Oct 24-27, 2017
8:00 am - 4:30 pm
Instructors: Tonya Ward, Bianca Peterson, Tomasz Sanko, Caroline Ajilogba, Andries van der Walt, Leani Bothma
Data 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 project organization, data management, task automation, 16S amplicon analysis, and microbial community diversity analysis and visualization in R. 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.
Where: Room 218, Building G23, 11 Hoffman Street, NWU, Potchefstroom. Get directions with OpenStreetMap or Google Maps.
When: Oct 24-27, 2017. 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 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 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 (using contact details below) and we will attempt to provide them.
Registration: Registrations are now closed.
Contact: Please email anelda.vanderwalt@nwu.ac.za for more information.
Surveys
Please be sure to complete these surveys before and after the workshop.
| 08:30 - 09:00 | Welcome & project design |
| 09:00 - 10:00 | Data organization in spreadsheets |
| 10:00 - 10:30 | Coffee/tea break |
| 10:30 - 12:00 | Unix shell |
| 12:00 - 13:00 | Lunch break |
| 13:00 - 14:30 | Unix shell (continue) |
| 14:30 - 15:00 | Coffee/tea break |
| 15:00 - 16:30 | Introduction to 16S amplicon analysis |
| 08:30 - 10:00 | 16S amplicon analysis (continue) |
| 10:00 - 10:30 | Coffee/tea break |
| 10:30 - 12:00 | 16S amplicon analysis (continue) |
| 12:00 - 13:00 | Lunch break |
| 13:00 - 14:30 | 16S amplicon analysis (continue) |
| 14:30 - 15:00 | Coffee/tea break |
| 15:00 - 16:30 | Introduction to R |
| 08:30 - 10:00 | Data manipulation in R |
| 10:00 - 10:30 | Coffee/tea break |
| 10:30 - 12:00 | Data visualization in R |
| 12:00 - 13:00 | Lunch break |
| 13:00 - 14:30 | Microbial community data analysis in R |
| 14:30 - 15:00 | Coffee/tea break |
| 15:00 - 16:30 | Microbial community data analysis in R (continue) |
| 08:30 - 10:00 | Applied 16S amplicon analysis |
| 10:00 - 10:30 | Coffee/tea break |
| 10:30 - 12:00 | Applied 16S amplicon analysis (continue) |
| 12:00 - 12:30 | Wrap-up |
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
To participate in this Data Carpentry workshop, you will need an up-to-date web browser and 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. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.
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 Mac OS X 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 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 Data Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.
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.
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
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.
Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager (e.g. for Debian/Ubuntu
run sudo apt-get install r-base and for Fedora run
sudo yum install R). Also, please install the
RStudio IDE.