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.github/ISSUE_TEMPLATE.md

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Please delete the text below before submitting your contribution. 



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Thanks for contributing! If this contribution is for instructor training, please send an email to checkout@carpentries.org with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  



Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck (k8hertweck@gmail.com).  



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.github/PULL_REQUEST_TEMPLATE.md

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Please delete the text below before submitting your contribution. 



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Thanks for contributing! If this contribution is for instructor training, please send an email to checkout@carpentries.org with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution.  



Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum.  If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck (k8hertweck@gmail.com).  



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_includes/dc/intro.html

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<p>

  <a href="{{site.dc_site}}">Data Carpentry</a>

  aims to help researchers get their work done

  in less time and with less pain

  by teaching them basic research computing skills.

  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>

_includes/dc/schedule.html

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<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>

_includes/dc/syllabus.html

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<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>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_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 class="col-md-6">

    <h3 id="syllabus-r">Open Refine</h3>

    <ul>

      <li>Introduction to OpenRefine</li>

      <li>Importing data</li>

      <li>Basic functions</li>

      <li>Advanced Functions</li>

      <li><a href="{{site.lc_pages}}library-openrefine/reference">Reference...</a></li>

    </ul>

  </div>

</div>