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OSC10- Introductory Webinar


- Identify Open Science principles and practices.

- Recognize how Open Science is relevant to my practice as a budding reseacher.
- Prepare an Open Science strategy for my PhD research.

What is Open Science?

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Learning objectives

Why did we open science?

How to open (my) science?

- Rationale and Principles of Open Science.

- Open Science: a large taxonomy of scientific activities.
- Open science benefits: from my research to society.

1. What is Open Science?

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Rationale and Principles of Open Science

"Open Science is the practice of science in such a way that others can collaborate and contribute, where research data, lab notes and other research processes are freely available, under terms that enable reuse, redistribution and reproduction of the research and its underlying data and methods."

https://www.fosteropenscience.eu/foster-taxonomy/open-science-definition

What is Open Science?

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https://www.enseignementsup-recherche.gouv.fr/sites/default/files/2021-10/2e-plan-national-pour-la-science-ouverte-version-anglaise--13715.pdf

Rationale and Principles of Open Science

What is Open Science?

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http://book.openingscience.org.s3-website-eu-west-1.amazonaws.com/basics_background/open_science_one_term_five_schools_of_thought.html

A recent update (and interview of Benedikt Fecher) on the five schools of open science:

https://www.cienciadainformacaoexpress.com/post/the-five-schools-or-currents-of-thought-in-open-science-an-interview-with-benedikt-fecher

Rationale and Principles of Open Science

What is Open Science?

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https://www.fosteropenscience.eu/themes/fosterstrap/images/taxonomies/os_taxonomy.png

A large taxonomy of research activities

What is Open Science?

https://www.swissbiotech.org/listing/open-up-science/

What is Open Science?

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A large taxonomy of research activities

https://think.f1000research.com/open-research-europe-submission/open-research-europe/?utm_source=third_party_list&utm_medium=email&utm_campaign=JQC19396

Benefits for my research and society.

What is Open Science?

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https://www.unesco.org/en/natural-sciences/open-science

- A worldwide movement for knowledge dissemination.

What is Open Science?

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- A plethora of activities in many domains, from publishing to software development through citizen science.

- A beneficial scientific practice for me as a young researcher and for society.

- The serial crisis and the academic publishing ecosystem.

- Reproductibility crisis and integrity concerns.
- Public research funders requirements towards Open Science.

2. Why did we open science?

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Why open science?

The serial crisis and the academic publishing ecosystem

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Academic publishing: a unique market

Adapted from: https://scienceouverte.couperin.org/la-publication-scientifique-aujourdhui/

Why open science?

The serial crisis and the academic publishing ecosystem

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Another way of putting it

When trying to read an article on Nature...

netflix.com

Why open science?

The serial crisis and the academic publishing ecosystem

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https://www.nytimes.com/1998/12/08/health/soaring-prices-spur-a-revolt-in-scientific-publishing.html

Why open science?

The serial crisis and the academic publishing ecosystem

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A very, very, very profitable market

- The arrival of digital technology has coincided with a consolidation of the academic publishing market around a few powerful actors.


- Publishers' rationale for increasing subscription prices: the digital era does not reduce costs but increases them: new expenses related to technology + increased volume of publications.

- Inlastic demand
- Very uncompetitive market
- Bundling practices in the 90s
->>> oligopoly situation, prices explosion and a very clear increase in publishers' revenues.

Why open science?

The serial crisis and the academic publishing ecosystem

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The "Big 5" oligopoly of academic publishing

Mongeon, P. (2015). Big Publishers, Bigger Profits: How the Scholarly Community Lost the Control of its Journals. MediaTropes, 5, 102-110.

© European University Association

Why open science?

The serial crisis and the academic publishing ecosystem

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Elsevier, the market giant (for better or worse)

Why open science?

The serial crisis and the academic publishing ecosystem

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Elsevier, the market giant (for better or worse)

http://bjoern.brembs.net/2019/12/elsevier-now-officially-a-predatory-publisher/

http://www.e-learn.nl/2015/07/06/dutch-boycott-of-elsevier

https://bluesyemre.com/2018/11/15/elsevier-1880-vs-elsevier-2018/

https://medium.com/@jasonschmitt/can-t-disrupt-this-elsevier-and-the-25-2-billion-dollar-a-year-academic-publishing-business-aa3b9618d40a

Why open science?

The serial crisis and the academic publishing ecosystem

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2012: the breakup year?

http://thecostofknowledge.com/

https://fr.wikipedia.org/wiki/The_Cost_of_Knowledge

Why open science?

The serial crisis and the academic publishing ecosystem

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2012: the breakup year?

September 5, 2011: Sci-hub was launched by Alexandra Elbakyan

2011-2012: United States v. Aaron Swartz

Why open science?

The serial crisis and the academic publishing ecosystem

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Open Access: a digital-era movement

1991 : arXiv (repository for mathematics and physics)

1996 : PubMed (medical sciences search engine)

2000 : Pubmed Central (repository for medical and life sciences)

2006: PLoS ONE (first peer-review open access megajournal)

In the United States:

And in France:

2001 : HAL (open archive for all disciplines)

1999 : Revues.org, now OpenEdition Journals (online open access journal portal)


Why open science?

The serial crisis and the academic publishing ecosystem

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From a "reader-pays" to an "author-pays" model of academic publishing

Diamond Open Access: Gold Open Access without charging APC.

Gold Open Access = all articles and related content are available for free immediately on the journal's website.

- All articles and related contents are availible for free immediately on the journal's website.

- The publisher does not charge authors for publishing fees (APC)

- Publication costs are internalized by not-for-profit, non-commercial organizations, associations, networks or public institutions.

- All articles and related contents are availible for free immediately on the journal's website.

- The publisher does charge authors for publishing fees (APC)

- Publication costs (APC) are paid by the researcher, his/her research institution or his/her research funder.

Majority of for-profit, gold OA journals

Hybrid journals

- Articles and related contents are behind a paywall and only availible through subscription unless an OA option was taken by the author.

- The publisher does charge authors for publishing fees (APC) for the OA option.

- A certain number of institutions/funders are not paying for APCs in hybrid journals (e.g. in France: ANR or ERC)

-70% of journals indexed in DOAJ are diamond OA

Examples:
- PLoS journals
- Scientific Reports

Examples:
- Nature
- Current Biology

Why open science?

The serial crisis and the academic publishing ecosystem

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Data for France, 2020
Source : OpenAPC

The APCs: a new serial crisis?

Why open science?

The serial crisis and the academic publishing ecosystem

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The APCs: a new serial crisis?

https://twitter.com/natureneuro/status/1480909476546891784

Why open science?

The serial crisis and the academic publishing ecosystem

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The APCs: a new serial crisis?

https://mobile.twitter.com/MootazSalman/status/1482291722730319872/photo/1

https://twitter.com/DGlaucomflecken/status/1484679759829209090

Why open science?

The serial crisis and the academic publishing ecosystem

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The APCs: a new serial crisis?

Why open science?

The serial crisis and the academic publishing ecosystem

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https://barometredelascienceouverte.esr.gouv.fr

Why open science?

The serial crisis and the academic publishing ecosystem

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A new actor in the publishing field: predatory journals

Par ManuRoquette — Travail personnel, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=83306493

Maybe you have received emails like this...

Why open science?

The serial crisis and the academic publishing ecosystem

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It is not just journals: predatory conferences exist as well.


https://medium.com/@westwise/ive-been-invited-to-a-super-predatory-conference-and-i-have-to-share-371ae7db6a72

https://medium.com/gradbunker/how-to-identify-predatory-conferences-688f1d4c4d82

Why open science?

The serial crisis and the academic publishing ecosystem

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How to know if a journal is predatory?

Why open science?

Reproductibility crisis and integrity concerns

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From Baker, M. Over half of psychology studies fail reproducibility test. Nature (2015). https://doi.org/10.1038/nature.2015.18248

https://slideplayer.com/slide/11234638/

Why open science?

Reproductibility crisis and integrity concerns

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https://www.cos.io/rpcb

Why open science?

Reproductibility crisis and integrity concerns

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A few possible explanations:

- Positive publication biais (i.e. tendancy of scientific journals to only publish statistically significant results), not encouraging researchers to share negative, non replicative results.

- Questionable research practices, espacially data snooping, even fraud.

- Inability to properly reproduce research artifacts (e.g. method, stimuli).

What may be the cause for the "Replication Crisis"?

https://www.nature.com/articles/533452a

Why open science?

Reproductibility crisis and integrity concerns

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If for any given experiment the rationale, datasets and methods are freely availible, then the robustness of scientific results could be constantly reassessed.

Researchers could then:

- attempt to replicate the original experiment, i.e. rerun the original method and compare obtained data with the original experiment's.

- attempt to re-analyse the original data, i.e. re-run the statistical tests described by the original method, and compare obtained results with the original experiment's

- avoid "wasting" time on further exploring a counter-intuitive result which looked promising but actually resulted from statistical chance or a poorly designed procedure.

- indentify scientific misconduct or even fraud by exposing statistical inconsistencies in datasets and inferences.





How can Open Science help with the Replication Crisis?

Why open science?

Reproductibility crisis and integrity concerns

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Why open science?

Reproductibility crisis and integrity concerns

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Corbyn, Z. Misconduct is the main cause of life-sciences retractions. Nature 490, 21 (2012).
https://doi.org/10.1038/490021a

Why open science?

Reproductibility crisis and integrity concerns

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source: Retraction Watch

- Former professor of social psychology at Tilburg University

- As of 2019, Stapel has had 58 of his publications retracted (#7 most retracted scientist of all time in the Retraction Watch Leaderboard).

- Among these 58 retractions: a 2011 Science paper.

- Cited 5892 times according to Semantic Scholar.

https://www.nytimes.com/2013/04/28/magazine/diederik-stapels-audacious-academic-fraud.html

Diedrik Stapel, the psychology biggest con man.

Why open science?

Reproductibility crisis and integrity concerns

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"I became increasingly cavalier and careless. I was tired of sitting at the dining table for long evenings on end, typing data into the computer. I made spreadsheet after spreadsheet to present my research ideas to the world as clearly as possible, and I made spreadsheet after spreadsheet with the data for the studies that I did with my colleagues and students. I was in a hurry, and in my haste I made mistakes. I copied rows of data from one study to another, which meant that the second dataset looked suspiciously like the first."

-Diedrick Stapel (2014) Faking Science: A True Story of Academic Fraud (trad. Nicholas J. L. Brown)

source: Retraction Watch


- Levelt Committee, Noort Committee, Drenth Committee (2012)
Flawed science:The fraudulent research practices of socialpsychologist Diederik Stapel

Why open science?

Reproductibility crisis and integrity concerns

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https://www.japantimes.co.jp/news/2021/03/20/world/science-health-world/pfizer-employee-anti-vaxxer-covid/

https://www.foxnews.com/health/fox-news-poll-coronavirus-vaccine-concerns

https://santecool.net/anti-vax-anti-5g-meme-combat/

Why open science?

Reproductibility crisis and integrity concerns

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Why open science?

Public research funders requirements towards Open Science.

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2014-2020

- Open Access mandatory for all publications
- Mandatory deposit into a repository
- Data Management Plan mandatory by 2017 (for certain projects)
- Open access publication fees are reimbursable

2021-2027

- Open Access mandatory for all publications
- Research data to be FAIR and open by default
- DMP mandatory
- Digital or physical access to the results needed to validate the conclusions of scientific publications
- In cases of public emergency, immediate open access to all research outputs, if requested by the granting authority
- Publication fees reimbursable only if publishing venue offers full open access (publication fees in hybrids not reimbursed)

https://ec.europa.eu/info/research-and-innovation/strategy/strategy-2020-2024/our-digital-future/open-science_en#future-of-open-science-under-horizon-europe

Why open science?

Public research funders requirements towards Open Science.

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The coordinator and partners of projects funded by the ANR from 2022 commit to:

1. Make available all scientific publications resulting from ANR projects in open access under the Creative Commons Licence (CC-BY) or equivalent via one of the following routes:
- Publication in a natively Open Access journal
- Publication in a subscription journal that is part of a transformative agreement or in a transformative journal
- Publication in a subscription journal using the Right Retention Strategy (RRS), in accordance with the procedures indicated in the grant agreement

2. Submitting, at the time of publication at the latest, the full text of the scientific publications (version Author Accepted Manuscript or Version of Record) in the national open archive HAL, and mention the ANR research project reference.


3. All projects funded in 2019 onwards are required to produce a Data Management Plan (DMP)

https://anr.fr/en/anrs-role-in-research/commitments/open-science/

Why open science?

Public research funders requirements towards Open Science.

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"4. All productions cited in the evaluation files must be accessible in HAL or possibly in another open archive: these are understood to be the actual outputs themselves and not their bibliographic reference. It should not be necessary to provide them in the file, as an active link to the archive may be sufficient."

https://www.science-ouverte.cnrs.fr/

Why did we open science?

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Science opened...

- To provide another way to insure scientific integrity and accountability in our research practices.

- To make accessible to the taxpayer publicly-funded research

- As a reaction to ever increasing journal subscription prices in the traditional publishing industry.

- Opening my methods and data.

- Opening my publications.
- Opening my tools.

3. How to open (my) science?

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How to open (my) science?

By taking the UPC library Open Science trainings !

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How to open (my) science?

By taking the UPC library Open Science trainings !

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How to open (my) science?

By taking the UPC library Open Science trainings !

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How to open (my) science?

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Why?
Why do I want to open my research? (to fulfill my obligations towards my research funders, to create easily reusable content, to reach a large audience...)

What?
What type of content am I going to produce during my PhD? (research articles, books, meta-analyses, code, softwares, coference posters, blog posts...)


When?
When do I plan to share/open my research? As soon as possible? Before/after the peer-review process?

How?
What tools will I use to do this sharing? Peer-review, multilingual abstracts, Creative Commons licenses...

Where?
Which platform will host my research? Open Access academic publishers without APC? Open access books? My own website? Open archives for code/data repository...

Identify ressources associated with each step of your Open Science strategy

Defining my Open Science strategy

How to open (my) science?

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Opening my methods and data

"Preregistration is the process of specifying key study and analysis details and decisions before conducting the experiment. The main goal of preregistering one’s research is to make it easier for readers (and yourself) to distinguish between what the you set out to do (confirmation) and what was discovered along the way (exploration). Both are vital to science, but conflating these two types of work can lead to misinterpretation of the context of any claim. Preregistration prevents us from tricking ourselves and allows the argument to have meaning."

Preregistration: A Plan, Not a Prison
Alexander DeHaven

https://www.cos.io/blog/preregistration-plan-not-prison

Pre-register your study...

How to open (my) science?

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Opening my methods and data

"Registered Reports is a publishing format that emphasizes the importance of the research question and the quality of methodology by conducting peer review prior to data collection. High quality protocols are then provisionally accepted for publication if the authors follow through with the registered methodology."

https://www.cos.io/initiatives/registered-reports

...or even publish it as registered report

How to open (my) science?

Opening my methods and data

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"Entities become data only when someone uses them as evi- dence of a phenomenon, and the same entities can be evidence of multiple phenomena. Photographs in an old family album or high school yearbook may become data when a researcher uses them as evidence for hair and clothing styles of a period. Another researcher may use them as evidence of family groupings or social identity. Weather records in old ship logs, gathered for business and navigation purposes, now are used as data to study climate change. Patent records may be a source of evidence for when and where some found object may have been manufactured."

How to open (my) science?

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https://researchdata.springernature.com/documents/web_a92645_what-are-research-data-revision

Data can be :


- collected (e.g. archives)
- produced (e.g. observations, measures)

Opening my methods and data

What is a data?

How to open (my) science?

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https://www.ouvrirlascience.fr/wp-content/uploads/2021/10/SO_21-10-14-WEB-EN.pdf

Opening my methods and data

Learn about the data life cycle

How to open (my) science?

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Make your data FAIR!

Opening my methods and data

https://open-science-training-handbook.github.io/Open-Science-Training-Handbook_EN//02OpenScienceBasics/

How to open (my) science?

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Opening my methods and data

https://dmp.opidor.fr/

Manage your data! Learn how to write a DMP

How to open (my) science?

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Manage your data! Learn how to write a DMP

Opening my methods and data

https://dmp.opidor.fr/

How to open (my) science?

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Opening my publications

Diamond Open Access: Gold Open Access without charging APC.

- All articles and related contents are availible for free immediately on the journal's website.

- The publisher does not charge authors for publishing fees (APC)

- Publication costs are internalized by not-for-profit, non-commercial organizations, associations, networks or public institutions.

- All articles and related contents are availible for free immediately on the journal's website.

- The publisher does charge authors for publishing fees (APC)

- Publication costs (APC) are paid by the researcher, his/her research institution or his/her research funder.

Majority of for-profit, gold OA journals

Hybrid journals

- Articles and related contents are behind a paywall and only availible through subscription unless an OA option was taken by the author.

- The publisher does charge authors for publishing fees (APC) for the OA option.

- A certain number of institutions/funders are not paying for APCs in hybrid journals (e.g. in France: ANR or ERC)

Find your way through the Open Access publishing ecosystem

How to open (my) science?

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Take advantage of the Digital Republic bill (Loi pour une République Numérique)

Opening my publications

Article 30

Research publications funded at least 50% by public funds and appearing in serials with at least an issue a year can be made available free of charge after an embargo period.

The right of the authors is non-waivable, so any contractual provision to the contrary is superseded irrespective of academic publishers' policies.

https://en.wikipedia.org/wiki/Loi_pour_une_R%C3%A9publique_num%C3%A9rique
https://www.legifrance.gouv.fr/jorf/id/JORFTEXT000033202746/

Self-archiving (of the manuscript approved for publication) is then possible for all authors after 6 or 12 months from the publication.

How to open (my) science?

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Opening my publications

Use digital repositories (HAL, or another one) to disseminate your research

How to open (my) science?

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https://101innovations.wordpress.com/workflows/

Opening my tools

Use non-proprietary software to ensure replicability and interoperability

How to open (my) science?

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Opening my tools

How to open (my) science?

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- by learning all about the various dimensions of Open Science :)
- by making my research process transparent from the very beginning - if possible.
- by sharing my data and methods to make my research reproductible.
- by learning my rights regarding publication and using them to disseminate my articles.
- by using open-source software to produce my research - if possible.

Thank you for your attention :)
Don't forget to sign the attendance Framaform!

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Contact: margaux.larre-perez@u-paris.fr