Metagenomics Data Carpentry-based Workshop

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

General Information

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.


Schedule

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Tuesday, 24 Oct

08:30 - 09:00Welcome & project design
09:00 - 10:00Data organization in spreadsheets
10:00 - 10:30Coffee/tea break
10:30 - 12:00Unix shell
12:00 - 13:00Lunch break
13:00 - 14:30Unix shell (continue)
14:30 - 15:00Coffee/tea break
15:00 - 16:30Introduction to 16S amplicon analysis

Wednesday, 25 Oct

08:30 - 10:0016S amplicon analysis (continue)
10:00 - 10:30Coffee/tea break
10:30 - 12:0016S amplicon analysis (continue)
12:00 - 13:00Lunch break
13:00 - 14:3016S amplicon analysis (continue)
14:30 - 15:00Coffee/tea break
15:00 - 16:30Introduction to R

Thursday, 26 Oct

08:30 - 10:00Data manipulation in R
10:00 - 10:30Coffee/tea break
10:30 - 12:00Data visualization in R
12:00 - 13:00Lunch break
13:00 - 14:30Microbial community data analysis in R
14:30 - 15:00Coffee/tea break
15:00 - 16:30Microbial community data analysis in R (continue)

Friday, 27 Oct

08:30 - 10:00Applied 16S amplicon analysis
10:00 - 10:30Coffee/tea break
10:30 - 12:00Applied 16S amplicon analysis (continue)
12:00 - 12:30Wrap-up

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Setup

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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

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.

Linux

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.

Text 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.

Windows

Video Tutorial

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.

Mac OS X

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.

Linux

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

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Windows

Video Tutorial

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.

Mac OS X

Video Tutorial

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

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.