Jan 15-16, 2019
9:00 am - 5:00 pm
Instructors: Elias Ozolor, Sateesh Peri
Helpers: Richard Tillett, Gurlaz Kaur, Jeremiah Reyes, Ning Chang, Kyle Wang
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 target audience is students (both undergraduate and graduate) who have little to no prior computational experience. The instructors will prioritize creating a friendly environment that will empower researchers and enable data-driven discovery. Even those with some experience will benefit, as the goal is to teach not only how to do analyses, but how to manage the process to make it as automated and reproducible as possible.
When: Jan 15-16, 2019. Add to your Google Calendar.
Food: Lunch, coffee, and snacks for both days will be provided free of cost. (Yay!)
Registrations for the workshop have closed. The registrations and wait-list for this workshop are currently full. Wait-listed candidates will be informed if there are any drop-outs by January 6th 2019.
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 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.
Please be sure to complete these surveys before and after the workshop.
|09:00-09:45am||Introduction and Genomics Workshop Overview|
|9:45-10:30am||Introduction to CyVerse Atmosphere Cloud|
|10:45-12:00pm||BASH- Command Line for Genomics|
|12:00-1:30pm||Lunch Break (lunch will be provided!)|
|1:30-2:45pm||BASH - continued and Bioconda|
|3:00-4:00pm||RNAseq overview and Trimming sequencing data|
|4:00-5:00pm||Version control with Github|
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 and an up-to-date web browser.
For this workshop we will be using CyVerse Atmosphere cloud, so you need to register for CyVerse to access their cloud during workshop.
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
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