Save the World with Bioinformatics

Before anything, let Steve Yegge tell you why this is important. Start at 5:50 if you’re impatient.

This may be a bold statement, but I believe this video will be the call to arms for the Computer Scientists, Programmers, Developers, Hackers of our generation to make the choice to make a difference. This is when we decide  to solve real world problems instead of first world problems.

I got excited when I heard this talk, but had no idea where to start. My background is in Computer Science, not Biology. Most of the articles, books, etc. that I’ve seen assume you know where to start. This is my attempt to create Step 1 and document my course of action and resources in the hopes that they will make your jump a bit easier.

Getting started in Bioinformatics from the US National Library of Medicine National Institutes of Health is a quick-to-read and useful article, it also includes names and links to a couple of projects.

Courses

We have some learning to do, and there are some great free online options. I’m using MIT OpenCourseWare. Take a look and see what appeals to you, courses from other schools are available here as well. Below are the classes I plan on taking. View the syllabus tab on the left side of each course page to see what books the course uses, or if it has pre-requisites you might want to look at as well.

Introduction to Biology (why not?)

Molecular Biology

Introduction to Computational Molecular Biology (seems similar to the next class)

Foundations of Computational and Systems Biology

Computational Biology: Genomes, Networks, Evolution (might be a bit advanced)

Protein Biochemistry and Evolutionary Biology are also suggested on the Bioinformatics.org Getting Started page. The bottom of that page has a Volunteering section along with a link to open source projects.

Books

Bioinformatics for Dummies

Start reading and never stop. After reading the first chapter of this book, you’ll have a basic understanding of the underlying principles. In chapter 2, this book introduces you to some tools and online resources while explaining how to use them. Since it does a great job with that, I’ll refrain from listing them all here.

I previously purchased Bioinformatics for Python and at this point I haven’t find those types of books to be helpful. Right now, building the foundation and having an understanding of the basics is more important and will make these types of books actually meaningful when you get to them.

Software

Pick your favorite language and grab the software for it on Open-Bio.org I’ll be using biopython

This looked appealing to me: Bioclipse and download

EMBOSS – The European Molecular Biology Open Software Suite

Q&A Sites

Once you dive in, you will have some questions. Chances are someone else has as well. Stack exchange is fantastic, you’ll find this to be a great resource while working through the classes and while working on more Bioinformatics-related problems. StackOverflow can help when dealing specifically with some of the software you will be using.

BioStar

Biology StackExchange I’m following the tags for bioinformaticsmolecular-biologyhuman-genome and computational-biology

Biopython questions on StackOverflow

Good Luck!

This a great presentation introducing the field as well as a brief history on where the field has come and where it’s going. Daniel Reda – An Introduction to Biotechnology and Bioinformatics

I hope this helps to steer you in the right direction. Please share any resources you find in the comments and feel free to get in touch. It’s easy to feel a bit lost in the beginning, but it gets better when there are more computer geeks around.