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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.

Syllabus (draft, subject to change)

Last year’s syllabus as a chart (for reference): https://docs.google.com/spreadsheets/d/1n5zCJlT9g_vyWx6z-5vmT300ZH-vC6AP4TYKFeJIMZo/edit#gid=0

Expected Outcomes

By working through an example project relevant to their interests, participants will practice open science skills using CyVerse, GitHub, R or Python, and other resources. At the end of the week, students will present a plan for how to integrate open science into their labs.

Day 1

AM

  • Course introduction and objectives
    • Clarify objectives and how course topics address participants’ goals (general summary from pre-camp surveys)
    • Participant introductions
    • Discussion: What is open science?
    • Introduce example lab/research project
    • Collaboration culture and roles (Michael Mandel, Eller Business College)

Lunch break: optional command line refresher

PM

  • Introduction to CyVerse
    • Platform overview
    • Data Store
      • Data Store Access
        • iCommands, WebDav, CyberDuck
      • Data management
        • Data organization
        • Data sharing
        • Metadata
    • Discovery Environment (DE)
      • Walkthough & Terminology
      • Data Analysis
        • running apps in batch mode (DE apps)
        • VICE: Visual Interactive Computing Environment
      • Creating tools and apps - overview

Day 2

AM

  • Data Management
    • FAIR data principle (Findable, Accessible, Interoperable, and Reusable)
      • Data organization
      • Data and metadata standards
      • Using metadata
      • Data licensing
      • Legal and ethical concerns
  • Data Management tools:
    • Open Science Framework (OSF)
    • Protocols.io
    • CyVerse Data Commons
  • Writing Actionable Data Management Plans
  • Budgeting for open, reproducible science

PM

*Introduction to reproducible science
  • The Research Object
  • Tools for collaboration
    • Version Control: GitHub,
    • Documentation: ReadTheDocs, Bookdown
    • Communication: Slack, Gitter, Microsoft Teams
    • How to Google: Stack Overflow, etc.
  • Hands on GitHub
    • In a web-browser, command line

Day 3

AM

  • Project Pitches
  • Introduction to cloud computing
    • Atmosphere - Jetstream for XSEDE (scale up your analyses)
      • Launching an instance
      • Mounting a volume
    • OpenScienceGrid, XSEDE HPC
    • Commercial Cloud Providers

PM

  • Computational Notebooks
    • Jupyter Lab Notebooks with R or Python
    • Connecting Notebooks and VICE to GitHub
  • Optional Project time

Evening: Happy hour at 1702! No trip to UA’s north campus is complete without a visit to 1702 for pizza and beer. It’s a local institution.

Day 4

AM

  • Introduction to Containers
    • Intro to BioContainers, Docker, Kubernetes, and Singularity
    • Install Docker
      • Atmosphere
    • Run a container in Docker

PM

  • Work on projects, practice specific skills

Group Dinner in Downtown Tucson - take the streetcar!

Day 5

AM

  • Work on Projects, practice specific skills

PM

  • Project presentations
  • Planning for continued involvement
  • Course assessment

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