Keynote Systems measures download times for selected web sites. For example, consider this data: Keynote Systems download times

Cytoscape is a network analysis package used quite often in systems biology. Cytoscape has scripting support for Python, Ruby, and Groovy. Or at least they say there is scripting support for Groovy, but there wasn’t a meaningful Groovy example that I could find. So I made a couple of minor changes to the Ruby example, along with logging added for debugging and, behold, an example Cytoscape Groovy script:

In a previous post I showed csvsql which is one program in my arsenel of TSV/CSV file handling tools. Today’s post highlights another tool, viewtab, which is a fast read-only spreadsheet for exploring data in tab files. I often get data files from scientists or from the supplements of journal papers with only a vague clue what is in the file. I can cat the file but if the file has many columns a simple cat quickly becomes illegible. There are fancier things you can do with cat such as:

The visualization code I’m writing using Processing.js needs a tooltip to display some information depending on where your mouse is in the canvas. Although there are many tooltip options for webpage elements, I didn’t find any that I could easily use with Processing.js to generate tooltips dependent on the mouse position in the canvas. After a few frustrating attempts with various libraries I finally just took this rounded corners demo by F1LT3R. and hacked together a ToolTip class of my own that works with Processing.js. I think it’s pretty nice for a quick hack.

I’ve been playing around with Processing.js to produce visualizations of some genomics data. The Java based Processing language/environment was originally developed by the noted data visualization guru Ben Fry and graphic artist Casey Reas. Processing.js is a port of the Processing language and libraries to javascript and the HTML 5 canvas by none other than John Resig, the creator of the jQuery javascript library. I was skeptical at first that Processing.js would be anything but a pale shadow of it’s Processing predecessor, but after using it for a bit I have to say that I am impressed. Most of the Processing sketches one can find scattered around the web and on such sites as Open Processing just work. Here, for example, is a sketch from the examples on Processing.org called reflection2.

I recently read a couple of nice articles by Darren Wilkinson about implementing MCMC in various languages. The posts are here and here. Wilkinson apparently uses, or is considering using, Python for a lot of prototyping and C for a lot of his actual MCMC runs. However, since he feels that Java is in some ways nicer than C, and almost as fast, he has been using Java for some of the final MCMC runs. I thought I’d see how Groovy performed on this task.

I’ve been learning a little about jQuery by going through the excellent jQuery tutorial over at the jQuery Docs page. The examples use PHP for server side code, but since I’m more familiar with Servlets/Groovlets, I decided do the server side code as a Groovlet.