University of Illinois

Sep 27–28, 2018

9:00 am - 4:30 pm

Instructors: Jenny Drnevich, Samniqueka Halsey, Jessica Holmes

Helpers: Neal Davis

General Information

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: 607 Institute for Genomic Biology. Get directions with OpenStreetMap or Google Maps.

When: Sep 27–28, 2018. Add to your Google Calendar.

Requirements: Participants may bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on OR they may use one of the PCs in the computer lab. If bringing a laptop, 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 training@cse.illinois.edu for more information.

Acknowledgments: Local Software Carpentry and Data Carpentry workshops are made possible by the generous support of Computational Science and Engineering, Technology Services, the National Center for Supercomputing Applications, HPCBio at the Roy J. Carver Biotechnology Center with support through the Office of the Vice Chancellor for Research, the Deloitte Center for Business Analytics at the Gies College of Business, and the home units of each of our instructors.


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 2 · Fri 9/28

MorningIntroduction to the command line
Afternoon Wrangling genomics data

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


Syllabus

Project Organization and Management

The Unix Shell

  • Accessing and using Biocluster
  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Reference...

Programming in R for Data Analysis and Visualization

  • Working with vectors and data frames
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Using R from the command line
  • Reference...

Data Wrangling for Genomics

  • Assessing read quality
  • Trimming and filtering
  • A simple variant calling workflow
  • Automating a variant calling workflow
  • Reference...

Setup

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 and a spreadsheet program such as Microsoft Excel or LibreOffice.

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.

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.

macOS

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 dnf install R). Also, please install the RStudio IDE.

The Bash Shell

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

Windows

  1. Download MobaXTerm Home Edition for Windows installer.

macOS

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.

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 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.

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.

macOS

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.