We could still use more applicants for this position, so bumping the open position...
SymBioSys is a consortium of computational scientists and molecular biologists at the University of Leuven, Belgium focusing on how individual genomic variation leads to disease through cascading effects across biological networks (in specific types of constitutional disorders and cancers).
As a colleague of mine said a couple of weeks ago: "if you don't publish it, it didn't happen". Scientific publications are the currency to advance a researcher's career.
Just a short note...
Even though my position in Leuven only starts in October, I've already been involved in writing and defending a major grant.
Even though my position in Leuven only starts in October, I've already been involved in writing and defending a major grant.
I have been a bit frustrated lately by the fact that for many of my analyses I have to write a ruby script to mangle my data first, then resort to R to add a statistic to each of the datapoints, go back to ruby to mangle the result, repeat, rinse, and finally make plots in R.
I should create an online labbook with code examples of how I do things. Keep going back to an example script I have to copy/paste the code for handling different threads in ruby.
Read the excellent post by Neil Saunders on using ruby and mongodb to archive his posts on FriendFeed, prompting me to finally write down my own experiences with mongodb. So here goes...
Let's have a look at the pilot SNP data from the 1000genomes project.
Let's have a look at the pilot SNP data from the 1000genomes project.
Received an email this week from Sanger helpdesk that they installed a test hadoop system on the farm with 2 nodes. Thanks guys! First thing to do, obviously, was to repeat the streaming mapreduce exercise I did on my own machine (see my previous post).
After investigating git for the bioruby project, I started using it on basically every project I run. And what do I use it for? Two things: keeping track of changes (duh) and syncing between server and laptop.
Just a quick plug to see if I can find people interested in helping me out in some of my projects.
In the last 2 years, I started four open source projects (well: the last one was today...), each of which scratches my own itch and does what it needs to do for me.
In the last 2 years, I started four open source projects (well: the last one was today...), each of which scratches my own itch and does what it needs to do for me.
Did you ever have data lying around that you couldn't figure out where you got it from?
You downloaded and imported data from an FTP site into your database ages ago and you actually want to use it now.
You downloaded and imported data from an FTP site into your database ages ago and you actually want to use it now.
Seasoned programmers know this: testing should be an integral part of developing any script/program/software suite. Part and parcel is the unit test, where you test every little aspect of your program little by little.
One of the issues in a library like Bio::Graphics, is the plethora of glyph types that users will want. Here's a little showcase of what's provided by the library:
Features on a DNA sequences can be represented as filled boxes, open boxes, boxes with arrows, lines, triangles, ...
Features on a DNA sequences can be represented as filled boxes, open boxes, boxes with arrows, lines, triangles, ...
