test – IRIC's Bioinformatics Platform

A javascript implementation of the non-central version of Fisher’s exact test

In a previous post, I presented a case for choosing a non-central version of Fisher's exact test for most of bioinformatics' uses of this test. I will now present an implementation of this test in javascript that could easily be embedded in web interfaces. Although javascript is probably the least likely language to implement statistical methods, I hope this article will fill in as many details as possible to make it trivial to port it to other languages if the need arises. At [...]

By Sébastien|2017-04-29T17:47:57+00:00January 13, 2017|Categories: Data Analysis|Tags: javascript, Statistics, test|0 Comments

Fast network transfers?

Recently, everyone and their mother started using various tools in order to optimize large data transfer to, from and between supercomputers. Historically, we have seen tools like FDT, BBCP that tried to exceed the performance obtained from other transfer methods, like scp, rsync, ftp, etc. One tool in particular is now gaining traction and is being deployed on most supercomputers: GridFTP and its front-end Globus. The Globus frontend interface. Before jumping into the bandwagon, I thought it would [...]

By Patrick|2017-04-29T17:04:17+00:00October 13, 2016|Categories: Computer science, Performance|Tags: file manipulation, test|0 Comments

Simple multiprocessing in R (2nd edition)

The last time I spoke about this subject, I presented a really simple way to change an lapply call into its multicore sibling mclapply. Now while this is an extremely easy modification to implement in your code to gain substantial performance benefits, it kinda required you to be making use of the lapply function in the first place. So let's look at another way to introduce multiprocessing into your existing codebase with the use of the foreach and doMC packages. [...]

By Jean-Philippe|2017-04-29T16:24:45+00:00September 19, 2016|Categories: Performance, R|Tags: multiprocessing, test|0 Comments