner. The networks on my homepage are from real data, and the colors mapped in Cytoscape. All I had to do was rasterise it.

And so, with great pleasure, I give you my new home on the web: