Day 1

Day 2

The Unix Shell

• Files and directories: pwd, cd, ls, mkdir, ...
• History and tab completion
• Pipes and redirection
• Looping over files
• Creating and running shell scripts
• Finding things: grep, find, ...
• Reference...

Programming in Python

• Using libraries
• Working with arrays
• Reading and plotting data
• Creating and using functions
• Loops and conditionals: for, if, else, ...
• Reference...

Version Control with Git

• 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...

Introduction to R

• RStudio
• Understand the various mode of vectors
• Inspect objects
• Filter vectors and data frames
• Use vectorized functions
• Make basic plots

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.

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.

Git

Git is a state-of-the-art version control system. It 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.

Python

Python is becoming very popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We teach with Python version 2.7, since it is still the most widely used. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we will use RStudio, an interactive development environment (IDE).

SQL

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite, either directly or through a browser plugin.

Python

• Download and install Anaconda CE.
• Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Git Bash

Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.

Software Carpentry Installer

This installer requires an active internet connection

After installing Python and Git Bash:

• Download the installer.
• If the file opens directly in the browser select File→Save Page As to download it to your computer.
• Double click on the file to run it.

Editor

nano is the editor installed by the Software Carpentry Installer, it is a basic editor integrated into the lesson material.

Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this.

R

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

SQLite

Download the sqlite3 program and put it in the directory where you are running examples. Alternatively, you may install the Firefox SQLite browser plugin described below.

Bash

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.

Editor

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.

Git

Install Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.

Python

• Download and install Anaconda CE.
• Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

R

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

SQLite

sqlite3 comes pre-installed on Mac OS X. Alternatively, you may install the Firefox SQLite browser plugin described below.

Bash

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

If Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get or yum).

Editor

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.

R

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

SQLite

sqlite3 comes pre-installed on Linux. Alternatively, you may install the Firefox SQLite browser plugin described below.

Python

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 boot camp.)

1. Download the installer that matches your operating system and save it in your home folder.
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).

Firefox SQLite Plugin

Instead of using sqlite3 from the command line, you may use this plugin for Firefox instead. To install it:

• Start Firefox.
• Go to the plugin homepage.
• Click the "Add Now" button.
• Click "Install Now" on the dialog that appears after the download completes.
• Restart Firefox when prompted.
• Select "SQLite Manager" from the "Tools" menu.

Virtual Machine

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:

1. Install VirtualBox.
2. Download our VM image. Warning: this file is 1.7 GByte, so please download it before coming to your bootcamp.
3. Load the VM into VirtualBox by selecting "Import Appliance" and loading the .ova file.