index.html

---
layout: workshop      # DON'T CHANGE THIS.
root: .               # DON'T CHANGE THIS EITHER.  (THANK YOU.)
carpentry: "SWC"    # what kind of Carpentry (must be either "dc" or "swc")
venue: "Wrangle Some Data at the University of Arizona!"        # brief name of host site without address (e.g., "Euphoric State University")
address: "Integrated Learning Center (ILC); 1503 E. University Blvd., Tucson, AZ 85721"      # full street address of workshop (e.g., "Room A, 123 Forth Street, Blimingen, Euphoria")
country: "us"      # lowercase two-letter ISO country code such as "fr" (see https://en.wikipedia.org/wiki/ISO_3166-1)
language: "en"     # lowercase two-letter ISO language code such as "fr" (see https://en.wikipedia.org/wiki/ISO_639-1)
latlng: "32.231901,-110.9495000"       # decimal latitude and longitude of workshop venue (e.g., "41.7901128,-87.6007318" - use http://www.latlong.net/)
humandate: "Feb 25-26, 2017"    # human-readable dates for the workshop (e.g., "Feb 17-18, 2020")
humantime: "8:30 AM - 5:00 PM"    # human-readable times for the workshop (e.g., "9:00 am - 4:30 pm")
startdate: 2017-02-25      # machine-readable start date for the workshop in YYYY-MM-DD format like 2015-01-01
enddate: 2017-02-26       # machine-readable end date for the workshop in YYYY-MM-DD format like 2015-01-02
instructor: ["Marnee Dearman", "Upendra Devisetty", "Travis Struck", "Frank Ventura", "test"] # boxed, comma-separated list of instructors' names as strings, like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["Gaius Augustus", "Tushar Garg", "Uwe Hilgert", "Amit Juneja", "Jennifer Lumbres", "Blake Joyce", "Elizabeth Miller", "Julian Pistorius", "Andreina Siri", "Edwin Skidmore", "Anandraj Thiyagarajaperumal"]     # boxed, comma-separated list of helpers' names, like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: ["hilgert@email.arizona.edu"]    # boxed, comma-separated list of contact email addresses for the host, lead instructor, or whoever else is handling questions, like ["marlyn.wescoff@example.org", "fran.bilas@example.org", "ruth.lichterman@example.org"]
etherpad:  http://pad.software-carpentry.org/2017-02-25-CyVerse           # optional: URL for the workshop Etherpad if there is one
eventbrite: # optional: alphanumeric key for Eventbrite registration, e.g., "1234567890AB" (if Eventbrite is being used)
---

<!-- See instructions in the comments below for how to edit specific sections of this workshop template. -->

<!--
  HEADER

  Edit the values in the block above to be appropriate for your workshop.
  If the value is not 'true', 'false', 'null', or a number, please use
  double quotation marks around the value, unless specified otherwise.
  And run 'tools/check' *before* committing to make sure that changes are good.
-->

<!--
  EVENTBRITE

  This block includes the Eventbrite registration widget if
  'eventbrite' has been set in the header.  You can delete it if you
  are not using Eventbrite, or leave it in, since it will not be
  displayed if the 'eventbrite' field in the header is not set.
-->
{% if page.eventbrite %}
<iframe
  src="https://www.eventbrite.com/tickets-external?eid={{page.eventbrite}}&ref=etckt"
  frameborder="0"
  width="100%"
  height="248px"
  scrolling="auto">
</iframe>
{% endif %}

<!--
<h4>This is the workshop template.  Use it to create your own website.
Delete these lines and please fill in 
<a href="{{site.amy_site}}/submit">this self-organized workshop form</a>
and the administrator will contact you if we need any extra information.</h4>
-->

<h2 id="general">General Information</h2>

<!--
  INTRODUCTION

  Edit the general explanatory paragraph below if you want to change
  the pitch.
-->
<p>
<br><center><strong>The workshop is taking place during the annual
  <a href="http://www.tucsonrodeo.com/" target="blank">Rodeo Week</a> in Tucson, AZ.<br>
  <h3>Come for the rodeo, stay to wrangle some data!</h3></strong></center><br>
  <a href="{{site.swc_site}}">Software Carpentry</a>
  aims to help researchers get their work done
  in less time and with less pain
  by teaching them basic research computing skills.
  This hands-on workshop will cover basic concepts and tools,
  including program design, version control, data management,
  and task automation.
  Participants will be encouraged to help one another
  and to apply what they have learned to their own research problems.
<em>
    For more information on what we teach and why,
    please see our paper
    "<a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745">Best Practices for Scientific Computing</a>".
  </em>
</p>

<!--
  AUDIENCE

  Explain who your audience is.  (In particular, tell readers if the
  workshop is only open to people from a particular institution.
-->
<p id="who">
  <strong>Who:</strong>
  The course is aimed at practicing researchers - postdocs, graduate students, and other researchers. Undergraduate students can be admitted if space is available.<br>
  <center><strong>Prior knowledge of the tools presented at the workshop is <u>not</u> required.</strong></center>
</p>

<p>
  <b>APPLY</b> at <a href="https://cyverse-sdc.eventbrite.com">https://cyverse-sdc.eventbrite.com</a>
</p>
<!--
  LOCATION

  This block displays the address and links to maps showing directions
  if the latitude and longitude of the workshop have been set.  You
  can use http://itouchmap.com/latlong.html to find the lat/long of an
  address.
-->
{% if page.latlng %}
<p id="where">
  <strong>Where:</strong>
  {{page.address}}.
  Get directions with
  <a href="//www.openstreetmap.org/?mlat={{page.latlng | replace:',','&mlon='}}&zoom=16">OpenStreetMap</a>
  or
  <a href="//maps.google.com/maps?q={{page.latlng}}">Google Maps</a>.
</p>
{% endif %}

<!--
  SPECIAL REQUIREMENTS

  Modify the block below if there are any special requirements.
-->
<p id="requirements">
  <strong>Requirements:</strong> Participants must bring a laptop with a
  Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges
  on. They should have a few specific software packages installed (listed
  <a href="#setup">below</a>). They are also required to abide by
  Software Carpentry's
  <a href="{{site.swc_site}}/conduct.html">Code of Conduct</a>.
</p>

<!--
  ACCESSIBILITY

  Modify the block below if there are any barriers to accessibility or
  special instructions.
-->
<p id="accessibility">
  <strong>Accessibility:</strong> We are committed to making this workshop
  accessible to everybody.
  The workshop organisers have checked that:
</p>
<ul>
  <li>The room is wheelchair / scooter accessible.</li>
  <li>Accessible restrooms are available.</li>
</ul>
<p>
  Materials will be provided in advance of the workshop and
  large-print handouts are available if needed by notifying the
  organizers in advance.  If we can help making learning easier for
  you (e.g. sign-language interpreters, lactation facilities) please
  <a href="mailto:{{page.contact}}">get in touch</a> and we will
  attempt to provide them.
</p>

<!--
  CONTACT EMAIL ADDRESS

  Display the contact email address set in the configuration file.
-->
<p id="contact">
  <strong>Contact</strong>:
  Please email
  {% if page.contact %}
    {% for contact in page.contact %}
      {% if forloop.last and page.contact.size > 1 %}
        or
      {% else %}
        {% unless forloop.first %}
        ,
        {% endunless %}
      {% endif %}
      <a href='mailto:{{contact}}'>{{contact}}</a>
    {% endfor %}
  {% else %}
    to-be-announced
  {% endif %}
  for more information.
</p>

<hr/>

<!--
  SCHEDULE

  Show the workshop's schedule.  Edit the items and times in the table
  to match your plans.  You may also want to change 'Day 1' and 'Day
  2' to be actual dates or days of the week.
-->
<h2 id="schedule">Schedule</h2>

<!-- DO NOT EDIT SURVEY LINKS -->
<p><em>Surveys</em></p>
<p>Please be sure to complete these surveys before and after the workshop.</p>
<p><a href="{{ site.pre_survey }}{{ site.github.project_title }}">Pre-workshop Survey</a></p>
<p><a href="{{ site.post_survey }}{{ site.github.project_title }}">Post-workshop Survey</a></p>

<div class="row">
  <div class="col-md-6">
    <h3>Day 1</h3>
    <table class="table table-striped">
      <tr> <td>08:30</td>  <td>Automate tasks with the Unix shell and GitHub</td> </tr>
      <tr> <td>10:30</td> <td>Coffee</td> </tr>
      <tr> <td>12:30</td>  <td>Lunch break</td> </tr>
      <tr> <td>13:30</td>  <td>Conduct scientific analyses with Python and GitHub</td> </tr>
      <tr> <td>15:00</td>  <td>Coffee</td> </tr>
      <tr> <td>17:00</td>  <td>Dismissal</td> </tr>
    </table>
  </div>
  <div class="col-md-6">
    <h3>Day 2</h3>
    <table class="table table-striped">
      <tr> <td>08:30</td>  <td>Conduct scientific analyses with Python and GitHub, cont.</td> </tr>
      <tr> <td>10:30</td>  <td>Coffee</td> </tr>
      <tr> <td>12:30</td>  <td>Lunch break</td> </tr>
      <tr> <td>13:30</td>  <td>Bring it all together to manage and analyze data</td> </tr>
      <tr> <td>15:00</td>  <td>Coffee</td> </tr>
      <tr> <td>17:00</td>  <td>Dismissal</td> </tr>
    </table>
  </div>
</div>

<!--
  ETHERPAD

  At `_misc/etherpad.txt` you will find a template for the etherpad.

  Display the Etherpad for the workshop.  You can set this up in
  advance or on the first day; either way, make sure you push changes
  to GitHub after you have its URL.  To create an Etherpad, go to

      http://pad.software-carpentry.org/YYYY-MM-DD-site

  where 'YYYY-MM-DD-site' is the identifier for your workshop,
  e.g., '2015-06-10-esu'.
-->
{% if page.etherpad %}
<p id="etherpad">
<h3><strong>We will use an Etherpad (<a href="{{page.etherpad}}">{{page.etherpad}}</a>) for chatting, taking notes, asking questions and sharing URLs and bits of code.</strong></h3>
<br/>
</p>

<p>
<h3><strong>For a history of all commands typed during the Saturday morning session click <a href="https://www.dropbox.com/s/o0obmiht66ymprz/history.txt?dl=0" target="blank">Command Line History Travis</a> or
  <a href="https://dl.dropboxusercontent.com/u/27629977/history.txt" target="blank">Command Line History Upendra</a>.</strong></h3></p>
{% endif %}



<hr/>

<!--
  SYLLABUS

  Show what topics will be covered.

  1. If your workshop is R rather than Python, remove the comment
     around that section and put a comment around the Python section.
  2. Some workshops will delete SQL.
  3. Please make sure the list of topics is synchronized with what you
     intend to teach.
  4. You may need to move the div's with class="col-md-6" around inside
     the div's with class="row" to balance the multi-column layout.

  This is one of the places where people frequently make mistakes, so
  please preview your site before committing, and make sure to run
  'tools/check' as well.
-->
<h2 id="syllabus">Syllabus/Learning Objectives</h2>

<div class="row">
  <div class="col-md-6">
    <h3 id="syllabus-shell"><a href="{{site.swc_pages}}/shell-novice/reference/">The Unix Shell</a></h3>
    <ul>
      <li>Files and directories - in vs. "underneath" the GUI</li>
      <li>History and tab completion</li>
      <li>Pipes and redirection</li>
      <li>Loop over files</li>
      <li>Create and run scripts</li>
      <li>Find things</li>
    </ul>
  </div>
  <div class="col-md-6">
    <h3 id="syllabus-python"><a href="{{site.swc_pages}}/python-novice-inflammation/reference/">Programming With Python</a></h3>
    <ul>
      <li>Use libraries</li>
      <li>Work with arrays</li>
      <li>Read and plot data</li>
      <li>Create and use functions</li>
      <li>Use loops and conditionals</li>
      <li>Use Python from the command line</li>
      <li>Defensive programming</li>
    </ul>
  </div>
  <!--
  <div class="col-md-6">
    <h3 id="syllabus-r">Programming in R</h3>
    <ul>
      <li>Working with vectors and data frames</li>
      <li>Reading and plotting data</li>
      <li>Creating and using functions</li>
      <li>Loops and conditionals</li>
      <li>Using R from the command line</li>
      <li><a href="{{site.swc_pages}}/r-novice-inflammation/reference/">Resource...</a></li>
    </ul>
  </div>
  -->
  <!--
  <div class="col-md-6">
    <h3 id="syllabus-matlab">Programming in MATLAB</h3>
    <ul>
      <li>Working with arrays</li>
      <li>Reading and plotting data</li>
      <li>Creating and using functions</li>
      <li>Loops and conditionals</li>
      <li>Defensive programming</li>
      <li><a href="{{site.swc_pages}}/matlab-novice-inflammation/reference/">Resource...</a></li>
     </ul>
   </div>
   -->
</div>

<div class="row">
  <div class="col-md-6">
    <h3 id="syllabus-git"><a href="{{site.swc_pages}}/git-novice/reference/">Version Control with Git</a></h3>
    <ul>
      <li>Access a repository and pull files</li>
      <li>Create a repository</li>
      <li>Record changes: <code>add</code>, <code>commit</code>, ...</li>
      <li>View changes: <code>status</code>, <code>diff</code>, ...</li>
      <li>Ignore files</li>
      <li>Work on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
      <li>Resolve conflicts</li>
<!--      
      <li>Open licenses</li>
      <li>Where to host work, and why</li>
-->
    </ul>
  </div>
<!--<div class="col-md-6">
    <h3 id="syllabus-sql">Managing Data with SQL</h3>
    <ul>
      <li>Reading and sorting data</li>
      <li>Filtering with <code>where</code></li>
      <li>Calculating new values on the fly</li>
      <li>Handling missing values</li>
      <li>Combining values using aggregation</li>
      <li>Combining information from multiple tables using <code>join</code></li>
      <li>Creating, modifying, and deleting data</li>
      <li>Programming with databases</li>
      <li><a href="{{site.swc_pages}}/sql-novice-survey/reference/">Resource...</a></li>
    </ul>
  </div>
-->
</div>

<hr/>

<h2 id="Resources">Resources</h2>
<div class="row">
  <div class="col-md-6">
    <h3 id="referenc-shell">Unix Shell Resources</h3>
    <ul>
      <li><a href="http://explainshell.com/" target="_blank">Explain Shell: Parses shell commands and shows docs about the command.</a></li>
      <li><a href="http://www.shellcheck.net/" target="_blank">ShellCheck: Identifies bugs in shell scripts.</a></li>
    </ul>
  </div>
  <div class="col-md-6">
    <h3 id="reference-git">Git Resources</h3>
    <ul>
      <li><a href="https://git-scm.com/book/en/v2/Git-in-Other-Environments-Git-in-Bash" target="_blank"><i>Mac/Linux:</i> Integrating Git into your shell prompt</a></li>
      <li><a href="https://github.com/magicmonty/bash-git-prompt" target="_blank">An informative and fancy bash prompt for Git users</a></li>
      <li><a href="https://education.github.com/pack" target="_blank">Unlimited private repositories for free on Github, <i>while you are a student</i></a></li>
      <li><a href="https://git-annex.branchable.com/" target="_blank">Git for Archiving Data</a></li>
    </ul>
  </div>
<!--
  <div class="col-md-6">
    <h3 id="reference-r">R  Resources</h3>
    <ul>
      <li><a href="http://blog.moertel.com/posts/2006-01-20-wondrous-oddities-rs-function-call-semantics.html" target="_blank">R function call Semantics</a></li>
      <li><a href="https://www.r-bloggers.com/" target="_blank">R News and Tutorials contributed by (600) R Bloggers</a></li>
      <li><a href="http://rmarkdown.rstudio.com/" target="_blank">R Markdown Site/Docs</a></li>
      <li><a href="https://www.tutorialspoint.com/r/r_operators.htm" target="_blank">Tutorial: R Operators</a></li>
    </ul>
  </div>
-->
  <div class="col-md-6">
    <h3 id="reference-r">Python Resources</h3>
    <ul>
      <li><a href="https://www.codecademy.com/learn/python" target="_blank">Codecademy: Interactive Python practice lessons</a></li>
      <li><a href="http://rosalind.info/problems/list-view/?location=python-village" target="_blank">Rosalind Python Bioinformatics Practice</a></li>
      <li><a href="https://www.datacamp.com/community/tutorials/tutorial-jupyter-notebook#gs.mz7KeNQ" target="_blank">Jupyter Notebook tutorial</a></li>
      <li><a href="https://plot.ly/python/" target="_blank">Interactive plotting with Plotly (available for R and for Python)</a></li>
    </ul>
  </div>
  <div class="col-md-6">
    <h3 id="reference-r">General  Resources</h3>
    <ul>
      <li><a href="https://2017.resbaz.com/tucson" target="_blank">Research Bazaar Arizona: weekly events to help you out with code and computation</a></li>
      <li><a href="www.cyverse.org" target="_blank">CyVerse: cyberinfrastructure for scientists</a></li>
    </ul>
  </div>

</div>

<!--
  SETUP

  Delete irrelevant sections from the setup instructions.  Each
  section is inside a 'div' without any classes to make the beginning
  and end easier to find.

  This is the other place where people frequently make mistakes, so
  please preview your site before committing, and make sure to run
  'tools/check' as well.
-->

<h2 id="setup">Setup</h2>

<p>
  To participate in a Software Carpentry workshop, you will need
  access to the software described below. In addition, you will
  need an up-to-date web browser.
</p>
<p>
  We maintain a list of common issues that occur during installation as a reference for instructors
  that may be useful on the
  <a href = "{{site.swc_github}}/workshop-template/wiki/Configuration-Problems-and-Solutions">Configuration Problems and Solutions wiki page</a>.
</p>

<div id="shell"> <!-- Start of 'shell' section. -->
  <h3>The Bash Shell</h3>

  <p>
    Bash is a commonly-used shell that gives you the power to do simple
    tasks more quickly.
  </p>

  <div class="row">
    <div class="col-md-4">
      <h4 id="shell-windows">Windows</h4>
      <a href="https://www.youtube.com/watch?v=339AEqk9c-8">Video Tutorial</a>
      <ol>
        <li>Download the Git for Windows <a href="https://git-for-windows.github.io/">installer</a>.</li>
        <li>Run the installer and follow the steps bellow:
          <ol>
            <!-- Git 2.8.2 Setup -->
            <!-- Information -->
            <li>Click on "Next".</li>
            <!-- Select Components -->
            <li>Click on "Next".</li>
            <!-- Adjusting your PATH environment -->
            <li>
              <strong>
                Keep "Use Git from the Windows Command Prompt" selected and click on "Next".
              </strong>
                If you forgot to do this programs that you need for the workshop will not work properly.
                If this happens rerun the installer and select the appropriate option.
            </li>
            <!-- Choosing the SSH executable -->
            <li>Click on "Next".</li>
            <!-- Configuring the line ending conversions -->
            <li>
              <strong>
                Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
              </strong>
            </li>
            <!-- Configuring the terminal emulator to use with Git Bash -->
            <li>
              <strong>
                Keep "Use Windows' default console window" selected and click on "Next".
              </strong>
            </li>
            <!-- Configuring experimental performance tweaks -->
            <li>Click on "Install".</li>
            <!-- Installing -->
            <!-- Completing the Git Setup Wizard -->
            <li>Click on "Finish".</li>
          </ol>
        </li>
        <li>
          If your "HOME" environment variable is not set (or you don't know what this is):
          <ol>
            <li>Open command prompt (Open Start Menu then type <code>cmd</code> and press [Enter])</li>
            <li>
              Type the following line into the command prompt window exactly as shown:
              <p><code>setx HOME "%USERPROFILE%"</code></p>
            </li>
            <li>Press [Enter], you should see <code>SUCCESS: Specified value was saved.</code></li>
            <li>Quit command prompt by typing <code>exit</code> then pressing [Enter]</li>
          </ol>
        </li>
      </ol>
      <p>This will provide you with both Git and Bash in the Git Bash program.</p>
    </div>
    <div class="col-md-4">
      <h4 id="shell-macosx">Mac OS X</h4>
      <p>
        The default shell in all versions of Mac OS X is Bash, so no
        need to install anything.  You access Bash from the Terminal
        (found in
        <code>/Applications/Utilities</code>).
        See the Git installation <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">video tutorial</a>
        for an example on how to open the Terminal.
        You may want to keep
        Terminal in your dock for this workshop.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="shell-linux">Linux</h4>
      <p>
        The default shell is usually Bash, but if your
        machine is set up differently you can run it by opening a
        terminal and typing <code>bash</code>.  There is no need to
        install anything.
      </p>
    </div>
  </div>
</div> <!-- End of 'shell' section. -->

<div id="git"> <!-- Start of 'Git' section. GitHub browser compatability
           is given at https://help.github.com/articles/supported-browsers/-->
  <h3>Git</h3>
  <p>
    Git is a version control system that lets you track who made changes
    to what when and has options for easily updating a shared or public
    version of your code
    on <a href="https://github.com/">github.com</a>. You will need a
    <a href="https://help.github.com/articles/supported-browsers/">supported</a>
    web browser (current versions of Chrome, Firefox or Safari,
    or Internet Explorer version 9 or above).
  </p>
  <p>
    You will need an account at <a href="https://github.com/">github.com</a>
    for parts of the Git lesson. Basic GitHub accounts are free. We encourage
    you to create a GitHub account if you don't have one already.
    Please consider what personal information you'd like to reveal. For
    example, you may want to review these
    <a href="https://help.github.com/articles/keeping-your-email-address-private/">instructions
    for keeping your email address private</a> provided at GitHub.
  </p>

  <div class="row">
    <div class="col-md-4">
      <h4 id="git-windows">Windows</h4>
      <p>
        Git should be installed on your computer as part of your Bash
        install (described above).
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="git-macosx">Mac OS X</h4>
      <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">Video Tutorial</a>
      <p>
        <strong>For OS X 10.9 and higher</strong>, install Git for Mac
        by downloading and running the most recent "mavericks" installer from
        <a href="http://sourceforge.net/projects/git-osx-installer/files/">this list</a>.
        After installing Git, there will not be anything in your <code>/Applications</code> folder,
        as Git is a command line program.
        <strong>For older versions of OS X (10.5-10.8)</strong> use the
        most recent available installer labelled "snow-leopard"
        <a href="http://sourceforge.net/projects/git-osx-installer/files/">available here</a>.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="git-linux">Linux</h4>
      <p>
        If Git is not already available on your machine you can try to
        install it via your distro's package manager. For Debian/Ubuntu run
        <code>sudo apt-get install -y git</code> and for Fedora run
        <code>sudo yum install -y git</code>.
      </p>
    </div>
  </div>
</div> <!-- End of 'Git' section. -->

<div id="editor"> <!-- Start of 'editor' section. -->
  <h3>Text Editor</h3>

  <p>
    When you're writing code, you want to use a text editor that is
    optimized for writing code, with features like automatic
    color-coding of key words.  The default text editor on Mac OS X and
    Linux is usually set to <a href="http://www.vim.org/" target="_blank">Vim</a>, which is not famous for being
    intuitive.  if you accidentally find yourself stuck in it, try
    typing the escape key, followed by <code>:q!</code> (colon, lower-case 'q',
    exclamation mark), then hitting Return to return to the shell.
  </p>

  <div class="row">
    <div class="col-md-4">
      <h4 id="editor-windows">Windows</h4>
      <a href="https://www.youtube.com/watch?v=339AEqk9c-8">Video Tutorial</a>
      <p>
        <b><i>nano</i></b> is a basic editor and the default that instructors use in the workshop.
        To install it,
        download the <a href="{{site.swc_installer}}">Software Carpentry Windows installer</a>
        and double click on the file to run it.
        <strong>This installer requires an active internet connection.</strong>
      </p>
      <p>
        Others editors that you can use are
        <a href="http://notepad-plus-plus.org/">Notepad++</a> or
        <a href="http://www.sublimetext.com/">Sublime Text</a>.
        <strong>Be aware that you must
          add its installation directory to your system path.</strong>
        Please ask your instructor to help you do this.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="editor-macosx">Mac OS X</h4>
      <p>
        nano is a basic editor and the default that instructors use in the workshop.
        See the Git installation <a href="https://www.youtube.com/watch?v=9LQhwETCdwY ">video tutorial</a>
        for an example on how to open nano.
        It should be pre-installed.
      </p>
      <p>
        Others editors that you can use are
        <a href="http://www.barebones.com/products/textwrangler/">Text Wrangler</a> or
        <a href="http://www.sublimetext.com/">Sublime Text</a>.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="editor-linux">Linux</h4>
      <p>
        nano is a basic editor and the default that instructors use in the workshop.
        It should be pre-installed.
      </p>
      <p>
        Others editors that you can use are
        <a href="https://wiki.gnome.org/Apps/Gedit">Gedit</a>,
        <a href="http://kate-editor.org/">Kate</a> or
        <a href="http://www.sublimetext.com/">Sublime Text</a>.
      </p>
    </div>
  </div>
</div> <!-- End of 'editor' section. -->

<div id="python"> <!-- Start of 'Python' section. Remove the third paragraph if
           the workshop will teach Python using something other than
           the IPython notebook.
           Details at http://ipython.org/ipython-doc/2/install/install.html#browser-compatibility -->
  <h3>Python</h3>

  <p>
    <a href="http://python.org">Python</a> is a popular language for
    research computing, and great for general-purpose programming as
    well. <strong>All workshop participants should newly install Pyton (currently version 3.6), regardless of whether they already have Python or not,
    using the all-in-one installer <a href="https://www.continuum.io/anaconda">Anaconda</a>.</strong>
  </p>
    <p>
      We will teach Python using the <a href="https://jupyter-notebook.readthedocs.io/en/latest/"
      target="_blank">Jupyter notebook</a>, a programming environment that runs in a web browser and is being inlcuded in the
      Anaconda installation.
      For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and
      Firefox browsers are all
      <a href="http://ipython.org/ipython-doc/2/install/install.html#browser-compatibility">supported</a>
      (some older browsers, including Internet Explorer version 9 and below, are not).
    </p>

  <div class="row">
    <div class="col-md-4">
      <h4 id="python-windows">Windows</h4>
      <a href="https://www.youtube.com/watch?v=xxQ0mzZ8UvA">Video Tutorial</a>
      <ol>
        <li>Open <a href="http://continuum.io/downloads">http://continuum.io/downloads</a> with your web browser.</li>
        <li>Download the most recent Python 3 installer for Windows. (Currently version 3.6.)</li>
        <li>Install Python 3 using all of the defaults for installation <em>except</em> make sure to check 
          <strong>Make Anaconda the default Python</strong>.</li>
      </ol>
    </div>
    <div class="col-md-4">
      <h4 id="python-macosx">Mac OS X</h4>
      <a href="https://www.youtube.com/watch?v=TcSAln46u9U">Video Tutorial</a>
      <ol>
        <li>Open <a href="http://continuum.io/downloads">http://continuum.io/downloads</a> with your web browser.</li>
        <li>Download the Python 3 installer for OS X. (Currently version 3.6.)</li>
        <li>Install Python 3 using all of the defaults for installation.</li>
      </ol>
    </div>
    <div class="col-md-4">
      <h4 id="python-linux">Linux</h4>
      <ol>
        <li>Open <a href="http://continuum.io/downloads">http://continuum.io/downloads</a> with your web browser.</li>
        <li>Download the Python 3 installer for Linux. (Currently version 3.6.)</li>
        <li>Install Python 3 using all of the defaults for installation.
        (Installation requires using the shell. If you aren't
        comfortable doing the installation yourself
        stop here and request help at the workshop.)</li>
        <li>
          Open a terminal window.
        </li>
        <li>
          Type <pre>bash Anaconda3-</pre> and then press
          tab. The name of the file you just downloaded should
          appear.
        </li>
        <li>
          Press enter. You will follow the text-only prompts.  When
          there is a colon at the bottom of the screen press the down
          arrow to move down through the text. Type <code>yes</code> and
          press enter to approve the license. Press enter to approve the
          default location for the files. Type <code>yes</code> and
          press enter to prepend Anaconda to your <code>PATH</code>
          (this makes the Anaconda distribution the default Python).
        </li>
      </ol>
    </div>
  </div>
<!--
  <p>
  Once you are done installing the software listed above,
  please go to <a href="setup/index.html">this page</a>,
  which has instructions on how to test that everything was installed correctly.
  </p>
-->
</div> <!-- End of 'Python' section. -->

<!-- Start of 'R' section. -->
<!-- 
<div id="r">  <h3>R</h3>

  <p>
    <a href="http://www.r-project.org">R</a> is a programming language
    that is especially powerful for data exploration, visualization, and
    statistical analysis. To interact with R, we use
    <a href="http://www.rstudio.com/">RStudio</a>.
  </p>

  <div class="row">
    <div class="col-md-4">
      <h4 id="r-windows">Windows</h4>
      <a href="https://www.youtube.com/watch?v=q0PjTAylwoU">Video Tutorial</a>
      <p>
        Install R by downloading and running
        <a href="http://cran.r-project.org/bin/windows/base/release.htm">this .exe file</a>
        from <a href="http://cran.r-project.org/index.html">CRAN</a>.
        Also, please install the
        <a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
        Note that if you have separate user and admin accounts, you should run the 
        installers as administrator (right-click on .exe file and select "Run as 
        administrator" instead of double-clicking). Otherwise problems may occur later, 
        for example when installing R packages.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="r-macosx">Mac OS X</h4>
      <a href="https://www.youtube.com/watch?v=5-ly3kyxwEg">Video Tutorial</a>
      <p>
        Install R by downloading and running
        <a href="http://cran.r-project.org/bin/macosx/R-latest.pkg">this .pkg file</a>
        from <a href="http://cran.r-project.org/index.html">CRAN</a>.
        Also, please install the
        <a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="r-linux">Linux</h4>
      <p>
        You can download the binary files for your distribution
        from <a href="http://cran.r-project.org/index.html">CRAN</a>. Or
        you can use your package manager (e.g. for Debian/Ubuntu
        run <code>sudo apt-get install r-base</code> and for Fedora run
        <code>sudo yum install R</code>).  Also, please install the
        <a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
      </p>
    </div>
  </div>
</div>
-->
<!-- End of 'R' section. -->

<!-- Start of 'SQLite' section. -->
<!--
<div id="sql"> 

<h3>SQLite</h3>

  <p>
    SQL is a specialized programming language used with databases.  We
    use a simple database manager called
    <a href="http://www.sqlite.org/">SQLite</a> in our lessons.
  </p>

  <div class="row">
    <div class="col-md-4">
      <h4 id="sql-windows">Windows</h4>
      <p>
        The <a href="{{site.swc_installer}}">Software Carpentry Windows Installer</a>
        installs SQLite for Windows.
        If you used the installer to configure nano, you don't need to run it again.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="sql-macosx">Mac OS X</h4>
      <p>
        SQLite comes pre-installed on Mac OS X.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="sql-linux">Linux</h4>
      <p>
        SQLite comes pre-installed on Linux.
      </p>
    </div>
  </div>

  <p><strong>If you installed Anaconda, it also has a copy of SQLite
    <a href="https://github.com/ContinuumIO/anaconda-issues/issues/307">without support to <code>readline</code></a>.
    Instructors will provide a workaround for it if needed.</strong></p>
</div> 
-->
<!-- End of 'SQLite' section. -->

<!--
  Uncomment this section if you are using our virtual machine.

<div id="vm">
  <h3>Virtual Machine</h3>

  <p>
    Some instructors prefer to have learners use a virtual machine (VM)
    rather than install software on their own computers.  If your
    instructors have chosen to do this, please:
  </p>
  <ol>
    <li>
      Install <a href="https://www.virtualbox.org/">VirtualBox</a>.
    </li>
    <li>
      Download our <a href="{{site.swc_vm}}">VM image</a>.
      <strong>Warning:</strong> this file is 1.7 GByte, so please
      download it <em>before</em> coming to your workshop.
    </li>
    <li>
      Load the VM into VirtualBox by selecting "Import Appliance" and
      loading the <code>.ova</code> file.
    </li>
  </ol>
</div>
-->