readiab.org/index.html at master · applied-bioinformatics/readiab.org · GitHub

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<!DOCTYPE html>
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<head>
    <title>An Introduction to Applied Bioinformatics</title>
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    <a href="https://github.com/applied-bioinformatics/An-Introduction-to-Applied-Bioinformatics"><img style="position: absolute; top: 0; right: 0; border: 0;" src="https://camo.githubusercontent.com/38ef81f8aca64bb9a64448d0d70f1308ef5341ab/68747470733a2f2f73332e616d617a6f6e6177732e636f6d2f6769746875622f726962626f6e732f666f726b6d655f72696768745f6461726b626c75655f3132313632312e706e67" alt="Fork me on GitHub" data-canonical-src="https://s3.amazonaws.com/github/ribbons/forkme_right_darkblue_121621.png"></a>

    <div class="container">
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            <div class="page-header">
                <h1>An Introduction to Applied Bioinformatics</h1>
                <p class='lead'>An <strong>I</strong>ntroduction to <strong>A</strong>pplied <strong>B</strong>ioinformatics (or IAB) is a free, open source interactive text that introduces readers to core concepts of bioinformatics in the context of their implementation and application.</p>
            </div>
            <div class="col-xs-4 col-centered">
                <p><img src="http://readiab.org/IAB_files/logo.png" width=250px/></p>
                <p>IAB is primarily being developed by <a href="http://caporasolab.us/people/greg-caporaso/">Greg Caporaso</a> (GitHub/Twitter: <a href="https://github.com/gregcaporaso">@gregcaporaso</a>) in the <a href="http://www.caporasolab.us/">Caporaso Lab</a> at <a href="http://www.nau.edu/">Northern Arizona University</a>. You can find information on the courses I teach on <a href="http://www.caporasolab.us/teaching">my teaching website</a> and information on my research and lab on <a href="http://www.caporasolab.us/">my lab website</a>.</p>
                <br/><br/>
            </div>
            <div class="col-xs-8 col-centered">


                  <div class="panel panel-primary">
                      <div class="panel-heading"><h4>Read Interactively on Binder (recommended)</h4></div>
                      <div class="panel-body">
                          <p><a href="https://mybinder.org">Binder 2.0</a> is a platform for interactively working with Jupyter notebooks without installing any software on your computer. Reading IAB on Binder will work on different operating systems, and shouldn't require you to install any software (provided you already have a modern web browser).</p><br/>

                      <a href="https://mybinder.org/v2/gh/applied-bioinformatics/built-iab/master?filepath=IAB-notebooks/index.ipynb" class="btn btn-success btn-lg pull-right" target="_blank"><span class="glyphicon glyphicon-chevron-right" aria-hidden="true"></span>Read Latest Development Version</a>
                      </div>
                  </div>

                <div class="panel panel-info">
                    <div class="panel-heading"><h4>Read Statically (All Platforms)</h4></div>
                    <div class="panel-body">
                        <p>Here you can find statically published copies of IAB with full output. There are several version to choose from:</p>
                        <ul><li><a href="/book/latest/">the latest development version</a> (recommended: links may be unstable, but most recent content)
                        </li><li><a href="/book/0.1.3/">the latest release version</a> (the most recent stable release)
                        </li></ul><br/>

                    <a href="http://readiab.org/book/latest/" class="btn btn-success btn-lg pull-right"><span class="glyphicon glyphicon-chevron-right" aria-hidden="true"></span> Read Latest Development Version</a>

                    </div>
                </div>


                <div class="panel panel-info">
                    <div class="panel-heading"><h4>Read Interactively on macOS and Linux</h4></div>
                    <div class="panel-body">
                        <p>First install <a href="https://conda.io/miniconda.html" target="_blank">miniconda</a> then follow these instructions to install either the latest release or the latest development version of the book locally:</p>

                        <!-- Nav tabs -->
                        <ul class="nav nav-tabs" role="tablist">
                            <li role="presentation" class="active"><a href="#interactive-dev" aria-controls="profile" role="tab" data-toggle="tab">Latest Development (Recommended)</a></li>
                            <li role="presentation"><a href="#interactive-release" aria-controls="home" role="tab" data-toggle="tab">Latest Release</a></li>
                        </ul>

                        <!-- Tab panes -->
                        <div class="tab-content">
				<div role="tabpanel" class="tab-pane active" id="interactive-dev"><p></p>
                        <p>First, download the latest development version of the book:</p>
                         <a href="https://github.com/applied-bioinformatics/built-iab/archive/master.zip" class="btn btn-success"><span class="glyphicon glyphicon-download-alt" aria-hidden="true"></span> Download Latest Development Version</a>
                        <p></p>
			<p>Unzip the book, <b>change to the new directory</b> that is created, and run:</p>
                        <pre>$ conda env create -n iab-latest -f environment.yml
$ conda activate iab-latest
$ ./start.sh</pre>
                            </div>
                            <div role="tabpanel" class="tab-pane" id="interactive-release">
<pre>$ 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/applied-bioinformatics/An-Introduction-to-Applied-Bioinformatics/archive/0.1.3.zip
</pre>
                        <p>Next download the latest release of the book:</p>
                            <a href="http://readiab.org/book/0.1.3/IAB-notebooks.zip" class="btn btn-success"><span class="glyphicon glyphicon-download-alt" aria-hidden="true"></span> Download Latest Release</a>
                        <p></p>
                        <p>Unzip the book, change to the new directory that is created, and run:</p>
                        <pre>$ source activate iab-0.1.3
$ jupyter notebook index.ipynb</pre>
                            </div>
                        </div>
                    </div>
                </div>


            </div>

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        <div class="row row-centered">
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                <h3>Getting Involved:</h3>
                <p>If you're interested in writing or editing content or code for IAB, begin by reading the <a href="https://github.com/applied-bioinformatics/An-Introduction-to-Applied-Bioinformatics/blob/master/CONTRIBUTING.md">contributing guide</a> and the <a href="https://github.com/applied-bioinformatics/An-Introduction-to-Applied-Bioinformatics/blob/master/CODE-OF-CONDUCT.md">IAB Code of Conduct</a>. You can also watch the following video which demonstrates how to contribute changes using the <i>Edit</i> links found throughout the text:</p>
                <div class="embed-responsive embed-responsive-16by9">
                  <iframe class="embed-responsive-item" src="https://www.youtube.com/embed/s9-aZrX5CY8" frameborder="0" allowfullscreen></iframe>
                </div>
                <br/>
                <p> You can see the full list of <a href="https://github.com/applied-bioinformatics/An-Introduction-to-Applied-Bioinformatics/graphs/contributors">IAB contributors here</a>.</p>

            </div>
            <div class="col-xs-6">
            <h3>Note:</h3>
            <p>The code in the <code>iab</code> module is <strong>not sufficiently tested, documented, or optimized for production use</strong>, but is rather intended for educational use only. As code reaches those quality standards it is ported to <a href="http://www.scikit-bio.org/">scikit-bio</a>. I do not recommend using the code in the <code>iab</code> module outside of the text. In other words, don't <code>import iab</code> outside of the text - if you want access to the functionality in your own code, you should <code>import skbio</code>.</p></div>
        </div>
        <div class="row row-centered">
             <div class="container">
                  <div class="col-xs-4" >
                      <a href="http://sloan.org" target="_blank"><img src="SloanLogo-primary-black.png" width=100%/></a>
                  </div>
                  <div class="col-xs-3 vcenter">
                      <p class="small">IAB is funded in part by the <a href="http://sloan.org" target="_blank">Alfred P. Sloan Foundation</a>. Initial prototyping was funded in part by <a href="http://nau.edu/Research/Funding/Technology-Research-Initiative-Fund/" target="_blank">Arizona's Technology and Research Initiative Fund</a>.</p>
                  </div>
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                  <div class="col-xs-1 pull-right vcenter">
                      <a href="http://creativecommons.org/licenses/by-nc-sa/4.0/" target="_blank"><img src="http://readiab.org/IAB_files/88x31.png"></a>
                  </div>
                  <div class="col-xs-3 pull-right vcenter">
                      <p class='small'>An Introduction to Applied Bioinformatics by <a href="http://caporasolab.us/" target="_blank">The Caporaso Laboratory</a> is licensed under a <a href="http://creativecommons.org/licenses/by-nc-sa/4.0/" target="_blank">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License</a>.</p>
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