index.html

---
layout: workshop
root: .
venue: CoDiMa - University of Manchester     # brief name of host site without address (e.g., "Euphoric State University")
address: University Place, Oxford Road, Manchester # street address of workshop (e.g., "123 Forth Street, Blimingen, Euphoria")
country: gb    # country (two-letter ISO code such as "fr" - see https://en.wikipedia.org/wiki/ISO_3166-1)
language: en   # language (two-letter ISO code such as "fr" - see https://en.wikipedia.org/wiki/ISO_639-1)
latlng: 53.466758, -2.233717  # fractional latitude and longitude (e.g., 41.7901128,-87.6007318)
humandate: Nov 16-18, 2015  # human-readable date (e.g., 'Feb 17-18, 2020' without the quotes)
humantime: 9:30 am - 17:00 pm  # human-readable time (e.g., '9:00 am - 4:30 pm' without the quotes)
startdate: 2015-11-16  # use YYYY-MM-DD format like 2015-01-01
enddate: 2015-11-18    # use YYYY-MM-DD format like 2015-01-02
instructor: ["Alexander Konovalov (University of St Andrews)",
             "Kwasi Kwakwa (Imperial College London)",
             "Leighton Pritchard (James Hutton Institute)"] # list of names like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
helper: ["Nick Loughlin (University of Newcastle)",
         "Michael Torpey (University of St Andrews)"] # list of names like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
contact: alexander.konovalov@st-andrews.ac.uk    # contact email address for workshop organizer, such as 'grace@hopper.org' (without the quotes)
etherpad: http://pad.software-carpentry.org/2015-11-16-manchester-codima
eventbrite: 18756706815 # 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.  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 %}

<div class="row">
  <div class="col-md-6"></br>
    <strong>This workshop is brought to you by <a href="http://www.codima.ac.uk">CoDiMa</a> -
      Collaborative Computational Project (CCP) in the area of Computational Discrete Mathematics
      (EPSRC grant EP/M022641/1). It constitutes the initial part of the
      <a href="http://www.codima.ac.uk/school2015/">First CoDiMa Training School in Computational Discrete Mathematics</a>
      (November 16th-20th, 2015). By registering for this workshop you will automatically register for the whole School.
    </strong>
  </div>
  <div class="col-md-6">
    <a href="http://www.codima.ac.uk"/>
    <img border="0" alt="CoDiMa" src="http://www.codima.ac.uk/wp-content/uploads/2015/09/codima-small-banner.png" height="100"></a>
  </div>
</div>

<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>

<!--
  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>
  The course is aimed at PhD students and other researchers from UK institutions.
  <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>
  <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>

<p>
This workshop constitutes the initial part of the
<strong><a href="http://www.codima.ac.uk/school2015/">First CoDiMa
Training School in Computational Discrete Mathematics</a></strong>
which runs until Friday November 20th. By registering for this
workshop you will automatically register for the whole School. Please see
<a href="http://www.codima.ac.uk/school2015/">the School's page</a> for further details.
</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: University Place, room 2.219</h3>
    <table class="table table-striped">
      <tr> <td>09:30</td>  <td>Automating tasks with the Unix shell</td> </tr>
      <tr> <td>11:00</td> <td>Coffee</td> </tr>
      <tr> <td>12:30</td>  <td>Lunch break</td> </tr>
      <tr> <td>13:30</td>  <td>Automation with Make </td> </tr>
      <tr> <td>15:00</td>  <td>Coffee</td> </tr>
      <tr> <td>16:30</td>  <td>Wrap-up</td> </tr>
    </table>
  </div>
  <div class="col-md-6">
    <h3>Day 2: University Place, rooms 5.211 (until 1pm), 2.220 (after 1pm)</h3>
    <table class="table table-striped">
      <tr> <td>09:00</td>  <td>Coffee - at Alan Turing Building, Atrium Bridge Level 1</td> </tr>	
      <tr> <td>09:30</td>  <td>Version control with Git </td> </tr>
      <tr> <td>11:00</td>  <td>Break</td> </tr>
      <tr> <td>11:20</td>  <td>Version control with Git - continued </td> </tr>
      <tr> <td>13:00</td>  <td>Lunch break (room 2.220)</td> </tr>
      <tr> <td>14:00</td>  <td>Programming with GAP</td> </tr>
      <tr> <td>15:00</td>  <td>Coffee</td> </tr>
      <tr> <td>15:30</td>  <td>School activities (see schedule
        <a href="http://www.codima.ac.uk/school2015/">here</a>)</td> </tr>
    </table>
  </div>
  <div class="col-md-6">
    <h3>Day 3: Alan Turing Building, Room Frank Adams 1</h3>
    <table class="table table-striped">
      <tr> <td>09:30</td>  <td>Programming in GAP</td> </tr>
      <tr> <td>11:00</td>  <td>Coffee</td> </tr>
      <tr> <td>12:00</td>  <td>Wrap-up</td> </tr>
      <tr> <td>12:30</td>  <td>Lunch break</td> </tr>
      <tr> <td>13:30</td>  <td>School activities (see schedule
        <a href="http://www.codima.ac.uk/school2015/">here</a>)</td> </tr>
    </table>
  </div>
</div>

<h3>The full programme for each day of the Training School is available <a href="http://www.codima.ac.uk/school2015/">here</a></h3>

<!--
  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://etherpad.mozilla.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/>

<!--
  SYLLABUS

  Show what topics will be covered.

  1. If your workshop is R rather than Python, remove the comment
     around that section and put a comment around the Python section.
  2. Some workshops will delete SQL.
  3. Please make sure the list of topics is synchronized with what you
     intend to teach.
  4. You may need to move the div's with class="col-md-6" around inside
     the div's with class="row" to balance the multi-column layout.

  This is one of the places where people frequently make mistakes, so
  please preview your site before committing, and make sure to run
  'tools/check' as well.
-->
<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_githubio}}/shell-novice/reference.html">Reference...</a></li>
    </ul>
  </div>
  <div class="col-md-6">
  <h3>Automation with Make</h3>
    <ul>
      <li>Basic Tasks</li>
      <li>Automatic Variables and Wildcards</li>
      <li>Patterns</li>
      <li>Variables</li>
      <li><a href="{{site.swc_githubio}}/make-novice/reference.html">Reference...</a></li>
    </ul>
    <!--
    <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_githubio}}/python-novice-inflammation/reference.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_githubio}}/r-novice-inflammation/reference.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_githubio}}/git-novice/reference.html">Reference...</a></li>
    </ul>
  </div>
  <div class="col-md-6">
    <h3>Programming in GAP</h3>
    <ul>
      <li>First session with GAP</li>
      <li>Functions in GAP</li>
      <li>Using regression tests</li>
      <li>Small groups search</li>
      <li>Attributes and methods</li>
      <li><a href="http://alex-konovalov.github.io/gap-lesson/reference.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_githubio}}/sql-novice-survey/reference.html">Reference...</a></li>
    </ul>
  </div>
  -->
</div>

<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>
      <p>
        Download the Git for Windows
	<a href="https://git-for-windows.github.io/">installer</a>. Run the
        installer. <strong>Important: on the 6th page of the installation wizard (the
        page titled `Configuring the terminal emulator...`) select `Use Windows'
        default console window`. 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.</strong> 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">OS X</h4>
      <p>
        The default shell in all versions of 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">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='gap'> <!-- Start of 'GAP' section. GitHub browser compatability
           is given at https://help.github.com/articles/supported-browsers/-->
  <h3>GAP</h3>

  <p>
    GAP is a system for discrete computational algebra. It provides a programming
    language, a library of thousands of functions implementing algebraic algorithms
    written in the GAP language as well as large data libraries of algebraic objects.
    Its latest version may be found on the
    <a href="http://www.gap-system.org/Releases/">GAP Downloads page</a>.
  </p>

  <div class="row">
    <div class="col-md-4">
      <h4 id="git-windows">Windows</h4>
      <p>
        From the <a href="http://www.gap-system.org/Releases/">GAP Downloads page</a>,
        download the <code>.exe</code> installer and double click on the file to run it. When you
        will be asked for the installation path, note that it should not contain spaces.
        For example, you may install GAP in <code>C:\gap4r7</code> (default),
        <code>D:\gap4r7p8</code> or <code>C:\Math\GAP\gap4r7</code>, but you must not
        install it in a directory named like <code>C:\Program files\gap4r7</code> or
        <code>C:\Users\alice\My Documents\gap4r7</code> etc.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="git-macosx">OS X</h4>
      <p>
        On OS X, we suggest to install GAP using <a href="http://brew.sh/">Homebrew</a>.
        After installing Homebrew, open the Terminal and call
        <code>brew install homebrew/science/gap --with-InstPackages</code>.
        Please be patient - this may take a while. If Homebrew is already installed
        on your Mac, you may have to call <code>brew update</code> first.
      </p>
      <p>
        Alternatively, you may also install GAP from source as explained at the
        <a href="http://www.gap-system.org/Releases/">GAP Downloads page</a>.
        The BOB installer, suggested in the next column for Linux, is also available
        for OS X.
      </p>
    </div>
    <div class="col-md-4">
      <h4 id="git-linux">Linux</h4>
      <p>
        We suggest to use an
        <a href="http://gap-system.github.io/bob/">alternative GAP source installer BOB</a>
        which will first check whether everything it needs from your system is installed and
        if not it will warn you and tell you what is needed.
        Please see <a href="http://gap-system.github.io/bob/">BOB</a>
        page for further instructions. To be able to compile GAP you may need to install
        some tools as described <a href="http://www.gap-system.org/Download/tools.html">here</a>.
        Alternatively, you may also install GAP from source as explained at the
        <a href="http://www.gap-system.org/Releases/">GAP Downloads page</a>.
      </p>
    </div>
  </div>
</div> <!-- End of 'GAP' 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 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">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. -->




<!--
  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>
-->