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.