Nov 6-7, 2018
9:00 am - 4:30 pm
Instructors: Shane Sanders, David McKenzie, Anne Deslattes Mays, Neil Kindlon, Jason Macklin, Diogo Troggian Veiga, Sandeep Namburi
Helpers: Bill Flynn, Harshpreet Chandok, Seda Arat, Ravi Pandey, Ada Zhan, Mandy Chen
Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. Its target audience is researchers who have little to no prior computational experience, and its lessons are domain specific, building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. 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 "Good Enough 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.
Where: Holt Conference Room, 10 Discovery Drive, Farmington CT. Get directions with OpenStreetMap or Google Maps.
When: Nov 6-7, 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.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Data 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 shane.sanders@jax.org or sandeep.namburi@jax.org for more information.
Please be sure to complete these surveys before and after the workshop.
| Before starting | Pre-workshop survey |
| 09:00 | Welcome and introductions |
| 09:15 | Project organization and management |
| 10:45 | Coffee |
| 11:00 | Introduction to the command line |
| 12:20 | Lunch |
| 13:20 | Introduction to the command line (continued) |
| 14:45 | Coffee |
| 16:30 | END |
| 09:00 | Data wrangling and processing |
| 10:45 | Coffee |
| 11:00 | Data wrangling and processing (continued) |
| 12:20 | Lunch |
| 13:20 | Introduction to cloud computing for genomics |
| 14:45 | Coffee |
| 15:00 | Introduction to cloud computing for genomics (continued) |
| 16:25 | Post-workshop survey |
| 16:30 | END |
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
To participate in a Data 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.
cmd and press [Enter])setx HOME "%USERPROFILE%"
SUCCESS: Specified value was saved.exit then 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
(found in
/Applications/Utilities).
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
install anything.
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 macOS 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. It is installed along with Git.
Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.
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.
Others editors that you can use are Text Wrangler or Sublime Text.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.
Others editors that you can use are Gedit, Kate or Sublime Text.