sheilasaia/reproducibili-tea

Brainstorm and resources for Reproducibili-Tea event at NC State University Libraries co-organized with Micah Vandegrift.

Open Science and Reproducibili-tea @ NC State University

Brainstorm, notes, and resources for the Open Science and Reproducibili-Tea events at NC State University Libraries, co-organized by Micah Vandegrift and Sheila Saia.

Livestreaming on NC State Library Twitch with recordings shared to the Libraries YouTube channel.

Summer/Fall 2021 Schedule

• Show Me the Open Science! (Part 1) Tuesday, July 27 from 12-1p EST (1600 UTC)
• Show Me the Open Science! (Part 2) Thursday, August 27 from 12-1pm EST (1600 UTC)
• Show Me the Open Science! (Part 3) Friday, October 22 from 12-1pm EST (1600 UTC)

Show me the Open Science! Part 3 - Dissecting a Publication Contract

Introductions

• Micah (he/him)
• Will Cross (he/him)
• Carlos Goller
• Maggie Simon

Tea Talk

1. Why reproducibili-tea?
2. Best tea for autumn/reading legal contracts?
3. Happy Open Access Week!

Discussion

1. Why do publication contracts matter?
2. Tell us about weird circumstances you've had with a publishing contract
3. What is your primary need/goal when you approach a contract?
4. How have you typically used your own work after publication?
5. What seems confusing about your most recent contract or publishing experience?
6. What situation would be most ideal for you when publishing and using your work after the fact?

Resources

• SPARC's Authors Addendum
• Author's Alliance
• Your local friendly scholarly communication or open publishing librarian!

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Show me the Open Science! (in Ten Simple Rules or Less; Part 2)

Introductions

• Micah (he/him)
• Sheila (she/her)
• Dr. Natalie Nelson, professor and lead of the Biosystems Analytics Lab (BAL) in the Dept. of Bio & Ag Engineering at NC State. Natalie uses data analytics and machine learning to study complex biological system dynamics in lots of different applications from aquaculture to water resources management and beyond.
• Dr. Sierra Young, professor and lead of the Digitial Agroecology and Intelligent Systems Lab (DAISy Lab) in the Dept. of Bio & Ag Engineering at NC State. Sierra develops human-centered robots and sensors that help monitor agricultural systems and natural processes.

Tea Talk

1. Why reproducibili-tea?
2. Do Natalie and Sierra like tea? If so, which kinds?
3. Do you have a few simple rules for making a great cuppa? :)

Discussion

1. Can you tell us a little bit about the research you do?
2. Can you tell us about how you first got interested in open science/reproducible research?
3. Can you describe one of your favorite open science project (that you've participated in)?
4. Can you describe the idea behind the Ten Simple Rules paper?
5. What do you see as the link between the Ten Simple Rules paper and open science?
6. What surprised you most about developing an open source web app like ShellCast?
7. Do you have a favorite rule?

Ten Simple Rules (for reference)

1. Start with user-centered design
2. Test, test, then test again
3. Make it accessible
4. Protect your users
5. Hire a web developer, or become one
6. Expect expenses
7. Leverage institutional expertise
8. Track your progress with existing collaboration tools
9. Estimate task times, then double them (and then some)
10. Make it last: Plan for the long haul

Resources

• Ten Simple Rules preprint by Sheila, Natalie, Sierra, and Micah

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Show Me the Open Science! (Part 1)

The theory and practice of open science in real life (IRL)

Introductions

• Micah (he/him)
• Sheila (she/her)

Tea Talk

1. Why reproducibili-tea?
2. Real talk - Sweet Tea vs Unsweet Tea (which is better)

Discussion

• Working towards being as open as possible, where you improve with each iteration
• Project directory structures - what to do with code and data?
• Example Sheila's first reproducible repo
• Example Sheila's latest (work in progress) reproducible repo
• Check out collaboration and issue organization with GitHub projects, see example
• Using Git and R (demo) and/or using Git in the terminal (demo)
• Zenodo and GitHub connection
• How to save/version control data? Check out Zenodo and pancaderm (warning: Sheila hasn't actually used this yet)
• Preprints in practice, for example, EarthArXiv
• What happens when you can't be open? See this preprint and appendix for ideas
• Code as scholarly artifact?
• Is 'science' the product (written results) or the process?

Resources

• Research Object
• Octopus
• hypergraph
• OpenMimosa
• Zenodo and GitHub connection
• The Carpentries tutorial on Git
• The Carpentries tutorial on the Unix shell
• Open Hydrology

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Spring 2021 Schedule

Earl Grey Literature

The evolving scholarly record and reproducibility

Introductions

Micah (he/him) and Sheila (she/her) introduce themselves!

Tea Talk

1. What exactly is Earl Grey?
2. Is it gauche to order a 'London Fog' at the local coffee shop?
3. London is cool, right?
4. Why reproducibili-tea?

Discussion Questions:

1. Oxford Reproducible Research Initiative
2. What is 'grey literature' anyways?

• "That which is produced on all levels of government, academics, business and industry in print and electronic formats, but which is not controlled by commercial publishers." From the 4th International Conference on Grey Literature (1999)

3. Where might one find grey literature and how would one know?
4. Are pre-prints the future of publishing?
5. What do I do with a conference poster?
6. What is pre-registration?
7. Any papers, resources, experts, etc. you want to share on this topic?

Resources & Examples to Share:

• Pollock, M. C. (2018). Art of the Tea Latte. Tea & Coffee Trade Journal, 190(4), 47–49.
• Bazalgette, P. (2013). The taste test: Earl grey tea. FT.Com
• Lavoie, Brian, Eric Childress, Ricky Erway, Ixchel Faniel, Constance Malpas, Jennifer Schaffner, and Titia van der Werf. 2014. The Evolving Scholarly Record. Dublin, Ohio: OCLC Research. https://doi.org/10.25333/C3763V.
• Preprinting the COVID-19 pandemic. Nicholas Fraser, Liam Brierley, Gautam Dey, Jessica K Polka, Máté Pálfy, Federico Nanni, Jonathon Alexis Coates. bioRxiv 2020.05.22.111294; doi: https://doi.org/10.1101/2020.05.22.111294
• Chiarelli A, Johnson R, Pinfield S and Richens E. Preprints and Scholarly Communication: An Exploratory Qualitative Study of Adoption, Practices, Drivers and Barriers [version 2; peer review: 3 approved, 1 approved with reservations]. F1000Research 2019, 8:971 (https://doi.org/10.12688/f1000research.19619.2)
• Chiarelli, Andrea, Johnson, Rob, Pinfield, Stephen, & Richens, Emma. (2019, September 24). Accelerating scholarly communication: The transformative role of preprints. Zenodo. http://doi.org/10.5281/zenodo.3357727
• Rieger, O. Y. (2020, May 27). Preprints in the Spotlight: Establishing Best Practices, Building Trust. https://doi.org/10.18665/sr.313288
• OpenGrey.eu
• Some grey Literature at NC State
• Intnl Journal of Grey Lit <--- SO META!!

• Pre-printing Microbiolgy by P.D. Schloss (paper here)
• Blog post by Sheila on pre-prints
• Center for Open Science on Preregistration definition and resources (link here)
• The preregistration revolution by Nosek et al. (paper here)
• Ten Simple Rules to Consider Regarding Preprint Submission by Bourne et al. (paper here)

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Open Kombucha Knowledge

Universities/Institutions and open knowledge

Introductions

Micah (he/him) and Sheila (she/her) introduce themselves!

Tea Talk

1. What is that science experiment on your counter?
2. How does kombucha work?
3. Why is brewing kombucha fun?
4. What's your favorite kombucha flavor?
5. Why reproducibili-tea?

Discusion Questions:

1. When does something move from information to knowledge?
2. What is open knowledge, open science, open (fill in blank)?
3. What started you on your open access/open science journey? (Origin story!)
4. What are our open knowledge roles as librarians and researchers?
5. What is metadata and why is it important?

Resources & Examples to Share:

• Reusable Research webinar (happening just as we finish!)
• Open Knowledge Institutions: Reinventing Universities
• NC State Dept. of Applied Ecology Fermentology Mini-Seminars
• Kombucha microbiolgy explainer blogpost by Dr. Benjamin Wolfe
• The Big Book of Kombucha by Hannah Crum and Alex LaGory for all things kombucha and kombucha brewing
• Hannah Crum's website on Mold vs Not Mold
• Example README template for metadata - Shout out to my library mentors Gail Steinhart and Erica Johns at Cornell Libraries!
• Find your metadata standard here and here
• WaterML metadata standard as an example (for hydrology and related fields)
• The Open Science Training Handbook by Bezjak et al. (2018)
• "Open science is a spectrum rather than an on/off switch." - Micah, from Micah Vandegrift. (2021, February 4). Defining Open Science. Scholarly Communication Librarianship and Open Culture: Law, Economics, and Publishing. Association of College and Research Libraries. http://doi.org/10.5281/zenodo.4501795
• A Taxonomy for Learning, Teaching, and Assessing: A Revision of Bloom's Taxonomy of Educational Objectives by Anderson and Krathworth (2001)
• Multimicrobial Kombucha Culture Tolerates Mars-like Conditions Simulated on Low Earth Orbit. Olga Podolich, Olga Kukharenko, Andriy Haidak, Iryna Zaets, Leonid Zaika, Olha Storozhuk, Larysa Palchikovska, Iryna Orlovska, Oleg Reva, Tatiana Borisova, Ludmila Khirunenko, Mikhail Sosnin, Elke Rabbow, Volodymyr Kravchenko, Mykola Skoryk, Maksym Kremenskoy, Rene Demets, Karen Olsson-Francis, Natalia Kozyrovska, and Jean-Pierre Paul de Vera. Astrobiology. Feb 2019.183-196. http://doi.org/10.1089/ast.2017.1746
• Microbial Diversity of Kombucha, from Microbialfoods.org
• Scholia built on/from wikidata

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Credit, Contributors, and Chai

Attributing open knowledge

Introductions

Micah and Sheila (she/her) introduce themselves!

With special guest, Dr. Cassidy Sugimoto.

Tea Talk

1. What are Micah's feelings/thoughts about giving kombucha a second chance since our conversation last week? (Is it still a weird, sour science experiment?)
2. What's the difference between chai and cha?
3. What spices are key to a good chai?
4. What's Cassidy's favorite type of tea?
5. Why reproducibili-tea?

Discusion Questions:

1. What is the CRediT taxonomy?
2. What is Altmetric?
3. What is it like to be on the inside of a lab (i.e., Micah's vs Sheila & Cassidy's perspective on credit and open science collaborations)?
4. What is the evolution (and diversity?) of authorship to contributorship?
5. How do academic systems currently value/evaluate contribution?
6. What are some barriers to open science being the norm? (evaluation/research outputs and training)
7. How did you get started on your open science journey?

Resources & Examples to Share:

• Visual matrices for clarity in contributor roles
• National Academies incentives
• Example of tidycensus R package by Dr. Kyle Walker and "research output" evaluation mis-match
• CRediT stands for Contributor Roles Taxonomy and is describe here by the Consortia Advancing Standards in Research Administration (CASRAI) and National Information Standards Organization (NISO)
• Example of the journal Cell adopting CRediT taxonomy to standardize author contribution statements in peer-reviewed articles (see more at https://casrai.org/credit/ > "Adopters")
• Example of science communication by Dr. Christopher Jackson who was invited along with two other scientists to give this year's Royal Institution Christmas Lecture
• Using ORCID (along with CRediT) to get recognition for your work, see this article from ORCID
• NTRES 6490 (~2012 but as of 2017 is NTRES 6600?) at Cornell University taught by Erica Johns (librarian) and Dr. Cliff Kraft (faculty): Special Topics Grad Course: Managing data to facilitate graduate student research, see the library guide here
• Altmetric for researchers website
• Holcombe, A. (2019). Farewell authors, hello contributors. Nature, 571, 147. https://doi.org/10.1038/d41586-019-02084-8
• Holcombe, A. (2020, July 13). Announcing Tenzing. Medium. https://medium.com/@ceptional/announcing-tenzing-ceca6789d88c
• Larivière, V., Desrochers, N., Macaluso, B., Mongeon, P., Paul-Hus, A., & Sugimoto, C. R. (2016). Contributorship and division of labor in knowledge production: Social Studies of Science. https://doi.org/10.1177/0306312716650046
• Nowviskie, B. (2012, December 19). Evaluating Collaborative Digital Scholarship (or, Where Credit is Due). Journal of Digital Humanities. http://journalofdigitalhumanities.org/1-4/evaluating-collaborative-digital-scholarship-by-bethany-nowviskie/
• Transparency in Author Contributions in Science (TACS). (n.d.). Retrieved June 7, 2019, from http://www.nasonline.org/publications/Transparency_Author_Contributions.html
• Vasilevsky, N. A., Hosseini, M., Teplitzky, S., Ilik, V., Mohammadi, E., Schneider, J., Kern, B., Colomb, J., Edmunds, S. C., Gutzman, K., Himmelstein, D. S., White, M., Smith, B., O’Keefe, L., Haendel, M., & Holmes, K. L. (2020). Is authorship sufficient for today’s collaborative research? A call for contributor roles. Accountability in Research, 1–21. https://doi.org/10.1080/08989621.2020.1779591
• Papers on why contributions/credit matters to early career researchers?
• Lieden University announcement about reevaluating academic recognition
• Robinson-Garcia, N., Costas, R., Sugimoto, C. R., Larivière, V., & Nane, G. F. (2020). Meta-Research: Task specialization across research careers. ELife, 9, e60586. https://doi.org/10.7554/eLife.60586
• Saia, S.M., Suttles, K.M., Cutts, B.B. et al. Applying Climate Change Risk Management Tools to Integrate Streamflow Projections and Social Vulnerability. Ecosystems 23, 67–83 (2020). https://doi.org/10.1007/s10021-019-00387-5
• Contributorship methodology for Immersive Scholar
• Special Issue of Digital Humanities Quarterly on Invisible Labor
• Zuberi, T., & Bonilla-Silva, E. (2008). White logic, white methods: Racism and methodology. Lanham: Rowman & Littlefield Publishers. http://www.worldcat.org/oclc/181910126
• Zuberi, T. (2001). Thicker than blood: How racial statistics lie. Minneapolis: University of Minnesota Press. http://www.worldcat.org/oclc/1175643815

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Diversity, Documentation, and Darjeeling

Accessible open knowledge and open science for all

Introductions

Micah and Sheila (she/her) introduce themselves!

With special guest, Dr. Y. Douglas Rao.

Tea Talk

1. What's your take on Darjeeling in the tea-sphere?
2. Do you think of Wes Anderson while drinking darjeeling? (Bonus: What's your favorite Wes Anderson film?)
3. This is our last week! :/ Any other tea types you recommend?
4. Why reproducibili-tea?

Discusion Questions:

1. What is it like to be a scientist doing open science?
2. What are some potential barriers to doing/reproducing open science?
3. What are some common questions the library gets about doing open science?
4. What role do relationships play when doing open science? (not a one way street)
5. What is FAIR (Findable, Accessible, Interoperable, Reproducible) and CARE (Collective Benefit, Authority to Control, Responsibility, Ethics)? Why are they important?
6. How do we make open science training open and more inclusive?
7. How can we make documentation accessible to non-English speakers and folks that use assistive technologies?

Resources & Examples to Share:

• What is Darjeeling Tea on The Spruce Eats blog
• Protected Origin Status for Darjeeling Tea
• The Darjeeling Distinction : Labor and Justice on Fair-Trade Tea Plantations in India by Sarah Besky https://hdl.handle.net/2027/heb.33049
• People First Tourism Lab
• Knowledge Equity Lab
• Chan, Leslie, Hall, Budd, Piron, Florence, Tandon, Rajesh, & Williams, Wanósts'a7 Lorna. (2020, July 15). Open Science Beyond Open Access: For and with communities, A step towards the decolonization of knowledge (Version 1). Zenodo. http://doi.org/10.5281/zenodo.3946773
• OpenCider Open Computational Inclusion & Digital resources
• Medium article on writing Alt Text for data visualizations
• WEBAIM resources for accessible websites
• Equity in Author Order: A Feminist Laboratory Approach by M. Liboiron et al. (2017) --> also related to last week's discussion on contributions
• Ten simple rules for making training materials FAIR by Garcia et al. (2020)
• The CARE Principles for Indigenous Data Governance by Russo Carroll et al. (2020) - "The ‘CARE Principles for Indigenous Data Governance’ (Collective Benefit, Authority to Control, Responsibility, and Ethics) (RDA IG 2019) empower Indigenous Peoples by shifting the focus from regulated consultation to value-based relationships that position data approaches within Indigenous cultures and knowledge systems to the benefit of Indigenous Peoples (Castellano 2004; Anderson et al. 2003). This shift ultimately promotes equitable participation in processes of data reuse, which will result in more equitable outcomes."
• OpenScapes website for open science training materials
• 10-week plan for open science by Lowndes et al., (2017) - This is a great cirriculumn for lab groups!
• Example of open, accessible, but un-usable data...made usable, talk by Shelmith Kariuki