December 3-4, 2016
9:00 am - 4:00 pm
Instructors: Matthew Collins, Alex Thompson, Deborah Paul
Helpers: Rogelio Gonzalez Quiros
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. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
This Software Carpentry course is being offered in conjunction with the upcoming Biodiversity Information Standards (TDWG) 2016 Conference, December 5 - 9, 2016. We anticipate that many who take this workshop will also be attending TDWG 2016. iDigBio is sponsoring this workshop, and parts of the workshop will focus on using biological and paleontological specimen data.
**UPDATE: only 7 spots left.** Last chance to sign up.
Cost: Students $50.00, non-students $100.00
Go to the registration for TDWG 2016 to pay for and reserve your spot. Students enrolled in a degree program can request a discount code from the TDWG Treasurer by emailing an image of your student ID or a note from your advisor to "firstname.lastname@example.org". The discount code will secure reduced rates for both the conference registration and the course fee.
Spots are limited to 25 participants, so don't wait, register now.
Hotel Information: the following hotels are very close to CTEC (the workshop location). Please reserve at one of these, if possible, to make getting to the workshop easier. Participants going to TDWG can then check out on Sunday Dec 4th and will be transported to check-in to La Fortuna hotels on Sunday 5 PM in time for TDWG Sunday evening reception.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.
Course Overview: Sign up for a two-day Software Carpentry Workshop covering core skills needed to be productive in a small research team. Short tutorials alternate with practical exercises, and all instruction is done via live coding. All workshop participants are required to abide by our code of conduct to ensure that all attendees to have an enjoyable and fulfilling experience. The specific programming languages and tools taught will be customized based on your preferences. Core topics include:
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers 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 and we will attempt to provide them.
Contact: Please mail email@example.com for more information.
Please be sure to complete these surveys before and after the workshop.
|09:00||Automating tasks with the Unix shell|
|13:00||R for Reproducible Scientific Analysis|
|09:00||Version control with Git|
|13:00||Managing data with SQL|
We will use this Etherpad 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.
This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of Mac OS X 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 yum install git.
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.
nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.
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.
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.
SQLite comes pre-installed on Mac OS X.
SQLite comes pre-installed on Linux.
If you installed Anaconda, it also has a copy of SQLite
without support to
Instructors will provide a workaround for it if needed.