index.html

---
layout: workshop
root: .
venue: FIXME (brief name of host site)
address: FIXME (street address of home location)
country: FIXME (country (hyphenated if need be, like 'United-Kingdom')
language: FIXME (language code like 'en' or 'fr')
latlng: (fractional latitude and longitude like 41.7901128,-87.6007318)
humandate: FIXME (use the format 'Feb 17-18, 2020' (without the quotes)
humantime: FIXME (use the format '9:00 am - 4:30 pm' (without the quotes)
startdate: FIXME (use YYYY-MM-DD format like 2015-01-01)
enddate: FIXME (use YYYY-MM-DD format like 2015-01-02)
instructor: (list of names like ["Kay McNulty", "Betty Jennings", "Betty Snyder"])
helper: (list of names like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"])
contact: FIXME (contact email address for workshop organizer)
etherpad: # FIXME (insert the URL for your Etherpad if you're using one)
eventbrite: # FIXME (delete this if not used, otherwise uncomment and provide 1234567890AB key for Eventbrite registration)
---
<!--
  HEADER

  Edit the values in the block above to be appropriate for your
  workshop.  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="206px"
  scrolling="auto">
</iframe>
{% endif %}

<h2>General Information</h2>

<!--
  INTRODUCTION

  Edit the general explanatory paragraph below if you want to change
  the pitch.
-->
<p>
  <a href="{{site.swc_site}}">Software Carpentry</a>'s mission
  is to help scientists and engineers get more research done in less
  time and with less pain by teaching them basic lab skills for
  scientific computing.  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.
</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>
  <strong>Who:</strong>
  The course is aimed at graduate students and other researchers.
</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>
  <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>
  <strong>Requirements:</strong> Participants must bring a laptop with
  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>

<!--
  CONTACT EMAIL ADDRESS

  Display the contact email address set in the header.  If an address
  isn't set in the header, the Software Carpentry admin address is
  used.
-->
<p>
  <strong>Contact</strong>:
  Please mail
  {% if page.contact %}
    <a href='mailto:{{page.contact}}'>{{page.contact}}</a>
  {% else %}
    <a href='mailto:{{site.contact}}'>{{site.contact}}</a>
  {% 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>Schedule</h2>

<div class="row">
  <div class="col-md-6">
    <h3>Day 1</h3>
    <table class="table table-striped">
      <tr> <td>09:00</td>  <td>Automating tasks with the Unix shell</td> </tr>
      <tr> <td>10:30</td> <td>Coffee</td> </tr>
      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
      <tr> <td>13:00</td>  <td>Building programs with Python</td> </tr>
      <tr> <td>14:30</td>  <td>Coffee</td> </tr>
      <tr> <td>16:00</td>  <td>Wrap-up</td> </tr>
    </table>
  </div>
  <div class="col-md-6">
    <h3>Day 2</h3>
    <table class="table table-striped">
      <tr> <td>09:00</td>  <td>Version control with Git</td> </tr>
      <tr> <td>10:30</td>  <td>Coffee</td> </tr>
      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
      <tr> <td>13:00</td>  <td>Managing data with SQL</td> </tr>
      <tr> <td>14:30</td>  <td>Coffee</td> </tr>
      <tr> <td>16:00</td>  <td>Wrap-up</td> </tr>
    </table>
  </div>
</div>

<!--
  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://etherpad.mozilla.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>
  <strong>Etherpad:</strong> <a href="{{page.etherpad}}">{{page.etherpad}}</a>.
  <br/>
  We will use this Etherpad 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>Syllabus</h2>

<div class="row">
  <div class="col-md-6">
    <h3>The Unix Shell</h3>
    <ul>
      <li>Files and directories</li>
      <li>History and tab completion</li>
      <li>Pipes and redirection</li>
      <li>Looping over files</li>
      <li>Creating and running shell scripts</li>
      <li>Finding things</li>
      <li><a href="{{site.swc_lessons}}/ref/01-shell.html">Reference...</a></li>
    </ul>
  </div>
  <div class="col-md-6">
    <h3>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_lessons}}/ref/03-python.html">Reference...</a></li>
    </ul>
  </div>
  <!--
  <div class="col-md-6">
    <h3>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_lessons}}/ref/06-R.html">Reference...</a></li>
    </ul>
  </div>
  -->
</div>

<div class="row">
  <div class="col-md-6">
    <h3>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_lessons}}/ref/02-git.html">Reference...</a></li>
    </ul>
  </div>
  <div class="col-md-6">
    <h3>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_lessons}}/ref/04-sql.html">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 a Software Carpentry workshop, you will need 
  access to the software described below. In addition, you will 
  need an up-to-date web browser.
  Once you are done installing the software listed below,
  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 id="editor"> <!-- Start of 'editor' section. -->
  <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 ':q!' (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>
      <p>
	<code>nano</code> is the editor installed by the Software
	Carpentry Installer, it is a basic editor integrated into the
	lesson material.
      </p>
      <p>
	<a href="http://notepad-plus-plus.org/">Notepad++</a> is a
	popular free code editor for Windows.  Be aware that you must
	add its installation directory to your system path in order to
	launch it from the command line (or have other tools like Git
	launch it for you).  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>
	We recommend
	<a href="http://www.barebones.com/products/textwrangler/">Text Wrangler</a> or
	<a href="http://www.sublimetext.com/">Sublime Text</a>.
	In a pinch, you can use <code>nano</code>,
	which should be pre-installed.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="editor-linux">Linux</h4>
      <p>
	<a href="http://kate-editor.org/">Kate</a> is one option for
	Linux users.  In a pinch, you can use <code>nano</code>, which
	should be pre-installed.
      </p>
    </div>
  </div>
</div> <!-- End of 'editor' section. -->

<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>
	Install Git for Windows by downloading and running
	<a href="http://msysgit.github.io/">the installer</a>.
	This will provide you with both Git and Bash in the Git Bash program.
      </p>
      <h4>Software Carpentry Windows Installer</h4>
      <p>It installs and configures <code>nano</code> (<a href="{{site.swc_github}}/windows-installer">Among other things</a>)</p>
      <p><em>This installer requires an active internet connection.</em></p>
      <p>After installing Git Bash:</p>
      <ul>
	<li>
          Download the <a href="{{site.swc_installer}}">Software Carpentry Windows installer</a>.
	</li>
	<li>
          Double click on the file to run it.
	</li>
      </ul>
    </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 <code>bash</code>, 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>

  <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>
      <p>
	<strong>For OS X 10.8 and higher</strong>, install Git for Mac
	by downloading and running
	<a href="http://sourceforge.net/projects/git-osx-installer/files/latest/download">the installer</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 (10.5-10.7)</strong> use the
	most recent available installer for your
	OS <a href="http://sourceforge.net/projects/git-osx-installer/files/">available
	  here</a>.  Use the Leopard installer for 10.5 and the Snow
	Leopard installer for 10.6-10.7.
      </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> <!-- End of 'Git' 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
    scientific computing, and great for general-purpose programming as
    well.  Installing all of its scientific packages individually can be
    a bit difficult, so we recommend an all-in-one installer.
  </p>

    <p>
      Regardless of how you choose to install it,
      <strong>please make sure you install Python version 2.x and not version 3.x</strong>
      (e.g., 2.7 is fine but not 3.4).
      Python 3 introduced changes that will break some of the code we teach during the workshop.
    </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>
      <ul>
	<li>
          Download and
          install <a href="https://store.continuum.io/cshop/anaconda/">Anaconda</a>.
	</li>
	<li>
          Download the default Python 2 installer (do not follow the link to version 3).
	  Use all of the defaults for installation
          <em>except</em> make sure to check
	  <strong>Make Anaconda the default Python</strong>.
	</li>
      </ul>
    </div>
    <div class="col-md-4">
      <h4 id="python-macosx">Mac OS X</h4>
      <ul>
	<li>
          Download and
          install <a href="https://store.continuum.io/cshop/anaconda/">Anaconda</a>.
	</li>
	<li>
          Download the default Python 2 installer (do not follow the link to version 3).
	  Use all of the defaults for installation.
	</li>
      </ul>
    </div>
    <div class="col-md-4">
      <h4 id="python-linux">Linux</h4>
      <p>
	We recommend the all-in-one scientific Python installer
	<a href="http://continuum.io/downloads.html">Anaconda</a>.
	(Installation requires using the shell and if you aren't
	comfortable doing the installation yourself just
	download the installer and we'll help you at the boot
	camp.)
      </p>
      <ol>
	<li>
          Download the installer that matches your operating
          system and save it in your home folder.
	  Download the default Python 2 installer (do not follow the link to version 3). 
	</li>
	<li>
          Open a terminal window.
	</li>
	<li>
          Type <pre>bash Anaconda-</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>
</div> <!-- End of 'Python' section. -->

<div id="r"> <!-- Start of 'R' section. -->
  <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>
      <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>.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="r-macosx">Mac OS X</h4>
      <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. -->

<div id="sql"> <!-- Start of 'SQLite' section. -->
  <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_github}}/windows-installer">Software Carpentry
          Windows Installer</a> installs <code>sqlite3</code> 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>
	<code>sqlite3</code> comes pre-installed on Mac OS X.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="sql-linux">Linux</h4>
      <p>
	<code>sqlite3</code> comes pre-installed on Linux.
      </p>
    </div>
  </div>
</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>
-->