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layout carpentry venue address country language latlng humandate humantime startdate enddate instructor helper email collaborative_notes
workshop
swc
National Institutes of Health
Building 10 Library, 10 Center Drive, Bethesda MD 20892
USA
en
39.002777,-77.10446
April 4-5, 2018
9:00 am - 5:00 pm
2018-04-04
2018-04-05
Abhijit Dasgupta
Doug Joubert
David McGaughey
Denise Liberton
Vinai Roopchansingh
adasgupta@araastat.com
joubertd@ors.od.nih.gov

{% comment %} See instructions in the comments below for how to edit specific sections of this workshop template. {% endcomment %} {% comment %} 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 'make workshop-check' before committing to make sure that changes are good. {% endcomment %} {% comment %} 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. {% endcomment %} {% 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 %}

General Information

{% comment %} INTRODUCTION Edit the general explanatory paragraph below if you want to change the pitch. {% endcomment %} {% if page.carpentry == "swc" %} {% include sc/intro.html %}{% elsif page.carpentry == "dc" %} {% include dc/intro.html %}{% elsif page.carpentry == "lc" %} {% include lc/intro.html %} {% endif %} {% comment %} AUDIENCE Explain who your audience is. (In particular, tell readers if the workshop is only open to people from a particular institution. {% endcomment %} {% if page.carpentry== "swc" %} {% include sc/who.html %}{% elsif page.carpentry == "dc" %} {% include dc/who.html %}{% elsif page.carpentry == "lc" %} {% include lc/who.html %} {% endif %}

{% comment %} 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. {% endcomment %} {% if page.latlng %}

Where: {{page.address}}. Get directions with OpenStreetMap or Google Maps.

{% endif %} {% comment %} DATE This block displays the date and links to Google Calendar. {% endcomment %} {% if page.humandate %}

When: {{page.humandate}}. {% include workshop_calendar.html %}

{% endif %} {% comment %} SPECIAL REQUIREMENTS Modify the block below if there are any special requirements. {% endcomment %}

Materials from workshop

Requirements: 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 below). There may be a very limited number of pre-loaded laptops available. Please contact the instructors if you cannot bring a laptop with appropriate software loaded. They are also required to abide by {% if page.carpentry == "swc" %} Software Carpentry's {% elsif page.carpentry == "dc" %} Data Carpentry's {% elsif page.carpentry == "lc" %} Library Carpentry's {% endif %} Code of Conduct.

{% comment %} ACCESSIBILITY Modify the block below if there are any barriers to accessibility or special instructions. {% endcomment %}

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

  • The room is wheelchair / scooter accessible.
  • Accessible restrooms are available.

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 get in touch (using contact details below) and we will attempt to provide them.

{% comment %} CONTACT EMAIL ADDRESS Display the contact email address set in the configuration file. {% endcomment %}

Contact: Please email {% if page.email %} {% for email in page.email %} {% if forloop.last and page.email.size > 1 %} or {% else %} {% unless forloop.first %} , {% endunless %} {% endif %} {{email}} {% endfor %} {% else %} to-be-announced {% endif %} for more information.

{% comment %} 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. {% endcomment %}

Schedule

{% comment %} DO NOT EDIT SURVEY LINKS {% endcomment %}

Surveys

{% if page.carpentry == "swc" %}

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

{% elsif page.carpentry == "dc" %}

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

{% elsif page.carpentry == "lc" %}

Ask your instructor about pre- and post-workshop Survey details.

{% endif %} {% if page.carpentry == "swc" %} {% include sc/schedule.html %} {% elsif page.carpentry == "dc" %} {% include dc/schedule.html %} {% elsif page.carpentry == "lc" %} {% include lc/schedule.html %} {% endif %} {% comment %} Collaborative Notes If you want to use 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'. {% endcomment %} {% if page.collaborative_notes %}

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

{% endif %}

Materials and links from class

Script from R modules
Links to resources

{% comment %} 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. {% endcomment %}

Syllabus

{% if page.carpentry == "swc" %} {% include sc/syllabus.html %} {% elsif page.carpentry == "dc" %} {% include dc/syllabus.html %} {% elsif page.carpentry == "lc" %} {% include lc/syllabus.html %} {% endif %}

{% comment %} 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. {% endcomment %}

Setup

To participate in a {% if page.carpentry == "swc" %} Software Carpentry {% elsif page.carpentry == "dc" %} Data Carpentry {% elsif page.carpentry == "lc" %} Library Carpentry {% endif %} workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

{% comment %} Start of 'shell' section. {% endcomment %}

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
      {% comment %} Git 2.8.2 Setup {% endcomment %} {% comment %} Information {% endcomment %}
    1. Click on "Next".
      2. {% comment %} Select Components {% endcomment %}
    2. Click on "Next".
      3. {% comment %} Adjusting your PATH environment {% endcomment %}
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". 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.
      4. {% comment %} Choosing the SSH executable {% endcomment %}
    4. Click on "Next".
      5. {% comment %} Configuring the line ending conversions {% endcomment %}
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
      6. {% comment %} Configuring the terminal emulator to use with Git Bash {% endcomment %}
    6. Keep "Use Windows' default console window" selected and click on "Next".
      7. {% comment %} Configuring experimental performance tweaks {% endcomment %}
    7. Click on "Install".
      8. {% comment %} Installing {% endcomment %} {% comment %} Completing the Git Setup Wizard {% endcomment %}
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

macOS

The default shell in all versions of macOS is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

Linux

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

{% comment %} End of 'shell' section. {% endcomment %}
{% comment %} Start of 'Git' section. GitHub browser compatability is given at https://help.github.com/articles/supported-browsers/{% endcomment %}

Git

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 github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Windows

Git should be installed on your computer as part of your Bash install (described above).

macOS

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

Linux

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 sudo apt-get install git and for Fedora run sudo dnf install git.

{% comment %} End of 'Git' section. {% endcomment %}
{% comment %} Start of 'editor' section. {% endcomment %}

Text Editor

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 macOS 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.

Windows

Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. To install it, download the {% if page.carpentry == "swc" %} Software Carpentry {% elsif page.carpentry == "dc" %} Data Carpentry {% elsif page.carpentry == "lc" %} Library Carpentry {% endif %} Windows installer and double click on the file to run it. This installer requires an active internet connection.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

macOS

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

{% comment %} End of 'editor' section. {% endcomment %}
{% comment %} Start of 'R' section. {% endcomment %}

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Windows

Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

macOS

Video Tutorial

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.

{% comment %} End of 'R' section. {% endcomment %}