Foundational Open Science Skills (FOSS)
February 17–21, 2020
The University of Arizona, Tucson, Arizona
Syllabus and Agenda
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.
Monday, February 17
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
Discovery Environment (DE)
Data management
Data organization
Data sharing
Metadata
Data analysis
Running apps in batch mode (DE apps)
VICE: Visual Interactive Computing Environment
Creating new tools and apps – overview
Creating workflows
Data Store
iCommands, WebDav, CyerDuck
Tuesday, February 18
AM
Introduction to reproducible science – challenges and solutions
Tools for collaboration
Slack, GitHub, ReadTheDocs, Gitter, Stack Overflow, etc.
Hands on GitHub
In a web-browser, command line
PM
Introduction to cloud computing, OpenScienceGrid, XSEDE HPC
Atmosphere
Launching an instance
Mounting a volume
Creating images
Jetstream – Atmosphere for XSEDE (scale up your analyses)
Commercial cloud providers
Wednesday, February 19
AM
Data management
FAIR data principles (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
Jupyter Notebooks with R or Python (in VICE)
Connecting Notebooks and VICE to GitHub
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.
Thursday, February 20
AM
Introduction to Containers
Intro to BioContainers, Docker, and Singularity
Install Docker on Atmosphere and run a container
Introduction to workflow managers
PM
BIO5 tour
Work on projects, practice specific skills
Evening: Group dinner in Downtown Tucson – take the streetcar!
Friday, February 21
AM
Collaboration culture recap
Project presentations
Planning for continued involvement
Course assessment
This is a draft syllabus and subject to refinement. Please direct any questions to 411@cyverse.org.
