index.html

---
layout: workshop
root: .
venue: Bioinformatics, University of Cambridge
address: Craik-Marshall Building, Downing Site, Cambridge
country: United-Kingdom
language: en
latlng: 52.201965,0.122486,17 
humandate: June 15-16, 2015
humantime: 9:30 am - 17:30 pm
startdate: 2015-06-15
enddate: 2015-06-16
instructor: Aaron O'Leary, Myrto Kostadima
helper: 
contact: Gabriella Rustici <gr231@cam.ac.uk>
etherpad: # FIXME (insert the URL for your Etherpad if you're using one)
eventbrite:
---
<!--
  HEADER

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  workshop.  Run 'tools/check' *before* committing to make sure that
  changes are good.
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<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>

<!--
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<p>
  <strong>Who:</strong>
  The course is aimed at graduate students and other researchers.
</p>

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  <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

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-->
<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>

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  <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>

<p>
  <strong>Registration</strong>:
  See <a href='http://training.csx.cam.ac.uk/bioinformatics/event/1393220'>here</a>
  for more information.
</p>

<hr/>

<!--
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  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>

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  <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

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  2. Some workshops will delete SQL.
  3. Please make sure the list of topics is synchronized with what you
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<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/>

<!--
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<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="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>
    </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 10.8 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="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 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 workshop.)
      </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 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>
</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>
-->