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
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 susan.mcclatchy@jax.org for more information.
Surveys
Please be sure to complete these surveys before and after the workshop.
| 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-morning | Introduction 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 |
| 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 |
| Afternoon | Introduction 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.
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.
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.