index.html

---
layout: workshop      # DON'T CHANGE THIS.
root: .               # DON'T CHANGE THIS EITHER.  (THANK YOU.)
carpentry: "dc"    # what kind of Carpentry (must be either "dc" or "swc")
venue: "University of Connecticut, Storrs"        # brief name of host site without address (e.g., "Euphoric State University")
address: "Laurel Hall 306, Storrs, CT 06269"      # 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: "41.807232, -72.253436"       # decimal latitude and longitude of workshop venue (e.g., "41.7901128,-87.6007318" - use http://www.latlong.net/)
humandate: "Apr 17, 2017"    # human-readable dates for the workshop (e.g., "Feb 17-18, 2020")
humantime: "10:00 am - 12:00 pm"    # human-readable times for the workshop (e.g., "9:00 am - 4:30 pm")
startdate: 2017-04-17      # machine-readable start date for the workshop in YYYY-MM-DD format like 2015-01-01
enddate: 2017-04-17        # machine-readable end date for the workshop in YYYY-MM-DD format like 2015-01-02
instructor: ["Pariksheet Nanda"] # boxed, comma-separated list of instructors' names as strings, like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["Jingwen Pei", "Xin Li", "Tingyang Xu", "Christian Kuntz", "Luke Malinowski", "Dave Christianson", "Ed Swindelles"]     # boxed, comma-separated list of helpers' names, like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: ["hpc@uconn.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"]
collaborative_notes:             # optional: URL for the workshop collaborative notes, e.g. an Etherpad or Google Docs document
eventbrite: 33643014161          # 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="285px"
  scrolling="auto"
  vspace="0"
  hspace="0"
  marginheight="5"
  marginwidth="5"
  allowtransparency="true">
</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>
  The HPC Essentials workshop is for any researcher
  to use UConn's computer cluster
  with no prior experience of the command-line or programming.
  We will cover what the cluster can do for you,
  how to navigate the command-line interface to run your programs
  and transfer data.
</p>
<p align="center">
  <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 graduate students and other researchers.
  <strong>You don't need to have any previous knowledge of the tools that will
    be presented at the workshop.</strong>
</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 %}

<!--
  DATE

  This block displays the date and links to Google Calendar.
-->
{% if page.humandate %}
<p id="when">
  <strong>When:</strong>
  {{page.humandate}}.
  {% include workshop_calendar.html %}
</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 system (not a tablet, Chromebook, etc.) that they have administrative privileges
  on. They should have a few specific software packages installed and an account on the HPC cluster (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">
    <table class="table table-striped">
      <tr> <td>10:00</td> <td>What is a modern supercomputer?</td> </tr>
      <tr> <td>10:10</td> <td>Using the UNIX shell</td> </tr>
      <tr> <td>11:00</td> <td>Loading modules and submitting jobs to the cluster</td> </tr>
      <tr> <td>11:45</td> <td>Saving results with Globus</td> </tr>
      <tr> <td>12:00</td> <td>Wrap-up</td> </tr>
    </table>
  </div>
</div>

<!--
  Collaborative Notes

  If you want to use 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.collaborative_notes %}
<p id="collaborative_notes">
  We will use this <a href="{{page.collaborative_notes}}">collaborative document</a> for chatting, taking notes, and sharing URLs and bits of code.
</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</h2>

<div class="row">
  <div class="col-md-6">
    <h3 id="syllabus-shell">The Unix Shell</h3>
    <ul>
      <li>Files and directories</li>
      <li>History and tab completion</li>
      <li>Creating and running shell scripts</li>
      <li><a href="{{site.swc_pages}}/shell-novice/reference/">Reference...</a></li>
    </ul>
  </div>
  <!--
  <div class="col-md-6">
    <h3 id="syllabus-python">Programming in Python</h3>
    <ul>
      <li>Using libraries</li>
      <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>Using Python from the command line</li>
      <li><a href="{{site.swc_pages}}/python-novice-inflammation/reference/">Reference...</a></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/">Reference...</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/">Reference...</a></li>
     </ul>
   </div>
   -->
</div>
<!--
<div class="row">
  <div class="col-md-6">
    <h3 id="syllabus-git">Version Control with Git</h3>
    <ul>
      <li>Creating a repository</li>
      <li>Recording changes to files: <code>add</code>, <code>commit</code>, ...</li>
      <li>Viewing changes: <code>status</code>, <code>diff</code>, ...</li>
      <li>Ignoring files</li>
      <li>Working on the web: <code>clone</code>, <code>pull</code>, <code>push</code>, ...</li>
      <li>Resolving conflicts</li>
      <li>Open licenses</li>
      <li>Where to host work, and why</li>
      <li><a href="{{site.swc_pages}}/git-novice/reference/">Reference...</a></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/">Reference...</a></li>
    </ul>
  </div>
</div>
-->
<hr/>

<!--
  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 the 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>
      <p>You will need a terminal program to access the HPC cluster.</p>
      <ol>
	<li>Go to the Putty <a href="http://www.chiark.greenend.org.uk/%7Esgtatham/putty/download.html">download
	    page</a></li>
	<li>Click on <i>putty.exe</i> link under <strong>Alternative binary files</strong> to download putty</li>
	<li>To use it, double-click on the downloaded file</li>
      </ol>
    </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>).
        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="cluster">
  <h3>HPC cluster account</h3>
  <p>
    Please verify that you can connect to the HPC cluster via <code>login.storrs.hpc.uconn.edu</code>
    as described on our <a href="https://wiki.hpc.uconn.edu/index.php/HPC_Getting_Started">HPC wiki</a>.
    If you have not connected to the cluster before,
    you will need to login with your NetID and
    request an account using this form:
    <a href="http://hpc.uconn.edu/storrs/account-application">hpc.uconn.edu/storrs/account-application</a>.
  </p>
  <p>
    If you do not have a Net ID,
    please have a faculty member or other UConn employee
    setup an affiliate NetID for you: <a href="http://affiliate.uconn.edu">affiliate.uconn.edu</a>.
    Approval for a NetID takes about 1-2 business days.
  </p>
</div>

<!--
<div id="git">
  <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 git</code> and for Fedora run
        <code>sudo yum install git</code>.
      </p>
    </div>
  </div>
</div>

<div id="editor">
  <h3>Text Editor</h3>

  <p>
    When you're writing code, it's nice to have 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 Vim, 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>
        nano 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>

<div id="python">
  <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.  Installing all of its research packages individually can be
    a bit difficult, so we recommend
    <a href="https://www.continuum.io/anaconda">Anaconda</a>,
    an all-in-one installer.
  </p>

    <p>
      Regardless of how you choose to install it,
      <strong>please make sure you install Python version 3.x</strong>
      (e.g., 3.4 is fine).
    </p>

    <p>
      We will teach Python using the IPython notebook, a programming environment
      that runs in a web browser. 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 Python 3 installer for Windows.</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.</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.<br>
          (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. If it does not, navigate to the folder where you
          downloaded the file, for example with:
          <pre>cd Downloads</pre>
          Then, try again.
        </li>
        <li>
          Press enter. You will follow the text-only prompts. To move through
          the text, press the space key. 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>
        <li>
          Close the terminal window.
      </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>

<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>

<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>
-->