# Foundational Open Science Skills (FOSS) Lesson 1: Intro to Open Science
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**Date**: `2024-01-25`
**Today Lead Instructors:** Michele, Jeff
**Today Helpers:** Tina, Carlos
**Course Website:** https://foss.cyverse.org/
**Hack(pad)-of-Hack(pads):** https://hackmd.io/y9XyyinFToOJS3XPJ2TtGg

**Instant Feedback:** (please complete before you leave class) [Complete Form](https://docs.google.com/forms/d/e/1FAIpQLSdxgpv2TN2ArbFYml8nnv0Meda8H5Fx73OE9jgVm4lWTqlB1Q/viewform?usp=sf_link)
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## :stopwatch: Agenda

### Welcome:

- [Code of Conduct](https://cyverse-learning-materials.github.io/foss/code_of_conduct/)

### Staff Introductions

Hi, I'm [Tyson](https://tysonswetnam.com), I am co-PI of CyVerse and have a background in geoinformatics and fire :fire: ecology. :coffee:

[Jeff Gillan](https://www.gillanscience.com). My background is in remote sensing, photogrammetry, drones, and rangeland science.Decaf :coffee:

Greetings! I am [Michele Cosi](https://cosimichele.github.io/), science analyst and educator for CyVerse. My academic background consists of plant sciences, genomics and bioinformatics. :beer:

Tina Lee, Camp Cook: ping me via slack if you need logistics help, have questions (or better yet, answers!). left hand:tea:, right hand:coffee:

### Student Self-Introductions

your name, background and interests, :coffee: or :tea:
Kurt Riitters, Forestry/Biometrics, Research Ecologist graybeard, many interests -- esp deployment of spatial analysis software developed over past couple decades. Coffee.

N. Brandon Barba, PhD student in Clinical Translational Science at UofA Phoenix. I'm interested in clinical data analysis. :Coffee: > :Tea:

Sarah Yates, Technical Data Manager for Clinical Trials/Health Programs, i'm interested in clinical trial monitoring methods :coffee:

Mackenzie Waller, Assistant Professor at CAPLA (landscape architecture / design) :coffee: if I can't have :beer:
### Course Overview

- Website: https://foss.cyverse.org
- CyVerse Accounts: https://user.cyverse.org
- Course Content
- About Capstone Projects

## :clipboard: Open Science Overview (45 minutes)

Today' Lesson: https://foss.cyverse.org/01_intro_open_sci/

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**Learning objectives:**

After this lesson, you should be able to:

- Explain what Open Science is
- Explain the components of Open Science
- Describe the behaviors of Open Science
- Explain why Open Science matters in education, research, and society
- Understand the advantages of and the challenges to Open Science
- Identify who the practitioners of Open Science are
- Understand the underlying Ethos of Open Science
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## :studio_microphone: Breakout Discussion and Notes

**General notes**

Pros/cons of pre-prints:

Pros:

Cons:

**Questions**

Have you used/cited preprints?
Used: +
`+` = yes ++++++ +++++
`-` = no ++++++

Cited:
`+` = yes ++++
`-` = no ++++++++++

Have you authored a pre-print?
Authored:
`+` = yes +++
`-` = no ++++++++++

### Breakout 1 (10 minutes)

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- **What does Open Science mean to you?**
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Group 1: reproducibility/replicability, freely available data/code/resources, transparency, accessibility

Group 2: Making material open and reproducable so others can build on it.

Group 3:
- Reproducibility!
- Transparency in the science (making mistakes is ok!)

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- **What characteristics might a paper, project, lab group require to qualify as doing Open Science?**
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Group 1: lab website with protocols, Github repository, available datasets

Group 3: integrity and transparency (put things on GitHub! Version Control!)

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- **What are some limitations to you, your lab group, or your domain?**
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Group 1: working with communities (cultural competency), data principles for protected communities

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- **Discussion Question 1: Which of the pillars of Open Science is nearest to your own heart?**
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Group 1: ability to pay/afford to publish as a open access publication, open hardware

Group 2: Open Education Resources

:classical_building: Open Access publications: +

:classical_building: Open Data: +++

:classical_building: Open Peer Review:

:classical_building: Open Methodology: ++

:classical_building: Open Source Software:+ +++

:classical_building: Open Educational Resources: +++

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**Discussion Question 2: Are there any pillars not identified?**
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* Open Hardware (Arduino, RaspberryPI)

### Breakout 2 (10 minutes)

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- **What motivates you to do Open Science?**
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Group 1: collaboration w/ community and stakeholders, improve approach and leverage of health data, connections/expand networks,

Group 3: Make science freely available to everyone

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- **Do you feel that you fall into a particular "school"? If so, which one, and why?**
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Group 1: democratic - making things open access, pragmatic - utility/methodologies/expansion/makes science better;

Group 3: pragmatic

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- **Are there any motivating factors for doing Open Science that don't fit into this framework?**
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#### :school: School of Thought & :scales: Ethics

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**Which School do you belong to or want to?**
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:school: Democratic +++++

:school: Pragmatic ++++++++++

:school: Infrastructure +

:school: Public school ++

:school: Measurement +++

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**What are some examples of ethics that we did not discuss?**
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Group 1: citation matters, data embargo/govt industry, competiveness

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## Homework

Go to the Foss Reference Hub GitHub repository, branch 1: https://github.com/CyVerse-learning-materials/foss-reference-hub/tree/week-1

If you are following along [Option 1 of the Capstone](https://foss.cyverse.org/final_project/overview/#option-1), the homework for this week is to be able to recreate the week 1 branch:
- Create a GitHub Repository
- Add and populate:
- `AUTHOR.md`
- `LICENCE`
- `README.md`

Also, create your ORCID! https://orcid.org/

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