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Yale University

Dec. 18-19, 2014

9:00 am - 4:30 pm

Instructors: Dhavide Aruliah, Robert Till

Helpers: Camille Avestruz, Tomomi Sunayama, Nick Sawyer, Jieming Chen, Luis Vargas

General Information

Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on workshop will cover basic concepts and tools; 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 graduate students and other researchers.

Where: SPL Rm. 48, Sloane Physics Laboratory, 217 Prospect St, New Haven, CT. 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 admin@software-carpentry.org for more information.


Schedule

We will use this etherpad for collaborative note-taking throughout the session.

Day 1

09:00 Automating tasks with the Unix shell (data)
10:30 Coffee break
12:00 Lunch break
13:00 Building programs with MATLAB (dataMATLAB scripts from Day 1)
14:30 Coffee break
16:00 Wrap-up

Day 2

09:00 More programming with MATLAB (more data)
10:30 Coffee break
12:00 Lunch break
13:00 MATLAB exercises  MATLAB scripts from Day 2)
14:30 Coffee break
16:00 Wrap-up

Syllabus

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 MATLAB

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

Managing Data with SQL

  • 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 working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your workshop.

Overview

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.

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.

Windows

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.

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.

Mac OS X

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.

SQLite

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

Linux

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.

Editor

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

SQLite

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

All operating systems

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.
  • To check that the plugin installed correctly, select "SQLite Manager" from the "Tools" menu.

In newer versions of Firefox, the menu bar isn't always displayed. To make it appear, use the Alt key next to the space bar on your keyboard, or consult the support page from Firefox for additional help.