Find us on GitHub

University of Texas at Arlington



Oct 15-16, 2016

9:00 am - 5:00 pm

Instructors: Daren Card, Devendra Umbrajkar, Gaurav Kolekar, Kevin Vilbig, James Titus-McQuillan, Heath Blackmon

Helpers: Sailee Pawar, Anna Williford

Thank You




General Information

Software Carpentry's mission is to help scientists across all disciplines 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.

Who: The course is aimed at anyone who is interested in learning new tools. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: UTA campus, Geoscience building, room 100 . Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: If you have questions about the workshop please email to awillifo@uta.edu. For help with software installation please email to dcard@uta.edu .


Schedule

Day 1

09:00 Pre-workshop Survey
09:00 Unix Shell 1 Linux lesson; Linux Commands
10:45 Coffee
11:00 Unix Shell 2 Data; Shell History
12:30 Lunch break
1:30 Version Control with Git 1: Git Intro; Git lesson Lesson materials for both afternoon sessions
3:00 Coffee
3:15 Version Control with Git 2
4:45 Wrap-up

Day 2

09:00 Introduction to R 1: R basics lesson
10:45 Coffee
11:00 Introduction to R 2: R functions lesson; R functions files
12:30 Lunch break
1:30 Reproducible Research Workflows with R 1 Data analysis with R Lessons materials for both afternoon sessions
3:00 Coffee
3:15 Reproducible Research Workflows with R 2
4:30 Wrap-up
4:45 Post-workshop Survey

Lessons: Our lessons are based on lessons developed by Software Carpentry Foundation

Etherpad: http://pad.software-carpentry.org/2016-10-15-UTA.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Saved latest version of Etherpad (after the workshop) is here.

Setup

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.

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.

The Bash Shell

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

Windows

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Click on "Next".
    4. Click on "Next".
    5. Click on "Next".
    6. Select "Use Git from the Windows Command Prompt" 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.
    7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
    8. Select "Use Windows' default console window" and click on "Next".
    9. Click on "Next".
    10. Click on "Finish".

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

Mac OS X

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 /Applications/Utilities). 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.

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).

Windows

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

Mac OS X

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 yum install git.

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 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.

Windows

You can use your favorite text editor. If you do not have one, we recommend Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. To add Notepad++ to the path: 1) Open Git-Bash from the start menu. 2) Type: cd [enter] to make sure you are in your home directory. 3) Type: notepad .bashrc [enter]. This will create .bashrc file in Notepad. Add the following text to the file:
export PATH=$PATH:"C:\Program Files (x86)\Notepad++"
alias npp=notepad++

4) Save the file and exit Notepad. 5) Open a new Git-Bash window. You should now be able to launch Notepad++ by typing: npp [enter]. If you run into trouble please ask your instructor to help you with this.

Mac OS X

You can use your favorite text editor. If you do not have one, we recommend Text Wrangler or Sublime Text.

Linux

You can use your favorite text editor. If you do not have one, we recommend Gedit, Kate or Sublime Text.

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

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

Mac OS X

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 yum install R). Also, please install the RStudio IDE.