{ "metadata": { "name": "", "signature": "sha256:d2aaeb936946d20bcd915fed579c1222561be4246a56903890bd3c3c451a64a7" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "An Introduction To Applied Bioinformatics" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "
\n", "\n", "Bioinformatics, as I see it, is the application of the tools of computer science (things like programming languages, algorithms, and databases) to address biological problems (for example, inferring the evolutionary relationship between a group of organisms based on fragments of their genomes, or understanding if or how the community of microorganisms that live in my gut changes if I modify my diet). Bioinformatics is a rapidly growing field, largely in response to the vast increase in the quantity of data that biologists now grapple with. Students from varied disciplines (e.g., biology, computer science, statistics, and biochemistry) and stages of their educational careers (undergraduate, graduate, or postdoctoral) are becoming interested in bioinformatics.\n", "\n", "I teach bioinformatics at the undergraduate and graduate levels at Northern Arizona University. This repository contains some of the materials that I've developed in these courses, and represents an initial attempt to organize these materials in a standalone way. If you'd like to read a little more about the project, see my [blog post](http://microbe.net/2014/05/01/teaching-bioinformatics-using-ipython-notebooks/) on [microbe.net](http://microbe.net)." ] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Disclaimer" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "**This project is in very early development stage.** It's not ready for prime-time by any means, but I fall firmly into the \"publish early, publish often\" mindset, hence its public availability. I am very interested in feedback. The best way to get feedback to me is through [the IAB issue tracker](https://github.com/gregcaporaso/An-Introduction-To-Applied-Bioinformatics/issues), and the best way to contribute is through [pull requests](https://help.github.com/articles/using-pull-requests).\n", "\n", "The code in the iab module is **not sufficiently tested, documented, or optimized for production use**. As code reaches those quality standards it will be ported to [scikit-bio](http://www.scikit-bio.org). I do not recommend using the code in the iab module outside of these notebooks. In other words, don't `import iab` outside of the notebooks - if you want access to the functionality in your own code, you should `import skbio`.\n", "\n", "Currently, the **best example of where I'm hoping to go with these materials** is the [multiple sequence alignment](http://nbviewer.ipython.org/github/gregcaporaso/An-Introduction-To-Applied-Bioinformatics/blob/master/algorithms/4-multiple-sequence-alignment.ipynb) chapter." ] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Contents" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "0. [Getting started](getting-started/Index.ipynb): using the IPython Notebook and *An Introduction To Applied Bioinformatics*\n", "1. Fundamentals\n", " 1. [Pairwise alignment](fundamentals/pairwise-alignment.ipynb) ([exercise](fundamentals/pairwise-alignment-exercises.ipynb))\n", " 2. [Database searching and determining the statistical significance of an alignment](fundamentals/database-searching.ipynb)\n", " 3. [Phylogeny reconstruction: distances, distances matrices and hierarchical clustering with UPGMA](fundamentals/phylogeny-reconstruction.ipynb)\n", " 4. [Multiple sequence alignment](fundamentals/multiple-sequence-alignment.ipynb) ([exercise](fundamentals/msa-assignment.ipynb))\n", " 5. [Read mapping and clustering](fundamentals/sequence-mapping-and-clustering.ipynb?create=1)\n", "2. Applications\n", " 1. [Studying biological diversity](applications/biological-diversity.ipynb)\n", "3. Wrapping up" ] } ], "metadata": {} } ] }