index.html

---
layout: workshop      # DON'T CHANGE THIS.
root: .               # DON'T CHANGE THIS EITHER.  (THANK YOU.)
carpentry: "swc"    # what kind of Carpentry (must be either "dc" or "swc")
venue: "Software Carpentry @ University of Glasgow, Future of Computational Science Event"        # brief name of host site without address (e.g., "Euphoric State University")
address: "Level 5, School of Computing Science, Sir Alwyn Williams Building, University of Glasgow, Glasgow, G12 8QQ"      # full street address of workshop (e.g., "Room A, 123 Forth Street, Blimingen, Euphoria")
country: "UK"      # lowercase two-letter ISO country code such as "fr" (see https://en.wikipedia.org/wiki/ISO_3166-1)
language: "en"     # lowercase two-letter ISO language code such as "fr" (see https://en.wikipedia.org/wiki/ISO_639-1)
latlng: "55.873890,-4.291815"       # decimal latitude and longitude of workshop venue (e.g., "41.7901128,-87.6007318" - use http://www.latlong.net/)
humandate: "Oct 16-17, 2017"    # human-readable dates for the workshop (e.g., "Feb 17-18, 2020")
humantime: "9:00 - 17:00"    # human-readable times for the workshop (e.g., "9:00 am - 4:30 pm")
startdate: 2017-10-16      # machine-readable start date for the workshop in YYYY-MM-DD format like 2015-01-01
enddate: 2017-10-17        # machine-readable end date for the workshop in YYYY-MM-DD format like 2015-01-02
instructor: ["Manos Farsarakis", "Adrian Jackson"] # boxed, comma-separated list of instructors' names as strings, like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["Tom Wallis","Craig Reily","William Kavangh","Robbie Simpson","Stephen McQuistin"]     # boxed, comma-separated list of helpers' names, like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: ["support@archer.ac.uk"]    # boxed, comma-separated list of contact email addresses for the host, lead instructor, or whoever else is handling questions, like ["marlyn.wescoff@example.org", "fran.bilas@example.org", "ruth.lichterman@example.org"]
etherpad: http://pad.software-carpentry.org/2017-10-16-Glasgow         # optional: URL for the workshop Etherpad if there is one
eventbrite:           # optional: alphanumeric key for Eventbrite registration, e.g., "1234567890AB" (if Eventbrite is being used)
---

<!-- See instructions in the comments below for how to edit specific sections of this workshop template. -->

<!--
  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 %}

<!--
<h4>This is the workshop template.  Use it to create your own website.
Delete these lines and please fill in 
<a href="{{site.amy_site}}/submit">this self-organized workshop form</a>
and the administrator will contact you if we need any extra information.</h4>
-->

<h2 id="general">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>
  aims to help researchers get their work done
  in less time and with less pain
  by teaching them basic research computing skills.
</p>  
<p>
  This workshop is hosted by EPCC, Edinburgh Parallel Computing Centre, and organised in collaboration by ARCHER, the Software Sustainability Institute, and UoE Research Data Service.
</p>
<p>
  <a href="http://www.archer.ac.uk">ARCHER</a>, the UK's national
  supercomputing service, offers training in software development and
  high-performance computing to scientists and researchers across the
  UK. As part of our training service we are running a two-day Data
  Carpentry workshop. 
</p>
<!--
<p>
  The <a href="http://www.software.ac.uk">Software Sustanability Institute</a>'s mission is to cultivate better, more sustainable, research software to enable world-class research (<a href="http://softwaresaved.spreadshirt.co.uk/"><em>better software, better research</em></a>). Software is fundamental to research: <a href="http://www.software.ac.uk/blog/2014-12-04-its-impossible-conduct-research-without-software-say-7-out-10-uk-researchers">seven out of ten UK researchers report that their work would be impossible without it</a>.
</p>
<p>
The <a href="http://www.ed.ac.uk/information-services/research-support/research-data-service">Research Data Service</a> is a suite of tools and support for University staff and students to aid them in data management planning, working with data, sharing and preserving their data, and re-skilling. It is delivered by a virtual team spanning across a number of sections of Information Services including EDINA and Data Library, Library & University Collections, IT Infrastructure, User Services, and the Digital Curation Centre.
</p>
-->

<p>
  
  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 id="who">
  <strong>Who:</strong>
  The course is aimed at graduate students and other researchers.
  <strong>You need to have previous experience working with the Unix Shell. 
    For a brief introduction to bash, you can refer to the 
    <a href="http://swcarpentry.github.io/shell-novice/">SWC material available
    online</a> </strong>
  You don't need to have any previous knowledge of the tools that will
    be presented at the 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 id="where">
  <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 id="requirements">
  <strong>Requirements:</strong> Participants must bring a laptop with a
  Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges
  on. They should have 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>

<!--
  ACCESSIBILITY

  Modify the block below if there are any barriers to accessibility or
  special instructions.
-->
<p id="accessibility">
  <strong>Accessibility:</strong> We are committed to making this workshop
  accessible to everybody.
  The workshop organisers have checked that:
</p>
<ul>
  <li>The room is wheelchair / scooter accessible.</li>
  <li>Accessible restrooms are available.</li>
</ul>
<p>
  Materials will be provided in advance of the workshop and
  large-print handouts are available if needed by notifying the
  organizers in advance.  If we can help making learning easier for
  you (e.g. sign-language interpreters, lactation facilities) please
  <a href="mailto:{{page.contact}}">get in touch</a> and we will
  attempt to provide them.
</p>

<!--
  CONTACT EMAIL ADDRESS

  Display the contact email address set in the configuration file.
-->
<p id="contact">
  <strong>Contact</strong>:
  Please email
  {% if page.contact %}
    {% for contact in page.contact %}
      {% if forloop.last and page.contact.size > 1 %}
        or
      {% else %}
        {% unless forloop.first %}
        ,
        {% endunless %}
      {% endif %}
      <a href='mailto:{{contact}}'>{{contact}}</a>
    {% endfor %}
  {% else %}
    to-be-announced
  {% endif %}
  for more information.
</p>

<hr/>

<h2>Registration</h2>
<p>
To register, or to get more information, please, visit the <a
href="http://www.archer.ac.uk/training/">ARCHER training page</a>.
<!--You can also register directly <a href="https://events.prace-ri.eu/event/612/registration/register#/register">here</a>.-->
</p>


<!-- DO NOT EDIT SURVEY LINKS -->
<h2>Surveys</h2>
<p>Please be sure to complete these surveys before and after the workshop.</p>
<p><a href="{{ site.pre_survey }}{{ site.github.project_title }}">Pre-workshop Survey</a></p>
<p><a href="{{ site.post_survey }}{{ site.github.project_title }}">Post-workshop Survey</a></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-fluid">
  <div class="span6">
    <h3>Day 1</h3>
    <table class="table table-striped">
      <tr> <td>9:00</td> <td>Welcome and set-up</td> </tr>
      <tr> <td>9:30</td> <td>Version control with Git</td> </tr>
      <tr> <td><em>10:30</em></td> <td><em>Coffee break</em></td> </tr>
      <tr> <td>11:00</td> <td>Version control with Git</td> </tr>
      <tr> <td>12:30</td> <td>Lunch break</td> </tr>
      <tr> <td>13:30</td> <td>Automating tasks with Make</td> </tr>
      <tr> <td><em>15:00</em></td> <td><em>Coffee break</em></td> </tr>
      <tr> <td>15:30</td> <td>Automating tasks with Make</td> </tr>
      <tr> <td>17:00</td> <td>Close</td> </tr>
    </table>
  </div>
  <div class="span6">
    <h3>Day 2</h3>
    <table class="table table-striped">
      <tr> <td>9:00</td> <td>Python</td> </tr>
      <tr> <td><em>10:30</em></td> <td><em>Coffee break</em></td> </tr>
      <tr> <td>11:00</td> <td>Python</td> </tr>
      <tr> <td>12:30</td> <td>Lunch break</td> </tr>
      <tr> <td>13:30</td> <td>Data Management with SQL</td> </tr>
      <tr> <td><em>15:00</em></td> <td><em>Coffee break</em></td> </tr>
      <tr> <td>15:30</td> <td>Data Management with SQL</td> </tr>
      <tr> <td>16:30</td> <td>Wrap-up and feedback</td> </tr>
      <tr> <td>17:00</td> <td>Close</td> </tr>
    </table>
  </div>
</div>
<hr/>


<!--
  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>SQL session:</strong> <a href="https://docs.google.com/document/d/1Sz9-tAJZZYdEHpjsFI28n03yQX8pfH6jHbJdWkkmNDs/edit?usp=sharing">Google Document</a>.
  <br/>
  We will use this document for sharing exercises, URLs and bits of code.
</p>
<p>
  <strong>Workshop Feedback:</strong> <a href="http://bit.ly/171016-SWC-Glasgow">http://bit.ly/171016-SWC-Glasgow</a>.
  <br/>
  Feedback helps us improve and also helps us continue to get funding to run more workshops like this. Thank you!
</p>

{% endif %}

<hr/>

<h2>Syllabus</h2>

<div class="row-fluid">
  <div class="span6"> 
    <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="http://hpcarcher.github.io/git-novice/">Reference...</a></li>
    </ul>
  </div>
  
  <div class="row-fluid">
  <div class="span6"> 
    <h3>Automating tasks with Make</h3>
    <ul>
      <li>Make is not just for compiling code</li>
      <li>Basic Tasks</li>
      <li>Automatic Variables and Wildcards</li>
      <li>Patterns</li>
      <li>Variables</li>
      <li><a href="http://swcarpentry.github.io/make-novice/">Reference...</a></li>
    </ul>
  </div>
    
  <div class="span6">
    <h3>Building programs with 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: <code>for</code>, <code>if</code>, <code>else</code>, ...</li>
      <li>Defensive programming</li>
      <li>Using Python from the command line</li>
      <li><a href="http://swcarpentry.github.io/python-novice-inflammation/">Reference...</a></li>
    </ul>
  </div>
</div>
 
  <div class="span6">
    <h3>Data Management with SQL</h3>
    <ul>
      <li>Introduction to SQL</li>
      <li>Basic Queries</li>
      <li>Aggregation</li>
      <li>Joins and aliases</li>
      <li><a href="http://www.datacarpentry.org/sql-ecology-lesson/">Reference...</a></li>
     </ul>
  </div>
</div>


<hr/>

<!--
    Edit the setup instructions in _includes/setup.html to reflect your workshop.
    (In particular, most workshops teach either Python or R, not both.)
-->

<h2>Setup</h2>

<p>
  To participate in a Software Carpentry workshop, 
  you will need working copies of the software described below.
  Please make sure to install everything
  (or at least to download the installers)
  <em>before</em> the start of your workshop.
</p>

{% include setup.html %}

<h2>Check your setup</h2>

<p>
  To check you have the necessary software and tools:
</p>
<ul>
  <li>
    Download <a href="./setup/swc-installation-test-2.py">swc-installation-test-2.py</a>
  </li>
  <li>Open up a bash shell</li>
  <li>Change into the directory where you put the script</li>
  <li>Run the script:
    <pre>python swc-installation-test-2.py</pre>
  </li>
</ul>

<hr/>

<h2>Recognising prompts and how to exit</h2>
<!--
<p>
If you find yourself in a shell that you don't recognise, or in an editor that you can't get out of then see <a href="novice/ref/05-prompts-exits.html">Recognising prompts and how to exit</a>.
</p>
-->
<hr/>

<h2>Useful links</h2>

<p>
  Workshop Slides (password to download: "Glasgow"):
  </p
  <ul>
  <li><a href="https://datasync.ed.ac.uk/index.php/s/h3lKWaHiq52i6tQ">Opening slides</a></li>
  <li><a href="https://datasync.ed.ac.uk/index.php/s/U4zosJMaUghLnvN">Version Control with Git</a></li>
  <li><a href="https://datasync.ed.ac.uk/index.php/s/OPGcxk6Li7NkbDH">SQL</a></li>
  <li><a href="https://datasync.ed.ac.uk/index.php/s/qzkaXBrw0KQFW9h">Closing slides</a></li>
  </lu>

<p>
Software Carpentry online lessons:
</p>
<ul>
<li><a href="http://swcarpentry.github.io/git-novice/">Version Control with Git</a></li>
<li><a href="http://swcarpentry.github.io/python-novice-inflammation/">Programming with Python</a></li>
<li><a href="http://swcarpentry.github.io/make-novice/">Automating tasks with make</a></li>
<li><a href="http://swcarpentry.github.io/sql-novice-survey/">Databases and SQL</a></li>
</ul>
<p>
Git:
</p>
<ul>
<li>
GitHub <a href="https://try.github.io/levels/1/challenges/1">interactive Git tutorials</a>
</li>
<li>
<a href="http://justinhileman.info/article/git-pretty/">Git pretty</a> - a flowchart about how to recover from mistakes.
</li>
<a href="https://presentate.com/bobthecow/talks/changing-history">Changing History, or How to Git pretty</a> - slides relating to the above.
</li>
</ul>
<p>
Python:
</p>
<ul>
<li>
<a href="http://matplotlib.org/gallery.html">matplotlib examples gallery</a> - includes source code.
</li>
<li>
<a href="http://wiki.scipy.org/Cookbook">SciPy Cookbook</a> - examples of how to do useful stuff using numpy, scipy, matplotlib, interfacing, etc.
</li>
<li>
Scientific Python <a href="http://scipy-lectures.github.io/">lecture notes</a></li>
</ul>
<p>
Training:
</p>
<ul>
<li>
<a href="http://www.archer.ac.uk/training/">ARCHER Training</a> - free HPC training all over the UK.
</li>
<li>
<a href="http://www.codecademy.com/">Code Academy</a> - free online programming courses</a>
</li>
</ul>
<p>
Papers:
</p>
<p>
Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, et al. (2014)  
Best Practices for Scientific Computing. PLoS Biol 12(1): e1001745. <a 
href="http://dx.doi.org/10.1371/journal.pbio.1001745">doi:10.1371/journal.pbio.1001745</a>.
</p>
<p>
Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) Ten Simple Rules for  
Reproducible Computational Research. PLoS Comput Biol 9(10): e1003285. 
<a 
href="http://dx.doi.org/10.1371/journal.pcbi.1003285">doi:10.1371/journal.pcbi.1003285</a>.
</p>
<p>
Noble WS (2009) A Quick Guide to Organizing Computational Biology 
Projects. PLoS Comput Biol 5(7): e1000424. <a 
href="http://dx.doi.org/10.1371/journal.pcbi.1000424">doi:10.1371/journal.pcbi.1000424</a>.
</p>
<p>
Ram K (2013) "git can facilitate greater reproducibility and increased
transparency in science", Source Code for Biology and Medicine 2013,
8:7 <a
href="http://dx.doi.org/10.1186/1751-0473-8-7">doi:10.1186/1751-0473-8-7</a>.
</p>
<p>
Glass, R. (2002) Facts and Fallacies of Software Engineering, Addison-Wesley, 2002. (<a href="http://ff.tu-sofia.bg/~bogi/France/SoftEng/books/Addison%20Wesley%20-%20Robert%20L%20Glass%20-%20Facts%20and%20Fallacies%20of%20Software%20Engineering.pdf">PDF</a>).
</p>

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