May 29-30, 2018
8:30 am - 4:30 pm
Instructors: Carolina Johnson, Yee Mey Seah
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. 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: This workshop is for analysts, evaluators, and epidemiologists at the King County Department of Community and Human Services and Public Health - Seattle and King County You don't need to have any previous knowledge of the tools that will be presented at the workshop.
When: May 29-30, 2018. Add to your Google Calendar.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). If possible, participants should bring the laptop they use at the County, and should speak to their supervisor or the workshop coordinator if they need a laptop for this training. Participants should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:
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.
Contact: Please email firstname.lastname@example.org for more information.
Please be sure to complete these surveys before and after the workshop.
|08:30||Version control with Git|
|13:00||R for Reproducible Analysis|
|09:00||R for Reproducible Analysis (cont'd)|
|13:00||Managing data with SQL|
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
cmdand press [Enter])
setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.
exitthen pressing [Enter]
This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of macOS is Bash, so no
need to install anything. You access Bash from the Terminal
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.
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
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.
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
After installing Git, there will not be anything in your
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"
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.
We have developed a customized script that will install the text editor and SQL tools on your machines without requiring administrator privileges.
To install nano (our basic text editor) and SQLite
mkdir .swc curl -L -O http://www.nano-editor.org/dist/v2.2/NT/nano-2.2.6.zip unzip nano-2.2.6.zip -d .swc/nano curl -L -O https://sqlite.org/2015/sqlite-shell-win32-x86-3090200.zip unzip sqlite-shell-win32-x86-3090200.zip -d .swc/sqlite3 echo "alias nano='winpty `pwd`/.swc/nano/nano' alias sqlite3='winpty `pwd`/.swc/sqlite3/sqlite3'" >~/.bashrc
Installation of R and RStudio on King County machines will require going through the KCIT Software Center.
For reference, full installation instructions for non-King County machines are provided below for people who either have administrator privileges or who would like to follow along with these lessons on their personal computers.
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. Notepad++ us a decent text editor that is available for download from the KCIT software center. For this class we will default to nano a very simple editor with shell integration (installation instructions below), but Notepad++ is another decent text editor with syntax highlighting that is available for installation from the KCIT software center.
nano is a basic editor and the default that instructors use in the workshop. Running the installation commands in the "Setup for King County machines" section above will install nano for use with Bash. You can follow those steps for your personal Windows machine.
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.
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.
Running the installation commands in the "Setup for King County machines" section above will have installed SQLite for use with Bash for the workshop. If you have already run the installation script once for nano, you do not need to run it again.
SQLite comes pre-installed on macOS.
SQLite comes pre-installed on Linux.
R and the RStudio IDE are both available for download from the KCIT Software Center. If you are unable to access the files via the Software Center, please notify the workshop organizer and the KCIT Help Desk. If you want to install R/RStudio on a computer on which you have administrator rights, follow the instructions below.
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.