University of California Davis

Jan 24-25, 2018

9:00 am - 4:30 pm

Instructors: Karen Word, Daniel Standage, Lisa Johnson Cohen, Taylor Reiter, Sue McClatchy, Jeffrey Miller

Helpers: Jessica Mizzi, Ryan Peek, Shannon Joslin

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 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.

Where: Bennett Conference Room, Center for Companion Animal Health, Davis, CA 95616-8782. Get directions with OpenStreetMap or Google Maps.

When: Jan 24-25, 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 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.

Contact: Please email for more information.



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

Pre-workshop Survey

Post-workshop Survey

Day 1

Morning Project organization and management
09:00 Welcome and workshop introductions
09:30 Data Tidiness
10:00 Planning for NGS Projects
10:30 Examining Data on the NCBI SRA Database
10:45 Coffee
Mid-morningIntroduction to the command line
11:00 Introducing the Shell
11:30 Navigating Files and Directories
12:00 Lunch break
13:00 Working with Files and Directories
13:45 Redirection
14:30 Coffee
14:45 Writing Scripts
15:30 Project Organization
16:15 Wrap-up
16:30 END

Day 2

Morning Data wrangling and processing
09:00 Assessing Read Quality
10:00 Trimming and Filtering
10:45 Coffee
11:00 Variant Calling Workflow
12:00 Lunch break
13:00 Automating a Variant Calling Workflow
AfternoonIntroduction to cloud computing for genomics
13:45 Why of cloud computing
13:50 Logging onto Cloud
14:00 Fine tuning your Cloud Setup
14:30 Coffee
14:45 Data roundtripping
15:15 Which Cloud for my data?
16:15 Wrap-up
16:30 END

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


The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...


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.

The Bash Shell

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


  1. Download and install PuTTY for Windows .


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.