Agenda¶
This workshop runs under a Code of Conduct. Please respect it and be excellent to each other!
Twitter hash tag: #cyverse_foss
Agenda subject to change.
Instructors will review the agenda at the end of each day, and adjust based on participant input.
| Day | Time | Activity (Instructor) | Content |
|---|---|---|---|
| 06/03/19 (Monday) | 8:45-9:00 | Assemble near BSRL elevators | |
| 9:00-:9:30 | Course introduction and overview of the day’s and week’s activities (Ramona) | Course Introduction | |
| 9:30-10:00 | Opens Science, Introductory activity (Ramona) | Introduce the week long activity of setting up a lab for open science. Template | |
| 10:00-10:15 | Coffee break | ||
| 10:15-12:15 | Collaboration culture and roles (Michael Mandel, Eller Business College) | Interactive session. Please complete the self assessment by Sunday. | |
| 12:15-1:15 | Lunch break (on your own) | ||
| 1:15-2:45 | Tools for collaboration (Tyson) | Version Control Systems with Git | |
| 2:45-3:00 | Coffee break | ||
| 3:00-4:15 | Tools for collaboration cont. | Team Communication: Slack, Gitter, ZenHub, etc. | |
| 4:15-4:45 | Tools for collaboration cont. | Wikis & Documentation: Atlassian Confluence, ReadTheDocs | |
| 4:45-5:00 | Wrap-up, Discussion, Q&A | Brief survey of activities | |
| 5:00-6:00 | Instructor Debrief | ||
| 06/04/19 (Tuesday) | 8:45-9:00 | Assemble near BSRL elevators | |
| 9:00-10:15 | Introduction and overview of the day’s activities (Ramona) | Software Essentials | |
| 9:15-10:15 | Introduction to Bash: Command Line Interface (Amanda) | Command line and shell | |
| 10:15-10:30 | Coffee break | ||
| 10:30-12:00 | Programming with R with RStudio (Meghan) | Lesson | |
| 12:00-1:00 | Lunch Break (on your own) | ||
| 1:00-2:45 | Programming with R with RStudio, cont. (Meghan) | Lesson | |
| 2:45-3:00 | Coffee break | ||
| 3:00-4:45 | RStudio with Version Control (Meghan, Tyson) | Lesson | |
| 4:45-5:00 | Wrap-up, Discussion, Q&A | Brief survey of activities | |
| 5:15-6:00 | Happy Hour at 1702 | ||
| 06/05/19 (Wednesday) | 8:00-9:00 | Breakfast with DE team (optional) | CyVerse provides breakfast for participants who are interested in providing DE user feedback |
| 9:00-9:15 | Introduction and overview of the day’s activities (Ramona) | Using CyVerse | |
| 9:15-9:45 | Introduction to CyVerse cyberinfrastructure (Amanda) | Overview of CI, user portal, getting help, Learning Center | |
| 9:45-10:00 | Team Charter (Ramona) | ||
| 10:00-10:15 | Coffee break | ||
| 10:15-11:00 | Introduction to the Discovery Environment (Ramona) | Data and analyses in the DE | |
| 11:00-12:00 | CyVerse Data Store (Ramona) | iCommands, CyberDuck, Data Commons | |
| 12:00-1:00 | Lunch Break (on your own) | ||
| 1:00-2:45 | Introduction to VICE (Tyson) | Jupyter Notebook, Rstudio, RShiny | |
| 2:45-3:00 | Coffee break | ||
| 3:00-3:45 | VICE continued (Tyson) | Jupyter Notebook, Rstudio, RShiny | |
| 3:45-4:45 | Introduction Cloud Computing (Sateesh) | Using CyVerse Atmosphere | |
| 4:45-5:00 | Wrap-up, Discussion, Q&A | Brief survey of activities | |
| 5:00-5:30 | Instructor Debrief | ||
| 06/06/19 (Thursday) | 8:45-9:00 | Assemble near BSRL elevators | |
| 9:00-9:15 | Introduction and overview of the day’s activities (Ramona) | AM: Data Management, PM: Cloud Computing | |
| 9:15-10:15 | Introduction to Data Management (Ramona) | Data life cycle, organization, metadata, FAIR data | |
| 10:15-10:30 | Coffee break | ||
| 10:30-11:00 | Data management plans and tools (Ramona) | Draft a DMP | |
| 11:00-12:00 | Bio5 Tour | Meet in Bio5 (Keating) lobby | |
| 12:00-1:00 | Lunch Break (on your own) | ||
| 1:00-1:30 | Budgeting for open, reproducible science (Fernando, Tina) | Slides | |
| 1:30-2:00 | DMPs continued (if needed) | Draft a DMP | |
| 2:00-2:45 | Advanced cloud computing (Tyson) | XSEDE, Jetstream, commercial providers | |
| 2:45-3:00 | Coffee break | ||
| 3:00-4:45 | Time to catch up | Work on your own or in small groups on topics from throughout the week. | |
| 4:45-5:00 | Wrap-up, Discussion, Q&A | Brief survey of activities | |
| 5:00-5:30 | Instructor Debrief | ||
| 6:30-8:30 | Group dinner | Location TBD | |
| 06/07/19 (Friday) | 8:45-9:00 | Assemble near BSRL elevators | |
| 9:00-9:15 | Introduction and overview of the day’s activities (Ramona) | AM: Containers, PM: lab organization | |
| 9:15-9:35 | Introduction to Containers (Tyson) | ||
| 9:35-10:00 | Biocontainers (Amanda) | Biocontainers | |
| 10:15-10:30 | Coffee break | ||
| 10:30-11:00 | Creating DE apps (Amanda) | Tool and app creation | |
| 11:00-1:00 | Lunch Break - option to join the CyVerse potluck lunch | Coffee shop closes at 1:00, so this is the last chance for fine Catalyst coffee! | |
| 1:00-2:00 | Collaborative exercise (Michael Mandel) | Repeat exercise from day 1 and discuss | |
| 2:00-3:00 | Group activity on Open Science Labs (Ramona) | Complete plans for open science lab, next steps | |
| 3:00-3:15 | Coffee break | ||
| 3:15-4:00 | Report out on Open Science Labs (Team) | Everyone briefly describes their plans | |
| 4:00 | Wrap-up, Evaluations, Q&A (Team) | Post-workshop evaluation | |
| 4:30-5:00 | Instructor Final Debrief |
Fix or improve this documentation:
- On Github: Github Repo Link
- Send feedback: Tutorials@CyVerse.org