# Foundational Open Science Skills (FOSS) Lesson 1: Intro to Open Science
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**Date**: `9/02/2025`
**Today Lead Instructors:** Michele Cosi
**Today Helpers:** Tina Johnson
**Course Website:** https://foss.cyverse.org/

**Instant Feedback:** (please complete before you leave the session) [Complete Form](https://docs.google.com/forms/d/1dQbtjGYUpKrYP3zJ5BICwGiPNgQYuBG471EmGzuGh3g)
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## :stopwatch: Agenda

### Welcome

### Staff Introductions

### Course Overview

- Teaching Modalities
- Rundown of [calendar](https://foss.cyverse.org/schedule/) and the 12 sessions
- [Code of Conduct](https://cyverse-learning-materials.github.io/foss/code_of_conduct/)
- About Capstone Projects

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## Please Introduce Yourself

Michele Cosi - Instructor/Scientist for the Data Science Institute; I like plants but I have an extremely brown thumb (because I tend to look at them through a computer) :computer::seedling:
- Lance Picton
- Andrés Caballero
- Lori Hennessy 🐰🐰
- Karla Ajoy
- Gabe Geffen
- Saka Harvis
- Chidera Ejike
- Lourdes Fierro
- Mehedi Hasan
- Emily Davis
- Tina Johnson
- Anam Khalid

## :clipboard: Introduction to Open Science

Today's 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

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## :studio_microphone: Discussion of Open Science and 6 Pillars

**After hearing our definitions of open science, are we missing anything? Do you have a definition?**

Write something here please
Transparency needs to be included in our definition

Openess birth more ideas

### :classical_building: Open Access publications
**Have you ever read, cited, or published in an Open Access journal?**

| y = yes | n = no |
|---|---|

- Read: Y N Y N Y Y N Y Y Y
- Cited: Y N N N Y N Y Y Y Y
- Published: N N N N N N Y Y N Y

**Describe certain Pro or Cons of Open Access publications:**

- Pro: Access and transparency(!)
- Advancement of knowledge

- Cons:Sometimes associated with lower level journals (stigma)

**Pre-prints:**

| y = yes | n = no |
|---|---|

- Do you read Pre-prints?
- N Y Y YY Y N N Y
- Have you published a Pre-print?
-
- N N N N N N N N

**Describe certain Pro or Cons of Pre-Prints publications:**

- Pros:

- Cons:Without peer-review - big example was pre-print Covid-19 data that was later deemed as detrimental to human health

### :classical_building: Open Data
**Can you mention any examples where data should not be _Open_?**

- [HIPAA](https://www.hhs.gov/hipaa/for-professionals/privacy/laws-regulations/index.html) data should **never** be public
- It could cause harm by the state / Nation
- Tribal data
- Research sponsored by Industries
- Sensitive personal info about vulnerable communities

### :classical_building: Open Educational Resources
**What Open Educational Resources do you use?**

- [The Carpentries](https://carpentries.org/), for the basics of CLI, R, Python.
- [EDX](https://www.edx.org/school/edx)

### :classical_building: Open Methodology
**In FOSS, we will NOT do much coding. However, it will be useful to have some familiarity**

| y = yes | n = no |
|---|---|

**Do you write code?**
Y N Y N Y
**Have you ever used Github or similar to share code?**
N N Y N N
**Have you ever done pre-registration?**
N N N N N

### :classical_building: Open Peer Review
**Do you have any complaints with the peer-review process you have been through?**

- Yes I just had a conferene proposal rejected 😭 and I don't know why or by who.
-

**Do any of the open peer-review ideas seem useful?**

- Yes, potentially as a counterbalance to closed peer-review and gatekeeping
-

### :classical_building: Open Source Software
**Do you use open software?**

Y

- [Nextflow](https://github.com/nextflow-io/nextflow): a pipeline management tool (hosted on GitHub)

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## Why do Open Science

**Which School do you belong to or want to?**

| y = yes | n = no |
|---|---|

:school: Democratic

:school: Pragmatic

:school: Infrastructure

:school: Public school

:school: Measurement

:school: Compliance

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### Breakout

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**Discussion Question 1: Which of the pillars of Open Science is nearest to your own heart?**
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| A = agree/support | D = disagree/does not support |
|---|---|

:classical_building: Open Access publications:AAAADAA

:classical_building: Open Data:ADAAAA

:classical_building: Open Peer Review: AAAAAAA

:classical_building: Open Methodology:AAA AAAAAA

:classical_building: Open Source Software:AAAAAAAA

:classical_building: Open Educational Resources:Agree, AAAAAAAAA

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**Discussion Question 2: Are there any pillars not identified?**
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- Humanities? Potentially as a way of meaning making.
-

:::danger
**Discussion Question 3: What are some limitations to you, your lab group, or your domain?**
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- Identifiable data, especially clinical.
- Music educators (Phds) are social scientists and performers who teach are not. (DMA)
- Work with tribal data, that may not be publishable or open
- Some data like tribal data may not be as open because of tribal restrictions
- Research has to be simplyfied and pinpointed in order to be adapted to the art scene
- Data science principles aren't being taught to all engineering degrees
- Data availability might depend on political agendas

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