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FOSS 2019 Introduction

Welcome and staff introductions

Stuff to get out of the way

Learning Objectives

By the end of week one, participants should have the basic skills needed to:
  • Communicate and collaborate with other scientists and developers
  • Manipulate files on the command line
  • Write basic R scripts
  • Manage, share, and analyze data on CyVerse
  • Understand high performance and cloud-based computing
Our goal is to have each participant leave with a solid plan for how they will set up their own lab to conduct open science. This master plan will include plans for:
  • intra- and inter-lab communication and collaboration
  • data management
  • scaling analyses


FOSS camp focuses on hands on activities – participants should learn skills by practicing them. Most of the skill taught in this course are interdepent, and lessons are designed to reinforce skills learned earlier in the week. Some material may be completely new to you, and some may be familiar. If you have experience with a subject, please help your less-experienced neighbor.

During this week, we will introduce many new tools and technologies, but these are just a sample of what is available for you to use in your own Open Science Lab. Before choosing which technologies to adopt, you should look around and see what others in your community are using. This is a case where fitting in with your peers can make you more productive. For example, if everyone you know is already on Google Chat, you may have a hard time convincing them to use Slack or Gitter, and vice versa.

We don’t expect anyone to be experts at these skills after one week. Instead, we aim to give you enough hands on experience to confidently continue with your own self-pased learning. Each lesson includes links to addtional learning materials that can enhance or expand on what you have learned at FOSS camp.

For up to one year following FOSS camp, CyVerse will provide concierge service to participants, to ensure that they are able to take full advantage of CyVerse infrastructure for their open science projects.


Each day will start with an overview of the days activites and end with an assessment and discussion. Please speak up and let us know if we should go faster, slower, or do something different. Participants should feel free to drive the agenda to suit their needs.

Day Activity
Monday AM Open Science, Collaboration
Monday PM Tools for Collaboration
Tuesday AM Software essentials (command line, R)
Tuesday PM Software essentials (R)
Wednesday AM CyVerse (Discovery Environment)
Wednesday PM CyVerse (Data Store, VICE)
Thursday AM Data Management
Thursday PM Cloud computing
Friday AM Containers, Apps
Friday PM Open Science, Wrap up

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