No post this Monday as I spent Friday evening writing Bio::Blogs. However Shirley Wu has asked me to the mention the PSB session proposal. If you’d like to get involved in the Open Notebook Science movement, this is a good place to begin. Shirley’s post outlines the requirements and there’s a Google Doc for the proposal itself.
This is the February edition of Bio::Blogs, an aggregation of bioinformatics posts from the past month. This issue has a particular focus on Open Notebook Science - researchers sharing their work as they produce it.
For this edition, with the help of Cameron Neylon, Jean-Claude Bradley, and Pedro Beltrao, I’ve tried to write a short essay on open science as well as the open notebook variety. I’ve posted this on my research website.
In World of Bioinformatics QuestTM (WoBQ) having the right character that suits your style is essential. You may think that a hot shot Rubyist is the coolest class to be, but remember that you have to play this character for the next 50 years. In general it’s better to be a character that you’ll enjoy playing, rather than one that will get you more publications but have less fun with. This page will guide you through all the parts of character generation for WoBQ.
In a previous post I wrote about how great new web tools are making it easier for scientists to collaborate, find information, and share information. This light-hearted introduction was rather popular, so heres’s a tongue-in-cheek video version.
A common task in bioinformatics is to read data from a set of files, arrange into the required format, then run an analysis to verify or falsify your expectation. An example would be reading in the yeast interaction network, and protein evolution rates, then correlating the two sets of data to see if there is a trend. Using Perl, you would specify how each file gets read in, arrange the sets of data by gene name, then correlate the two.