index.html

---
layout: workshop
root: .
workshop: Reproducible Science Workshop - Tools, Resources, and Practices
venue: Duke Marine Lab, Auditorium
address: 135 Duke Marine Lab Rd, Beaufort, NC 28516
country: United-States
language: en
latlng: 34.7169124,-76.6721571
humandate: September 24-25, 2015
humantime: 9:00 am - 5:00 pm
startdate: 2015-09-24
enddate: 2015-09-25
instructor: ["Mine Çetinkaya-Rundel (Duke, <a href='https://stat.duke.edu/'
target='_blank'>Dept. of Statistical Science</a>)", "Karen Cranston (Duke, <a href='http://opentreeoflife.org' target='_blank'>Open Tree of Life</a>)", "Hilmar Lapp (Duke, <a href='http://genome.duke.edu' target='_blank'>GCB</a>)", "Dan Leehr (Duke, <a href='http://genome.duke.edu' target='_blank'>GCB</a>)"]
contact: hilmar.lapp@duke.edu
etherpad: https://etherpad.mozilla.org/cwfShOVreq
eventbrite: # 18455296288
---
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<h2 id="info">General Information</h2>

<!--
  INTRODUCTION

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  the pitch.
-->
<p>
  Making science more reproducible has the potential to advance
  scientific research and make researchers' work more effective and productive.
  For computational and data-intensive research, which is increasingly
  pervasive across the sciences, this is particularly true, and yet is often
  seen as difficult to achieve. In this 2-day bootcamp-style hands-on workshop,
  we will teach a number of tools, resources, and practices that can be used
  today to make one's computational science more reproducible.
</p>
<p>
  The course and the curriculum were developed by the participants of
  the <a href="https://github.com/Reproducible-Science-Curriculum/Reproducible-Science-Hackathon-Dec-08-2014">Reproducible
  Science Curriculum Hackathon</a> held at the
  National Evolutionary Synthesis Center (<a href="http://nescent.org">NESCent</a>) in
  December 2014. The hackathon and instructor travel are supported by the National
  Science Foundation (NSF).
</p>

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<p>
  <strong>Who:</strong>
  The course is aimed at graduate students, postdocs, and other
  researchers who perform computational analysis or work. The material
  on automation uses basic R for teaching and illustrating the key
  concepts. Advanced knowledge of R is not needed, but some familiarity with R
  will make the workshop more enjoyable.
</p>

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</p>
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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 our
  <a href="{{site.swc_site}}/conduct.html">Code of Conduct</a>, which we have adopted from Software Carpentry.
</p>
<p>The course is free but requires registration. We ask that as a
courtesy to others you cancel as early as possible if you register and
subsequently are prevented from taking your seat.
</p>

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  <strong>Contact</strong>:
  Please email
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  {% else %}
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  for more information.
</p>

<hr/>

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<h2 id="schedule">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>Introduction to Reproducible Research</td> </tr>
      <tr> <td>10:30</td>  <td>Coffee/Tea break</td> </tr>
      <tr> <td>10:45</td>  <td>Organizing your project to facilitate Reproducible Research</td> </tr>
      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
      <tr> <td>13:00</td>  <td>Literate programming</td> </tr>
      <tr> <td>15:00</td>  <td>Coffee/Tea break</td> </tr>
      <tr> <td>15:30</td>  <td>Literate programming</td> </tr>
      <tr> <td>17:00</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</td> </tr>
      <tr> <td>10:30</td>  <td>Coffee/Tea break</td> </tr>
      <tr> <td>10:45</td>  <td>Automating your workflows</td> </tr>
      <tr> <td>12:00</td>  <td>Lunch break</td> </tr>
      <tr> <td>13:00</td>  <td>Automating your workflows</td> </tr>
      <tr> <td>15:00</td>  <td>Coffee/Tea break</td> </tr>
      <tr> <td>15:30</td>  <td>Sharing and publishing your research workflow</td></tr>
      <tr> <td>16:30</td>  <td>Wrap-up</td> </tr>
    </table>
  </div>
</div>

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<!-- <hr/> -->

<!--
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<h2>Syllabus</h2>

<div class="row">
  <div class="col-md-4">
    <h3>Introduction to Reproducible Research</h3>
    <ul>
      <li>Recognize the problems that reproducible research helps address</li>
      <li>Identify pain points in getting your analysis to be reproducible.</li>
      <li>The role of documentation, sharing, automation, and organization in making your research more reproducible.</li>
      <li>Introducing some tools to solve these problems, specifically R/RStudio/RMarkdown.</li>
      <li>Slides:
       <ul>
       <li><a href="intro-slides/intro-01-slides.html">Intro I slides</a></li>
       <li><a href="intro-slides/intro-02-slides.html">Intro II slides</a></li>
       </ul></li>
    </ul>
  </div>
  <div class="col-md-4">
    <h3>Organizing your project to facilitate Reproducible Research</h3>
    <ul>
      <li>Organize projects and folders to enable reproducibility and reusability</li>
      <li>Understand the structure of data files and the importance of documenting all changes made</li>
      <li>Using these practices, create a reproducible project workflow using knitr in RStudio.</li>
      <li>Slides:
      <ul>
        <li><a href="organization-slides/">File organization</a></li>
        <li><a href="naming-slides/">File naming</a></li>
      </ul></li>
    </ul>
  </div>
  <div class="col-md-4">
    <h3>Literate programming</h3>
    <ul>
      <li>Understand the value of having question, source code, and
  result side by side</li>
      <li>Use literate programming to create executable documentation</li>
      <li>Create self-documenting data cleaning and quality control reports</li>
      <li>Slides:
      <ul>
        <li><a href="lit-prog-slides/">Literate programming</a></li>
      </ul></li>
    </ul>
  </div>
</div>


<div class="row">
  <div class="col-md-4">
    <h3>Version control</h3>
     <ul>
      <li>Exposure to the motivations of using version control.</li>
      <li>Learn the basics of Git via Git and Github.</li>
      <li>Slides:
        <ul><li><a href="slides/01-github-slides.html">Version control, Git, and Github</a></li>
      </ul></li>
     </ul>
  </div>
  <div class="col-md-4">
    <h3>Automating your workflows</h3>
    <ul>
      <li>Transforming scripts into functions</li>
      <li>Make files as a concept</li>
      <li>Utilizing free continuous integration tools</li>
      <li>Recreate figures automatically</li>
      <li>Slides:
      <ul>
        <li><a href="slides/01-automation-slides.html">Automation</a></li>
        <li><a href="slides/02-functions-slides.html">Functions</a></li>
        <li><a href="slides/03-functions-for-data-slides.html">Functions for data</a></li>
        <li><a href="slides/04-functions-for-figures-slides.html">Functions for figures</a></li>
        <li><a href="slides/05-testing-slides.html">Testing</a></li>
        <li><a href="slides/06-automating-slides.html">Putting it all together</a></li>
      </ul></li>
    </ul>
  </div>
  <div class="col-md-4">
    <h3>Sharing and publishing your research workflow</h3>
    <ul>
      <li>Ensuring your workflow is permanently archived and citable</li>
      <li>Documentation and metadata for reusability</li>
      <li>Choosing licenses for software and data</li>
      <li>Slides:
        <ul><li><a href="slides/01-publication-slides.html">Sharing, publishing, archiving, licensing</a></li></ul>
      </li>
    </ul>
  </div>
</div>


<hr/>

<!-- materials -- zip files to download -->
<h2 id="materials">Materials</h2>
<div class="row">
  <div class="col-md-4">
    <h3>Introduction</h3>
    <ul>
      <li><a href="https://github.com/Reproducible-Science-Curriculum/rr-intro/archive/data-v0.2.zip">Download</a></li>
    </ul>
  </div>
  <div class="col-md-4">
    <h3>Organization</h3>
    <ul>
      <li><a href="https://github.com/Reproducible-Science-Curriculum/rr-organization1/archive/data-v0.4.zip">Download</a></li>
    </ul>
  </div>
  <div class="col-md-4">
    <h3>Literate Programming</h3>
    <ul>
      <li><a href="https://github.com/Reproducible-Science-Curriculum/rr-literate-programming/archive/data-v0.4.zip">Download</a></li>
    </ul>
  </div>
</div>
<div class="row">
  <div class="col-md-4">
    <h3>Automation</h3>
    <ul>
      <li><a href="https://github.com/Reproducible-Science-Curriculum/rr-automation/archive/data-v0.2.zip">Download</a></li>
    </ul>
  </div>
  <div class="col-md-8">
    <h3>Reproducibility checklist</h3>
    <p>A <a href="checklist.html">checklist</a> to evaluate and stimulate thoughts
      about the reproducility of your project.</p>
  </div>
</div>

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<h2 id="setup">Setup</h2>
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<p>
  <a href="setup/index.html">This page</a> has instructions on testing
  that you have the right software installed.
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<!--
<div> <!-- 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>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>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>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> <!-- 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>Windows</h4>
      <p>
	Install Git for Windows by download 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 Installer</h4>
      <p><em>This installer requires an active internet connection.</em></p>
      <p>After installing Python and Git Bash:</p>
      <ul>
	<li>
          Download the <a href="{{site.swc_installer}}">installer</a>.
	</li>
	<li>
          If the file opens directly in the browser
          select <strong>File&rarr;Save Page As</strong> to download it
          to your computer.
	</li>
	<li>
          Double click on the file to run it.
	</li>
      </ul>
      <p>
	Information about the SWC Windows Installer,
	including the source code, can be found at
	<a href="https://github.com/swcarpentry/windows-installer">https://github.com/swcarpentry/windows-installer</a>.
      </p>
    </div>
    <div class="col-md-4">
      <h4>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>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> <!-- Start of 'Git' section. -->
  <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>. See the instructions
    below for your operating system. Windows and Mac Users (with OSX 10.9+) will
    install the GitHub GUI, while Linux and Mac users with older operating
    systems will install the command line utility.
  </p>

  <p>
    If you don't already have a GitHub account,
    please <a href="https://github.com/join">create one</a>.
  </p>

  <div class="row">
    <div class="col-md-4">
      <h4>Windows</h4>
      <p>
	Please download the GitHub GUI <a href="https://windows.github.com/">here</a>.
      </p>
    </div>
    <div class="col-md-4">
      <h4>Mac OS X</h4>
      <p>
	<strong>For OS X 10.9 and higher</strong>, install the GitHub GUI for Mac
        by downloading and running the installer from
        <a href="https://mac.github.com/">here</a>.
        <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>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> <!-- Start of 'Python' section. --><!--
  <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>

  <div class="row">
    <div class="col-md-4">
      <h4>Windows</h4>
      <ul>
	<li>
          Download and
          install <a href="https://store.continuum.io/cshop/anaconda/">Anaconda</a>.
	</li>
	<li>
          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>Mac OS X</h4>
      <ul>
	<li>
          Download and
          install <a href="https://store.continuum.io/cshop/anaconda/">Anaconda</a>.
	</li>
	<li>
          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>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.
	</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> <!-- 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>. After installing both R and
    RStudio, start RStudio and install some packages that we will need for the
    workshop (see bottom of the page).
  </p>

   <h5>There is brand new version of RStudio available as of May 26th
    (v0.99.441), make sure to update if you already have RStudio installed.</h5>

  <div class="row">
    <div class="col-md-4">
      <h4>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>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>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>

  <h4> After installing R and RStudio</h4>
  <p>
    Start RStudio, and type (or copy and paste) at the console:
    <code>
      install.packages(c("knitr", "rmarkdown", "ggplot2", "dplyr"))
    </code>
  </p>

</div> <!-- End of 'R' section. -->

<!--
<div> <!-- 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>Windows</h4>
      <p>
	Download the <a href="{{site.swc_files}}/sqlite3.exe">sqlite3
	  program</a> and put it in the directory where you are running
	examples.
      </p>
    </div>
    <div class="col-md-4">
      <h4>Mac OS X</h4>
      <p>
	<code>sqlite3</code> comes pre-installed on Mac OS X.
      </p>
    </div>
    <div class="col-md-4">
      <h4>Linux</h4>
      <p>
	<code>sqlite3</code> comes pre-installed on Linux.
      </p>
    </div>
  </div>
</div> <!-- End of 'SQLite' section. -->


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  Uncomment this section if you are using our virtual machine.

<div>
  <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>
-->

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