TITLE: The Selfish Reasons for Practicing Open Research
AUTHORS: Lenny  Teytelman

[DESCRIPTION]
Champions and practitioners of open research and FAIR data practices are realizing significant benefits to their research along with the impactful bonus of making the whole research enterprise better for everyone. In addition to the ethical and moral reasons for adopting these best practices, data and results show that scientists who work in an open science framework will have increased productivity, more credit and recognition and longer scientific longevity to their work.

This is based on my talk at the Singapore Open Research Conference, hosted by Nanyang Technological University. The Google slides from the talk are here, in addition to the steps below.

Please feel free to use and adapt! It's all about promoting openness and reuse!

If you and extend/edit this or have suggestions, please do share the ideas or link to your versions in comments here. Also, you can "fork" this entire document, and build on it, then publishing back into this same workspace.


(Image: UNESCO Recommendation on Open Science, CC BY-SA 3.0 IGO)

[STEPS]
SECTION: Introduction
1. Cancer Bio Reproducibility Project

As part of the background on why we created protocols.io, we like to talk about the Cancer Biology Reproducibility Project, which was a $1.5 million dollar initiative coordinated by the Center for Open Science and by Science Exchange with the goal of trying to independently replicate almost 200 experiments from about 50 high-profile papers on cancer biology.

 



SECTION: Introduction
2. Open Research sharing takes time

As much as open research is a public good, the truth is that sharing methods, data, code, and so on takes an effort. And time is one resource that all researchers lack. This is why it's important to highlight the many benefits of open science that apply directly to the research authors.

 Figure from: LaFlamme, M., Harney, J., & Hrynaszkiewicz, I. (2022, October 14). A survey of researchers' methods sharing practices and priorities. https://doi.org/10.31222/osf.io/7jxav

"It takes too long to prepare detailed methods information in a way that would be useful for others."
SECTION: Preprints
3. ASAPbio is a nonprofit promoting preprints. This superb graphic from them nicely captures the many helpful aspects of preprints (link).

 
SECTION: Preprints
4. 
 

SECTION: Preprints
5. Preprints boost article citations and mentions.

Nature Index Link

Darwin Y Fu, Jacob J Hughey (2019) Meta-Research: Releasing a preprint is associated with more attention and citations for the peer-reviewed article eLife 8:e52646

Nicholas Fraser, Fakhri Momeni, Philipp Mayr, Isabella Peters; The relationship between bioRxiv preprints, citations and altmetrics. Quantitative Science Studies 2020; 1 (2): 618–638.

 

SECTION: Reagent Repositories
6. “Repositories like the ones recommended by PLOS handle the logistics of material requests, letting the scientists focus on what’s important: doing research.”

“Saves authors the time and burden of shipping requested materials.”

https://theplosblog.plos.org/2019/05/depositing-and-reporting-of-reagents-accelerating-open-and-reproducible-science/

SECTION: Reagent Repositories
7.   

SECTION: Reagent Repositories
8. Addgene
ATCC (American Type Culture Collection)
ABRC (Arabidopsis Biological Resource Center)
Bloomington Drosophila Stock Center
Caenorhabditis Genetics Center
DSMZ
European Conditional Mouse Mutagenesis Program
European Mouse Mutant Archive
Knockout Mouse Project
Jackson Laboratory
Mutant Mouse Regional Resource Centers
PlasmID
RIKEN Bioresource Centre
Developmental Studies Hybridoma Bank
EUROSCARF (S.Cerevisiae)
National Xenopus Resource
ZIRC (Zebrafish International Resource Center)
SECTION: Reagent Repositories
9. (From Addgene, https://www.addgene.org/deposit/benefits/)
 

SECTION: Data
10. As with preprinting, sharing data seems to increase citations of a given research article.

“We also find an association between articles that include statements that link to data in a repository and up to 25.36% (± 1.07%) higher citation impact on average, using a citation prediction model. “

Colavizza G, Hrynaszkiewicz I, Staden I, Whitaker K, McGillivray B (2020) The citation advantage of linking publications to research data. PLoS ONE 15(4): e0230416. https://doi.org/10.1371/journal.pone.0230416

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“In a multivariate regression on 10,555 studies that created gene expression microarray data, we found that studies that made data available in a public repository received 9% (95% confidence interval: 5% to 13%) more citations than similar studies for which the data was not made available.”

Piwowar HA, Vision TJ. 2013. Data reuse and the open data citation advantage. PeerJ 1:e175 https://doi.org/10.7717/peerj.175

SECTION: Data
11. In Sept. 2022, I was asked to share scripts from a 2007 analysis. Good thing I uploaded it to figshare; there’s no way I’d find the laptop from 2007.  No cost, 10 seconds to find with Google.

  

SECTION: Data
12. Repositories

Re3data.org - Re3data is a global registry of research data repositories

General repositories:
Figshare (free up to 20GB total)
Zenodo (free; 50GB per dataset)
OSF from the Center for Open Science (5GB private for free, 50GB for public)

  

SECTION: Preregistration
13.  
SECTION: Preregistration
14.   

SECTION: Preregistration
15.  
SECTION: Methods
16. (You're reading this on protocols.io; of course we are going to mention methods!)

Public sharing on protocols.io is always open access, free to read and publish. 

  
And a huge part of our goal is to increase the credit for and recognition of the work of method development.

SECTION: Methods
17. Your methods on protocols.io are more discoverable. In the example below, if the protocol was shared only as a supplement of the research paper, no way people outside that field would find it.

  

SECTION: Methods
18. Increased Collaborations

 
https://www.protocols.io/researchers/luciano-martelotto/protocols 

SECTION: Methods
19. protocols.io also has a partnership with PLOS ONE, helping to turn protocols into peer-reviewed publications.

  
  

SECTION: Methods
20. Publishing Protocols: Lab Protocols in PLOS ONE 

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SECTION: Acknowledgements
21. More and more funders now require preprints, open data, methods, code. Many mandating immediate Open Access. There is a major shift from governments and funders, and adopting open practices now strengthens your future position. https://en.unesco.org/science-sustainable-future/open-science/recommendation, https://www.nature.com/articles/d41586-022-00402-1

  

SECTION: Importance of an early start
22. For data, methods, code - planning early is key. If you think of sharing them only when submitting a paper, it’s a lot of extra work to share a good dataset at that point. But if you think of a Data Management Plan and make early plans and use tools like protocols.io and GitHub, then sharing the methods and code is super easy at the time of publication.


  

SECTION: Importance of an early start
23.  
SECTION: Acknowledgements
24.