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IAB is primarily being developed by Greg Caporaso (GitHub/Twitter: @gregcaporaso) in the Caporaso Lab at Northern Arizona University. You can find information on the courses I teach on my teaching website and information on my research and lab on my lab website.



Read Statically (All Platforms)

Here you can find statically published copies of IAB with full output. There are several version to choose from:


Read Latest Development Version

Read Interactively (OS X and Linux only)

First install miniconda then follow these instructions to install either the latest release or the latest development version of the book locally:

$ conda create -n iab-0.1.3 -c etetoolkit -c conda-forge python=3.5 ete3 scikit-bio=0.4.2
$ source activate iab-0.1.3
$ pip install https://github.com/caporaso-lab/An-Introduction-To-Applied-Bioinformatics/archive/0.1.3.zip

Next download the latest release of the book:

Download Latest Release

Unzip the book, change to the new directory that is created, and run:

$ source activate iab-0.1.3
$ jupyter notebook index.ipynb
$ conda create -n iab-latest -c etetoolkit -c conda-forge python=3.5 ete3 scikit-bio=0.4.2
$ source activate iab-latest
$ pip install https://github.com/caporaso-lab/An-Introduction-To-Applied-Bioinformatics/archive/master.zip

Next download the latest development version of the book:

Download Latest Development Version

Unzip the book, change to the new directory that is created, and run:

$ source activate iab-latest
$ jupyter notebook index.ipynb

Getting Involved:

IAB is in early development stage. To see the plans for where the project will go, see the project milestones.

If you're interested in writing or editing content or code for IAB, see CONTRIBUTING.md and/or watch the below video:


You can see the full list of IAB contributors here.

Note:

The code in the iab module is not sufficiently tested, documented, or optimized for production use, but is rather intended for educational use only. As code reaches those quality standards it is ported to scikit-bio. I do not recommend using the code in the iab module outside of the text. In other words, don't import iab outside of the text - if you want access to the functionality in your own code, you should import skbio.

IAB is funded in part by the Alfred P. Sloan Foundation. Initial prototyping was funded in part by Arizona's Technology and Research Initiative Fund.

An Introduction to Applied Bioinformatics by The Caporaso Laboratory is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.