December 9-10, 2016

9:00 am - 4:30 pm

Instructors: Michelle Berry, Nora Mitchell

Helpers: Karla Lindquist, Natasha Strydom, Jieming Chen, Dima Lituiev, Jiashun Zheng

General Information

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. The focus of this workshop will be on working with biological and sequence data, but it will not be a "how to analyze your RNASeq data" tutorial. 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 life science researchers (e.g., students, postdocs, research staff, faculty) from UCSF. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Mission Hall rm 1401/1402, 550 16th Street, San Francisco, CA 94143. Get directions with OpenStreetMap or Google Maps.

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 Software 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 and we will attempt to provide them.

Contact: Please email michberr8@gmail.com for more information.



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

Pre-workshop Survey

Post-workshop Survey

Day 1

09:00 Automating tasks with the Unix shell
10:30 Coffee
12:00 Lunch break
13:00 Introduction to R
14:30 Coffee
16:00 Wrap-up

Day 2

09:00 Data analysis and visualization in R
10:30 Coffee
12:00 Lunch break
13:00 Version control with Git/Github
14:30 Coffee
16:00 Wrap-up

Etherpad: http://pad.software-carpentry.org/2016-12-09-UCSF-R.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Here are links to the data we will be using for the workshop.