Foundational Open Science Skills (FOSS) Lesson 1: Intro to Open Science

Date: 2023-01-26
Today Lead Instructors: Tyson, Jeff
Today Helpers: Michele, Jason, Tina
Course Website: https://cyverse-learning-materials.github.io/foss
Zoom Link: https://arizona.zoom.us/j/87386173667

Instant Feedback: (please complete before you leave class) Complete Form

Agenda

Welcome (10 minutes):

• Code of Conduct

Staff Introductions (2 minutes)

Hi, I'm Tyson, I am co-PI of CyVerse and have a background in geoinformatics and fire ecology.

Jeff Gillan. My background is in remote sensing, photogrammetry, drones, and rangeland science.Decaf

Greetings! I am Michele Cosi, science analyst and educator for CyVerse. My academic background consists of plant sciences, genomics and bioinformatics.

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

, right hand

I'm Jason, I am a CyVerse Education, Outreach, and Training lead, and a biologist/bioinformatician educator.

Student Self-Introductions (3 minutes)

Name; Institution/Org; what you do; primary goal / interests in FOSS;

, , or 🍸 ?

Hello Everyone, I am Siddiqua. My background is in Mathematics. My research interest is in Statistical Machine Learning. I am a Data Engineer working in RII KMAP institute (UofA). My primary interest is to brush up my skills and learning and about infrastructure in scientific research.

Hi, I'm Ajay Perumbeti, and am an clinical informatics fellow at UACOM-Phoenix. I'm interested in ML pipelines for health data & transcriptome analysis. Love coffee, tea, and all of the above

Hi, I am Nayani Ilangakoon and I am a postdoctoral researcher at Earth Lab, CU Boulder. My background is in remote sensing, photogrammetry and fire/ disturbnace ecology. :Tea:

Hello everyone. I'm Luca and I'm a PhD student in system engineering at the University of Arizona.
I'm definetly a cocktail person

, nothing beats a good gin and tonic at the end of a long day in the office. I hope to use the knowledge learned in this course for my research on computer vision.

Hello, I'm Ming, Executive Assistant at ESIIL and I joined FOSS to a bit of background on open data science that I hope will help me in my job supporting the real data scientists!

for me!

Hello! I am Samantha Werts. I am a PhD candidate in Public Health. My research focuses on lifestyle behavior change with older cancer survivors utilizing mHealht tools. I am interested in learning more about data management and visualization. I am a

person!

Hello everyone!,

I am Shashank Yadav. I am a PhD Student in Biomedical Engineering at University of Arizona. I work with Dr. Vignesh Subbian on Electronic Health Records. I am interested in FOSS to focus on reproducible science. No tea / coffee / beer.

Hello, I'm Tyler. I'm a project manager at Earth Lab at CU Boulder. Primary goal is learning to use CyVerse resources to run workshops and working groups.

person.

Hey I'm Matthew! I'm a data manager at Archbold Biological station. We've got a lot of new and data heavy projects starting up and I'd say I am a

person.

Hi there, I'm Ana Almeida, biologist and educator at Cal State East Bay. My research focus on plant development, evolution and genomics. My favorite drink is a dirty martini.

Hi I am David Lopez and I am a PhD student in Chemical Engineering and MS student in Pharmaceutical Sciences. I am working on developing prediction models for physical properties of pharmaceuticals. I do not drink coffee at all. I like matcha though!

Hello, I'm Yi Liu. You can call me Yi. I use prons She/Her. I am a first year Ph.D. student at University of Michigan School of Environment and Sustainability. I come from Nanyang city in China and I received my bachelor degree in hydrology and water resources at Southern University of Science and Technology in Shenzhen. Now I focused on climate change and health, especially the pollen penology in a warmer climate and allergy. I love

!

Hello, my name is Mia Swain. I am a PhD candidate at the U of Nevada, Reno. I study plant genomics and I am interested in learning more about data management and open science practices. I love

and !

Hellow, my name is Shike Zhang. I'm a first year PhD student at SEAS, University of Michigan. I'm broadly interested in climate change and forecasting the impact of human activities on global phenology with ecological modeling.

Hello

Hello! I'm Megh Krishnaswamy, a 4th Year PhD student in the Linguistics Department. I am an experimental linguist and speech scientist. My primary interest is in finding ways to apply my work with data modelling in behavioural science to FOSS goals, and learn more about data visualization, effective science communication and Open Access to improve communication among researchers from different fields.

Hello, my name is Lina Benitez, I am a master student of Agricultural and Resource Economics at the University of Arizona working in environmental justice specifically in the analysis of chemical water contamination in Arizona and the socio economic characteristics of the affected population.

Hello, my name is Beckett Hills, I am a PhD student at UW-Madison working with hyperspectral and LiDAR data from drones and a cessna-mounted system to understand phenological changes in functional traits.

Hello, I am Dinesh Ghimire, a master's student of Biotechnology from West Virginia State University. I am from Nepal where I completed my undergraduate degree in Agricultural Science.I am currently working on marker assisted breeding work in tomatoes at Liedl Lab, WVSU. I am looking for PhD in plant science focusing on quantitative genetics, phenomics and computational biology.

Hi all! My name is Ramzi Ibrahim. I am a resident physician in the University of Arizona Internal Medicine program and will be applying to a Cardiology fellowship this upcoming year. My research interests include population health/epidemiological studies related to cardiovascular diseases. I'm looking forward to learning from all of you. Happy to collaborate if anybody is interested in medicine/population health!

Course Overview (10 minutes)

• Website: https://foss.cyverse.org
• SLACK: cyverselearning.slack.com
• CyVerse Accounts: https://user.cyverse.org
• Course Content
• About Capstone Projects

Open Science Overview (45 minutes)

Today' Lesson: https://cyverse-learning-materials.github.io/foss/01_intro_open_sci/

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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Breakout Discussion and Notes

General notes

Pros/cons of pre-prints:
Pros:

• get your idea out there first (avoid/minimize being scooped)
• see bias of reviewers
• possibly higher self-citation

Cons:

• less feedback overall?

Questions

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

Cited: -++-±+ -±––-
+ = yes
- = no

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

Chat-Shared Links

Breakout 1 (20 minutes)

Discussion Question 1: Which of the pillars of Open Science is nearest to your own heart?

Room 1

Open Educational Resources, also open data.

Open data and methodology

All these three: Open Access Publications , Open Data, Open Educational Resources.

All of them are important to advance science

Room 2 is writing a lot more than room 1 (we're having a great discussion)!!!

Room 2

Open Data – my reseach revolves around the machine learning with deep learning models. For most of the models that I have a did my own datasets.

Open access publications–the fact that government funded research isn't available is crazy

Open data – My work relies on data a lot, open data will help for sure, actually the most boring and tough process of many of my works are searching for appliable database.

Open source software -

Open source software - many remote sensing technologies depend on fairly expensive (data, hardware and cost) workflows, which can impact how much science can be accomplished within a reasonable timeframe.

Open Data - To me, it feels most fundamental, or that the possibilities of what can be done with open data stretch a bit further than some of the other pillars.

Open data - Even public data sets are difficult to navigate with data use agreements. Biolincc requires you to be faculty. NHANES requires a nebulous process for GIS data. MIMIC asks you to fill forms, and they will reject as not meeting requirements, with difficult to identify the specific issue. Some issues that have consumed a lot of time for me in the past. Perhaps some standards and automation for access would be helpful. A virtual assistant for access may be helpful.

Open data- I am data mining a bunch of experimental data that is in peer-reviewed articles and books. Open data is crucial for my research.

School of Thought & Ethics

Questions

Which School do you belong to or want to?

Democratic ++

Pragmatic ++

Infrastructure +++++

Public school+ +++++
make science accesible to reduce misinformation

Measurement ++
Most of research end up in publication but not reaching to acutual end user or reaching to the descicion making entity. Feels like difinetly need some measurements other than journal impact factor to measure how usable/accesible the research outcomes to societal benifits.

What are some examples of ethics that we did not discuss?

Breakout 2 (20 minutes)

Discussion Question 2: Are any of the pillars more important than the others to you?

Open Access:

Open Data:

Open Peer Review:

Open Methodology:

Open Source Software: +

Open Educational Resources:

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