Schedule¶
Important
Please fill out the weekly lesson feedback form
Tuesdays: 9:00AM – 11:00AM US Pacific Time (12:00PM – 2:00PM US Eastern Time)
or
Wednesdays: 11:00AM – 1:00PM US Pacific Time (2:00PM – 4:00PM US Eastern Time)
The weekly schedule is listed below as Week Number: Month Tuesday’s Date, Wednesday’s Date
Week 1: Feb. 9, 10 - What is Open Science? Overview and Onboarding¶
Activity:
- Welcome
- Self-introductions
- Intro to FOSS
- CyVerse Tour
Content:
Overview of the course, meet your fellow learners, review code of conduct and course objectives. Start setting up a CyVerse account.
Goals:
Understand and align shared expectations. Start orientation to technology we will use to share and organize.
Homework:
Due by: Monday February 15 (Tuesday cohort), Tuesday February 16 (Wednesday cohort)
Take the Skills Self-assessment
- Make a SHORT video introducing yourself. You can use slides or not (your choice). Tell us:
- Who you are/what you do (career stage, research focus, location, etc.)
- What you most want to gain from the course
- Keep to 3 minutes or less
- Upload your video to the FOSS google drive
- Have fun!
- Recording suggestions:
- Use a smartphone movie/video function
- If you have access to Zoom, you can record this way
- You can also create a video on YouTube if you have an account (you can keep the video unlisted)
And if you haven’t yet, finish setting up your accounts on CyVerse, GitHub, and DockerHub and get an ORCID. Install any optional software you would like to use. Here is a link to the pre-setup instructions.
Week 2: Feb. 16, 17 - Working with Data: Intro to Data Store, Scale and Challenges of Data¶
Activity:
- Guest Speaker (Nirav Merchant)
- Managing Big Data
- Data Stewardship Wizard
Content:
Inspirational talk on data science. Launch into the course by discussing shared challenges for working with data.
Goals:
Understand how your research and associated data challenges fit into the context of this course. Use a tool to help develop a data management strategy.
Homework:
- Review videos
- Start forming a team
- Advanced Shell Users: Read carpentries instructor training
Week 3: Feb. 23, 24 - Essential Skills: Key Concepts of Linux Command Line, VICE Apps¶
Activity:
- Intro Linux skills
- Intro to VICE
Content:
Working in teams, beginner command line users will get introduced to basic tools and lessons for learning more. Advanced learners will help as TAs. We’ll learn just enough to make sense of the parts of this course that will use command line tools.
Goals:
Beginning learners will gain basic understanding of the command line (survival skills). Advanced learners will reinforce teaching skills. Learners will be able to use the VICE platform to launch a command-line interface.
Homework:
- Finish Carpentries Shell Lesson
Week 4: Mar. 2, 3 - Planning Your Open Science Lab¶
Activity:
- Reproducibility Crisis
- Tools for documenting and sharing (Markdown, text editing, communication tools, social media)
- Introducing Github
Content:
We will discuss the major challenges of doing reproducible science. We’ll cover some of the basic tools for organizing within your lab and community. We will also introduce Github as key platform for organizing and disseminating - including but not limited to open source software
Goals:
Know some of the basic tools for documenting and sharing your work in an open source way. Understand how to use some basic features of GitHub (without needing to program).
Homework:
- Find the Github of a tool(s) that you use and look through the issues
- Revisit your DMP given our discussion on reproducibility
Week 5: Mar. 9, 10 - Using Git: Issues, Pull Request, and more¶
Activity:
- Capstone I: Building a GitHub Page
Content:
To apply what we have learned so far, each team will build a shared GitHub page to introduce their FOSS team, and the work of the team members.
Goals:
Be able to use authoring tools and Github to develop a simple website that documents and shares their work.
Homework:
- Complete the GH page for your team
- Find a software tool you’d like to be able to install and use on your own
NOTE: Next Week is a break for FOSS we will resume March 23/24
Week 6: Mar. 23, 24 - Reproducibility Tutorial I¶
Activity:
- Reproducibility tutorial I: Setting up and installing tools
Content:
We will begin a three-part tutorial and gain an understanding of how to install and run command line tools in a reproducible way.
Goals:
Understand how to set up a repository to collect and document your work. Use package managers to install Linux tools.
Homework:
As assigned.
Week 7: Mar. 30, 31 - Reproducibility Tutorial II: Containers¶
Activity:
- Reproducibility tutorial II: Making tools portable
Content:
We will learn about Docker and how we can use this tool to make our research workflow portable to any computing environment.
Goals:
Understand the value of Docker and be able to make use of pre-built Docker containers.
Homework:
As assigned.
Week 8: Apr. 6, 7 - Reproducibility Tutorial III: Workflows¶
Activity:
- Reproducibility tutorial III: Making workflows
- Introduce Capstone II: Applying what you have learned
Content:
We will learn how tools can be linked in a documented workflow using Snakemake. We will also start on Capstone II projects
Goals:
Understand how automated workflows can save time and make research more reproducible.
Homework:
- Capstone II: Applying what you have learned
Week 9: Apr. 13, 14 - Putting It All Together I¶
Activity:
- Capstone II: Applying what you have learned
Content:
Each FOSS team will work on a self-directed project to apply what they have learned into a small shared challenge that applies the skills covered so far.
Goals:
Be able to collaborate as a team to deliver a product that makes use of the skills covered in this workshop and relates to their own research objectives
Homework:
- Presentation for Capstone II: Applying what you have learned
Week 10: Apr. 20, 21 - Putting It All Together II¶
Activity:
- Capstone II: Final presentations
- Final survey
Content:
FOSS Teams will present their Capstone project and reflect on what they have learned
Goals:
Understand how FOSS enable researchers to deliver research that is more reproducible, open, and impactful
Homework:
- Final skills assessment
- Share what you learned with your main research group
Fix or improve this documentation:
- On Github: Github Repo Link
- Send feedback: Tutorials@CyVerse.org