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Vanderbilt University

Aug 20-21, 2015

9:00 am - 4:30 pm

Instructors: Scott Burns, Daniel Fabbri, Christopher Fonnesbeck, Will French

General Information

Software Carpentry'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.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers.

Where: Featheringill Hall, 400 24th Avenue South, 134 Auditorium, Nashville, TN 37212. 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: Please mail chris.fonnesbeck@vanderbilt.edu for more information.


Schedule

Day 1

09:00 Welcome and introduction
09:15 Automating tasks with the Unix shell
10:45 Coffee (15 min)
12:15 Lunch break
13:00 Building programs with Python
14:30 Coffee (15 min)
16:00 Wrap-up

Day 2

09:00 ACCRE presentation
09:15 Version control with Git
10:45 Coffee (15 min)
12:15 Lunch break
13:00 Managing data with SQL
14:30 Coffee (15 min)
16:00 Wrap-up

Syllabus

The Unix Shell (Will French)

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Programming in Python (Chris Fonnesbeck)

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Defensive programming
  • Using Python from the command line
  • Reference...

Version Control with Git (Scott Burns)

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why
  • Reference...

Managing Data with SQL (Daniel Fabbri)

  • Reading and sorting data
  • Filtering with where
  • Calculating new values on the fly
  • Handling missing values
  • Combining values using aggregation
  • Combining information from multiple tables using join
  • Creating, modifying, and deleting data
  • Programming with databases
  • Reference...

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. Once you are done installing the software listed below, please go to this page, which has instructions on how to test that everything was installed correctly.

Workshop Materials

The Github repository, which includes any materials required for the individual modules, as well as this website can be downloaded from GitHub. You can either clone the repository, or download a zip file (see the right-hand column of the page).

Software Installation Help

For those requiring assistance with installing any of the software required for the workshop, we are offering in-person support on Wednesday, August 19 from 1pm to 3pm in the Garden Room of the Department of Biostatistics at 2525 West End Avenue (11th floor). Please try to install the software yourself, but if you run into difficulties, please drop by the installation support session, or post questions to Slack.

The Bash Shell

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

Windows

Install Git for Windows by downloading and running the installer. 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 10.8 and higher, install Git for Mac by downloading and running the installer. 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 (10.5-10.7) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.

If you happen to be a user of Homebrew, you can install Git by typing brew install git from the Terminal prompt.

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

Atom is an open-source text editor that works on multiple platforms, and is designed to work well with version control systems, such as Git.

Other editors that you can use on Windows include Notepad++ and Sublime Text. For both of these choices, be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

We recommend TextMate 2, which is a free, robust, open-source editor for Mac OS X. Some instructors will be using it during the bootcamp.

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

Linux

Atom is an open-source text editor that works on multiple platforms, and is designed to work well with version control systems, such as Git.

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

Python

Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we recommend an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x, not version 2.x (e.g., 3.4 is fine but not 2.7). We will teach this workshop using Python 3.

We will teach Python using the Jupyter notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows

  • Download and install Anaconda.
  • Download the Python 3 installer (do not install version 2). Use all of the defaults for installation except make sure to check Make Anaconda the default Python.
  • After you’ve installed Anaconda, start up a Windows command prompt and update Jupyter (IPython) by typing conda install jupyter.

Mac OS X

  • Download and install Anaconda.
  • Download the Python 3 installer (do not install version 2). Use all of the defaults for installation.
  • After you’ve installed Anaconda, open up a Terminal window and update Jupyter (IPython) by typing conda install jupyter.

Linux

We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the workshop.)

  1. Download the installer that matches your operating system and save it in your home folder. Download the Python 3 installer (do not install version 2).
  2. Open a terminal window.
  3. Type
    bash Anaconda-
    and then press tab. The name of the file you just downloaded should appear.
  4. Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  5. After you’ve installed Anaconda, update Jupyter (IPython) by typing conda install jupyter.

SQLite

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.

Windows

The Software Carpentry Windows Installer installs SQLite for Windows. If you used the installer to configure nano, you don't need to run it again.

Mac OS X

SQLite comes pre-installed on Mac OS X.

Linux

SQLite comes pre-installed on Linux.