Welcome to Bioinformatics for beginners!
As a beginner myself I am creating this blog as a place to organize what I have learned (and am learning) about coding and as a resource for other novice coders. If there are any terms/jargon/concepts you dont understand feel free to contact me either by leaving a comment below or via twitter (@MDunitz)
Although I am sometimes shocked by how far I have come in such a short time, I am doing my best to direct this blog towards myself a year ago, a girl who didn’t know an operating system from a…well basically I didn’t know what an operating system was. In this post I am going to summarize what I have learned so far and how/where I learned it. If there are terms you don’t understand don’t worry! I promise I will explain them in future posts.
A little about me
I graduated with a degree in microbiology and political science from UC Davis in December of 2013. I have always been vaguely interested in coding/knowing more about computers but sort of in the same way I was interested in learning French–it would be useful and cool for someday. In January I began working full time in the Eisen lab at the UC Davis Genome Center. I work on a variety of fascinating (at least to me) projects using bioinformatics to study microbes in the built environment. For more information check out:
Currently I am working on a workflow/methods paper From Swab to Publication: a comprehensive workflow for microbial genome sequencing. The goal of this paper is to make sequencing and de novo assembly of genomes, as well as basic bioinformatics more accessible to undergraduates and smaller labs.
I am lucky enough to work with an amazing group of scientists. My coworkers range in “computer literacy” from novice bioinformaticians like myself to PhDs designing amazing bioinformatic tools/pipelines for the scientific community (such as A5 and phylosift) and all of them have been happy to assist me in my introduction to bioinformatics.
My experience with coding prior to this past winter was limited to the occasional analysis in STATA (a data analysis/statistics program) for political science classes. I began learning the command line in order to utilize QIIME (a tool for comparing and analyzing microbial communities). I also began learning python from Codeacademy (which I highly recommend-although be warned it is insanely addictive, you may find yourself staying up until three or four in the morning for “just one more level”). I then did python village on Rosalind and I am currently working on the bioinformatics stronghold.
I am not entirely sure how I will organize this blog, but I am hoping to explain the basics of the command line, and then review the python I learned in code academy and Rosalind and potentially check out the python tutorial.