# Foundational Open Science Skills (FOSS) Lesson 1: Intro to Open Science
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**Date**: `9/05/2024`
**Today Lead Instructors:** Jeffrey Gillan, Michele Cosi
**Today Helpers:** Tina Lee
**Course Website:** https://foss.cyverse.org/
**[Hack(pad)-of-Hack(pads)](https://hackmd.io/-4TgToyFRU2eX7lmDZLRnQ):**

**Instant Feedback:** (please complete before you leave class) [Complete Form](https://docs.google.com/forms/d/e/1FAIpQLSe32jy6HbKgl02qVGUq4_CQSo_N9GkxMuvalPrWXsqE-beTtg/viewform)
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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
- [HackMD](https://hackmd.io/-4TgToyFRU2eX7lmDZLRnQ)

## Please Introduce Yourself

Jeff Gillan - Data Science Institute; FOSS instructor; I like to analyze geospatial imagery (mostly drone).

Michele Cosi -

Tina Lee - FOSS camp cook; cyverse user engagement officer

Sunday Usman - I am a 4th year Ph.D. student in the Department of Systems and Industrial Engineering. My research focuses on Lifecycle Assessment, Techno-economic Analysis, Optimization, and GIS.

Maliaca Oxnam - Deputy Director, Data Science Institute; I'm looking forward to hearing your questions and discussions

Tina L Johnson, R4R Ops mgr

Ariful Islam - I'm a 3rd year PhD student in Geography. I study flood management and adaptation practices in coastal Bangladesh

Ulises Hernandez - I'm a PhD candidate in the Ecology and Evlutionary Biology program. I study how high rates of deleterious mutations influence evolutionary dynamics.

Andrew Wheeler - I'm a 5th year PhD student in the Genetics GIDP program studying models of protein evolution

Chosen Obih - Hi all! My name is Chosen and I'm a PhD student in the School of Plant Sciences at UoA. I study abiotic stress tolerance in plants.

Maiya Block Ngaybe - hi everyone! I am a Phd candidate at the college of public health studying health behvior and health promotion. I study the acceptability and decision making around new health products like vaccines or injectable PrEP in Arizona and global health contexts.

Dan Nissley - Hey folks! I am a staff scientist at the Institute for Computational and Data Sciences at Penn State. I am here to learn about Open Science in CyVerse to help support the NSF synthesis center NCEMS (https://ncems.psu.edu/).

Joy Luzingu - Hi everyone, my name is Joy Luzingu. I am a 4th year PhD student in Epidemiology. My research consists on evaluating mobile applications used in preventing mosquito-borne diseases and preparing for evacuation with pets during extreme weather events.

Imran Mithu - PhD studnet in Environmental Health Science. My research interest is Climate change and Neural health.

Sudan Pandey -I am a 4th year PhD student in Structural Engineering. I am currently working on testing large scale steel seismic collectors.

Rachel Lieber - Community Engagement Specialist at the Environmental Data Science Innovation and Inclusion Lab (ESIIL) at CU Boulder

Dave Drainer - I'm a 2nd Year Master's Student in Hydrology and Atmospheric Science, studying flood inundation mapping with machine learning.

Garrett Smith - Lecturer in the School of Landscape Architecture and Planning. I study public land management, mostly focusing on recreation and impacts to landscapes, wildlife, and other recreational users.

Caleigh Curley: I am a Doctoral Candidate in the Public Health Policy and Management Program at the University of Arizona (UArizona) Mel and Enid Zuckerman College of Public Health (MEZCOPH). I earned a Bachelor of Science in Biomedical Sciences and a Master of Public Health in Health Promotion from Northern Arizona University. My research explores the intersection of Indigenous health, public health policy, and data governance.

Megan Friggens: Research Ecologist with USFS-RMRS. I work on climate change/wildlife disease topics.

"Sparky" Alice Sweedo - I'm a postdoc in Physiology studying the communication between the gut microbiome and the heart in menopause. My project is going to be using -omics data, so I'm working on building skills to analyze big(ger) data. I generally want to make my research analysis more automated, and learn the skills for automation, openness, and reproducibility while I'm still in a training stage.

Cassidy Soloff: 3rd year PhD student in atmospheric science. I research aerosol particles and clouds.

Erich Eisenhart: I am a first year student of the Master's of Landscape Architecture, I work as a data analyst on the side, and am excited to learn about these skills and tools.

Will Brasic: Hello all! I am a third-year doctoral student in economics interested in industrial organization, machine learning, and applied econometrics. Currently, my research uses reinforcement learning to study the competitive implications of pricing algorithms.

Edwin Alvarado-Mena: PhD Candidate in Government and Public Policy & Master's Student in Data Science at UA.

Saurabh Kaushik: Postdoctoral Research Associate within SGDE, Interested in building AI driven remote sensing solutions for earth observation.

Brielle Hadley: third-year law student in the College of Law.

## :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

Tina - OS represents a sea change in academic research...from my funding, my research, my discovery, to Our Community. Tenure now considers collaboration to be a valuable thing!

Dan N - Open science to me is an important facilitator of research, allowing people to reuse previously published methods to solve new problems in various disciplines.

Cassidy - Making results reproducible by anyone

Dave - Making collaboration on a particular topic available to anyone

Imran- Open science is sharing research among all level of the society. Everything should be accessable to the people of sciecne.

Mike - Many of the Open Sci principles apply to other domains/professions. If not fully 'open' to the general public, reproducibility is still critical.
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:classical_building: Open Access publications:
**Have you ever read, cited, or published in an Open Access journal?**
`+` = yes
`-` = no
Read:+++++++++++++++ +
Cited:+++++++++++++ -
Published:+++++-++++++- -

pro:

Cons:Open access publication is challenging for researchers in developing or underdeveloped countries, which hampers the overall goal of open science

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**Pre-prints:**

Do you read Pre-prints?++++--+++ -
Have you published a Pre-print?-++---+- -

Pros: faster release of results, equity of ability to publish increased

Cons: no/limited peer review so possibly lower quality, reliability of work is questionable.

So, do peer-reviewed articles never have bogus science? - no, they can 😅

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<br/>

:classical_building: Open Data:

**Can you mention any examples where data should not be _open_?**

PII - Personally Identifiable Information
Sensitive locations (cultural resources, species locations)
Data from indigenous populations that they may not consent to have shared
Data that has been obtained without consent
Locational data ie: cell phone data
Security information
Data that may harm anyone (socially and mentally)

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:classical_building: Open Educational Resources:
**What Open Educational Resources do you use?**
openclass.ai (started by UA alum)
OpenSees (FE analysis)

- Carpentries' community lessons: https://carpentries.org/community-lessons/
<br/>
<br/>

: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 y y y y y y y y y y Y y y y yY n y

Have you ever used Git
hub or similar to share code? y y n y y y y y y y y y y y n n
yY y

**Have you ever done pre-registration?**
n n n n n n n n n n n n n
n N
n n y

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

The long timelines of traditional peer review can be frustrating. I suspect a lot of this time is due to the process of an editor matching paper submissions with appropriate reviewers; I am not sure if open peer review can alleviate this problem.

Limited number of reviewers, often who are only sort-of experts in your area. Peer reviewers are often biased by their own work and preferences.
Being in a niche area can mean that you have a small group studying a topic where between the authors and the reviewers they promote their own stuff even when there are flaws that peer review is supposed to reveal.

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

Signed/published: by making the reviewers public, open peer review can prevent the rare problem of a reviewer who does not act in good faith - one example is a reviewer asking you to cite all of their work.

Publishing the names of the reviewers would make them more accountable to do a good job reviewing (sometimes you get minimal comments from them that aren't really that helpful)

As long as you can keep internet trolls off them. It could be scholar trolls--just want to damage your work

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

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## Why do Open Science

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

:school: Democratic y y y y

:school: Pragmatic y y y y y y y

:school: Infrastructure y y

:school: Public school y y y y y

:school: Measurement y y

:school: Compliance y y

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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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:classical_building: Open Access publications:

:classical_building: Open Data:x

:classical_building: Open Peer Review:

:classical_building: Open Methodology: x x

:classical_building: Open Source Software:

:classical_building: Open Educational Resources: x x x

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**Discussion Question 2: Are there any pillars not identified?**
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:::danger
**Discussion Question 3: What are some limitations to you, your lab group, or your domain?**
Open data and Open methodology
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