Foundational Open Science Skills (FOSS)
February 17–21, 2020
The University of Arizona, Tucson, Arizona
Syllabus and Agenda
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
Course introduction and objectives
Clarify objectives and how course topics address participants' goals (general summary from pre-camp surveys)
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
Introduction to CyVerse
Discovery Environment (DE)
Running apps in batch mode (DE apps)
VICE: Visual Interactive Computing Environment
Creating new tools and apps – overview
iCommands, WebDav, CyerDuck
Tuesday, February 18
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
Introduction to cloud computing, OpenScienceGrid, XSEDE HPC
Launching an instance
Mounting a volume
Jetstream – Atmosphere for XSEDE (scale up your analyses)
Commercial cloud providers
Wednesday, February 19
FAIR data principles (Findable, Accessible, Interoperable, and Reusable)
Data and metadata standards
Legal and ethical concerns
Data management tools:
Open Science Framework (OSF)
CyVerse Data Commons
Writing actionable data management plans
Budgeting for open, reproducible science
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
Introduction to Containers
Intro to BioContainers, Docker, and Singularity
Install Docker on Atmosphere and run a container
Introduction to workflow managers
Work on projects, practice specific skills
Evening: Group dinner in Downtown Tucson – take the streetcar!
Friday, February 21
Collaboration culture recap
Planning for continued involvement
This is a draft syllabus and subject to refinement. Please direct any questions to email@example.com.