Rosalind: A great resource for learning bioinformatics programming

Most well-versed bioinformaticians have likely heard, or perhaps used, Rosalind, but I decided to write about it for any visitors who haven’t. Rosalind teaches users bioinformatics programming using exercises. Basically, the student is given a bit of background that ties the programming to the real-world application, is given a clear set of instructions, and is able to download data to use to test his or her program. The student then uploads their answer and the website grades it as correct or incorrect. Each dataset generated is unique, so you can’t just copy a friends answer. More importantly, with the way the exercises are set up, any programming language can be used to solve the problems, which provides a huge amount of flexibility. Last, and certainly not least, Rosalind is free to use!

Overall, for anyone who wants to learn how to program for bioinformatics with real-life challenges, I encourage you to give Rosalind a try. Likewise, if you are teaching students or forming a graduate student learning group, this is a great resource to use. I am currently using it for a class and am getting a pretty good handle on Python. I plan to attempt most or all of the challenges (beyond just those assigned in class) and may even go through a subset with a new language (such as Perl) to build my skills set. Seeing as most of the postdoc and faculty position listings I see in evolutionary biology and genomics explicitly demand the ability to use programming languages, it makes perfect sense to start learning!

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Burmese python genome paper published in PNAS

For my first blog post I thought it would be fitting to highlight the recent publication of my first manuscript! In early December we published on the release of the first snake genome, that of the Burmese python (Python molurus bivittatus). The response to our PNAS paper was great, and news of the release was carried by many news outlets.

The work highlights the massive transcriptional fluctuations that occur when a Burmese python feeds, which facilitates enlargement of several vital organs (heart, liver, kidney, and small intestine) and allows the snake to digest its prey rapidly. Thousands of genes are differentially expressed during this physiological response and those with significant fluctuations are homologous with metabolism, development, and pathology in humans. An analysis of molecular evolution found that many genes have endured positive selection, making them distinct from forms found in all other vertebrate organisms. Additionally, characteristics of genome structure indicate massive genome remodeling. Overall, the extreme phenotypes evident in snakes appear to be a product of protein adaptation, coordinated gene expression, and changes in genome structure. Stay tuned for future work on physiological remodeling in the Burmese pythons and genome evolution in snakes and squamate reptiles.