A Data Carpentry Workshop
Stanford University
June 17-18, 2017
9:00 am - 5:00 pm
Instructors:
Naupaka Zimmerman, Ted Hart
Helpers:
Kris Sankaran, Ben Stenhaug, Claudia Engel, Mary-Ellen Petrich, Sarah Munro, Amy Hodge, Chris DeBoever
June 17-18, 2017
9:00 am - 5:00 pm
Instructors: Naupaka Zimmerman, Ted Hart
Helpers: Kris Sankaran, Ben Stenhaug, Claudia Engel, Mary-Ellen Petrich, Sarah Munro, Amy Hodge, Chris DeBoever
General Information
Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data.
We will cover Introduction to the Linux shell and cloud computing, Scripting your analyses, Data wrangling in R, and Data visualization and reproducible research in R. Participants should bring their laptops and plan to participate actively. By the end of the workshop learners should be able to more effectively manage and analyze data and be able to apply the tools and approaches directly to their ongoing research.
Who: The course is aimed at postdocs and other researchers.
Where: Saturday LK005/Sunday LK120, 291 Campus Drive, Palo Alto, CA. Get directions with OpenStreetMap or Google Maps.
Sponsors: Office of Postdoctoral Affairs, Stanford Libraries, and Lane Medical Library.
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (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.
Contact: Please mail amyhodge@stanford.edu for more information.
Materials and other resources referred to during the workshop
- GitHub repository for custom R scripts we used and misc data files, updated R lessons
- Data Carpentry Genomics Workshop Materials
- Other Data Carpentry Workshops
Preliminary Schedule
Surveys
Please be sure to complete these surveys before and after the workshop.
Day 1
Note: If you need help with setup, please show up at 8:30 am on Saturday, and we will check to make sure you're all set to go.
Also - this weekend is graduation at Stanford, so parking will be at a premium. Arrive early (by 8:30 or so) to avoid the rush.
| 09:00 | Intro to Data Carpentry, this workshop, and cloud computing |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Automating tasks with the Unix shell, scripting analyses |
| 14:30 | Coffee |
| 16:30 | Wrap-up |
Day 2
| 09:00 | Data Analysis and wrangling with R |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Visualization and reproducible research with R |
| 14:30 | Coffee |
| 16:30 | Wrap-up |
Etherpad: http://pad.software-carpentry.org/2017-06-17-stanford.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Setup
To participate in a Data Carpentry workshop, you will need working copies of the described software. Please make sure to install everything (or at least to download the installers) before the start of your workshop. Participants should bring and use their own laptops to insure the proper setup of tools for an efficient workflow once you leave the workshop.
For this workshop, you will need to have R and RStudio installed, as well as a secure shell (ssh) client. MacOS already has this installed, for Windows machines, please install PuTTY. We will not be using OpenRefine or SQLite for this workshop.
If you have additional questions, please take a look at these Setup Instructions.
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.