index.html

---
layout: workshop
root: .
venue: University of California Berkeley      # brief name of host site without address (e.g., "Euphoric State University")
address: 190 Doe Library    # street address of workshop (e.g., "123 Forth Street, Blimingen, Euphoria")
country: us    # country (lowercase two-letter ISO code such as "fr" - see https://en.wikipedia.org/wiki/ISO_3166-1)
language: en   # language (lowercase two-letter ISO code such as "fr" - see https://en.wikipedia.org/wiki/ISO_639-1)
latlng: "37.871593, -122.272747"     # fractional latitude and longitude (e.g., "41.7901128,-87.6007318"; you can use http://www.latlong.net/)
humandate: Dec 14-15, 2015  # human-readable date (e.g., "Feb 17-18, 2020")
humantime: 9:00 am - 5:00 pm  # human-readable time (e.g., "9:00 am - 4:30 pm")
startdate: 2015-12-14  # use YYYY-MM-DD format like "2015-01-01"
enddate: 2015-12-15    # use YYYY-MM-DD format like" 2015-01-02"
instructor: ["Justin Kitzes", "Kyle Barbary", "Daniel Turek"] # list of names like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["Yu Feng", "Kunal Marwaha", "Zhao Zhang"]     # list of names like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: "jkitzes@berkeley.edu"    # contact email address for workshop organizer, such as "grace@hopper.org"
etherpad: "http://pad.software-carpentry.org/2015-12-14-berkeley"        # optional (insert the URL for your Etherpad if you're using one)
eventbrite:       # optional (insert the alphanumeric key for Eventbrite registration, e.g., "1234567890AB")
---
<!--
  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 %}

<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 the shell, program design, version control, 
  testing, 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>
  This novice level course is aimed at graduate students and other
  researchers who wish to learn the foundational principles of how to do
  data and software driven research. If you have never programmed before
  in any language, this workshop will likely move too quickly for you. If you
  are already comfortable using the shell and frequently write scripts or
  programs longer than 50 lines in any language, you are likely
  too advanced for the material in this workshop. <strong>Students
  who have tried to write code to run their own analyses in a language like
  R, Python, or Matlab but who struggle to do so comfortably are the ideal audience for this 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>
  <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>Arrival</td>  <td><a href='https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id={{ site.github.project_title }}'>Pre-workshop Survey</a></td> </tr>
      <tr> <td>09:00-9:30</td>  <td>Setup and Introductions</td> </tr>
      <tr> <td>09:30-10:45</td>  <td><a href="lessons/shell/">Introducing the Shell</a></td> </tr>
      <tr> <td>10:45-11</td> <td>Break</td> </tr>
      <tr> <td>11:00-12:30</td> <td><a href="lessons/python/">Scientific Programming I</a></td> </tr>
      <tr> <td>12:30-1:30</td>  <td>Lunch break</td> </tr>
      <tr> <td>1:30-3:00</td>  <td><a href="lessons/python/">Scientific Programming I and II</a></td> </tr>
      <tr> <td>3:00-3:15</td>  <td>Break</td> </tr>
      <tr> <td>3:15-5:00</td>  <td><a href="lessons/python/">Scientific Programming II and Wrap Up</a></td> </tr>
    </table>
  </div>
  <div class="col-md-6">
    <h3>Day 2</h3>
    <table class="table table-striped">
      <tr> <td>09:00-10:30</td>  <td><a href="lessons/git/">Version control I</a></td> </tr>
      <tr> <td>10:30-10:45</td>  <td>Break</td> </tr>
      <tr> <td>10:45-12:30</td>  <td><a href="lessons/git/">Version control II</a></td> </tr>
      <tr> <td>12:30-1:30</td>  <td>Lunch</td> </tr>
      <tr> <td>1:30-3:00</td>  <td><a href="lessons/python/testing.html">Modules and Testing</a></td> </tr>
      <tr> <td>3:00-3:15</td>  <td>Break</td> </tr>
      <tr> <td>3:15-5:00</td>  <td><a href="lessons/python/reproducible_workflow.html">Reproducible Workflows</a></td> </tr>
      <tr> <td>Dismissal</td>  <td><a href='https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id={{ site.github.project_title }}'>Post-workshop Survey</a></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>
  <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/>

<!--
  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 = "https://github.com/swcarpentry/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>
      <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 2.6.1 Setup -->
            <!-- Welcome to the Git Setup Wizard -->
            <li>Click on "Next".</li>
            <!-- Information -->
            <li>Click on "Next".</li>
            <!-- Select Destination Location -->
            <li>Click on "Next".</li>
            <!-- Select Components -->
            <li>Click on "Next".</li>
            <!-- Select Start Menu Folder -->
            <li>Click on "Next".</li>
            <!-- Adjusting your PATH environment -->
            <li>
              <strong>
                Select "Use Git from the Windows Command Prompt" 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>
            <!-- Configuring the line ending conversions -->
            <li>
              Click on "Next".
              <strong>
                Keep "Checkout Windows-style, commit Unix-style line endings" selected.
              </strong>
            </li>
            <!-- Configuring the terminal emulator to use with Git Bash -->
            <li>
              <strong>
                Select "Use Windows' default console window" and click on "Next".
              </strong>
            </li>
            <!-- Configuring experimental performance tweaks -->
            <li>Click on "Next".</li>
            <!-- Installing -->
            <!-- Completing the Git Setup Wizard -->
            <li>Click on "Finish".</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>). 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>

  <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 10.9 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> <!-- End of 'Git' section. -->

<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 <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>
      <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.
        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
    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
    <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>
      <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>
      <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>
      </p>
      <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.</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 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>
  <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. -->

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

  <p>
    As a backup plan for any installation issues, you can download the
    Software Carpentry virtual machine (VM)
    rather than install software on your own computer.  To use the VM, 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>