Appendix
Previous offerings
Videos from August, 2021
The inaugural offering of this material was in August 2021, co-hosted by the UC Davis DataLab and the NIH Common Fund Data Ecosystem. The material from that workshop is hosted here, and all the sessions were recorded; videos below!
Video: Introduction to the UNIX Command Line
Video: Creating and modifying text files on remote computers
Video: Connecting to remote computers with ssh
Video: Running programs on remote computers and retrieving the results
Video: Installing software on remote computers with conda
Video: Structuring your projects for current and future you
Video: Automating your analyses and executing long-running analyses on remote computers
Video: Keeping track of your files with version control
Video: Automating your analyses with the snakemake workflow system
Video: Executing large analyses on HPC clusters with slurm
Video: Making use of on-demand “cloud” computers from Amazon Web Services
Workshop Protocol
Before workshop
- Instructor(s) create workshop notes on GitHub as an R markdown file
- Instructor(s) create/test computing environment (i.e., binder, Farm HPC) for workshop material
- Training coordinator creates pre- and post-workshop assessment surveys, with input from instructor(s)
- Training coordinator emails notes, pre-workshop survey, and Zoom link to participants the day before the workshop
During workshop
- Moderator begins by asking everyone to fill out the pre-workshop survey if they haven’t already, and to put up a raised hand Zoom reaction when they’ve completed the survey. Then, describe ways to ask for help during the workshop: 1) type in Zoom chat to everyone or as a direct message to moderator/helpers (introduce helpers), 2) unmute and ask; say that we prefer participants don’t use the raised hand reaction to ask a question, since that’s used for checking in. At this point, there should be a majority of raised hands up for the survey question. Turn over the mic to the instructor.
- Moderator will keep track of chat questions, time (including a 5-minute break ~10:15 or 10:30am), and help share workshop resource links (i.e., section of workshop notes, exercises, post-workshop survey)
- Helpers aide in tracking chat questions and participation during check ins (i.e., direct message participants who have not raised their hands to make sure they’re still following along)
- Training team writes down typos, suggestions, etc. for the workshop and notes in the associated GitHub issue
After workshop
- Training team updates workshop notes as needed
- Training coordinator emails notes, workshop recording, and post-workshop survey link to participants some time after the workshop