“Open notebook” science is a practice in which research scientists record their work online and make it publicly available while conducting research in near-real time. Such research is thus completely open to the public and includes all its aspects such as raw data and any associated material. The approach was described by Bradley (2007), the first to use the term, as “no insider information”. Open notebook science makes the research process transparent and provides unsuccessful, not very significant, or unpublished outcomes (sometimes called “dark data”) to anyone interested (Goetz 2007).

Let’s take a look at the primary advantages of this practice, according to the literature. According to Schapira, Harding and Consortium (2019, p. 3), open lab notebooks can save time, resources, and knowledge. Making the information accessible quickly means that other researchers will be able to build upon the open results, making it possible for others to avoid spending time and resources on redundant experiments (Powell 2016). Open lab notebooks should include detailed protocols to achieve experimental replicability. The necessity of more transparent, replicable experiments has been discussed recently (for example, by Nature 2016 and Wallach et al. 2018). Negative data from unpublished research might additionally provide important insights (Mlinarić et al. 2017; Nimpf and Keays 2020). Open lab notebooks can also give experts a space for discussion, to (for example) spot discrepancies in an experiment and so on.

Early career researchers can use their notebooks to connect with peers and experts in the field. One can also add a link to one’s research notebook in an academic CV when applying to a position in order to showcase technical skills (Schapira, Harding and Consortium 2019).

Possible drawbacks of open notebooks (Harding and Consortium 2019, Sanderson 2008, Schapira 2018, Zirnask 2014):

• Possible data theft (being “scooped”): Risk can be mitigated by using repositories such as Zenodo, which assign a citable DOI (or other citable record) to a notebook.
• Difficulty publishing open notebook results in traditional peer-reviewed journals.
• Influencing other research projects before the research documented in the open notebook is complete and/or well-analysed (this is why there are experimental collaborations without open notebook use with strict rules to avoid data leakage and issues with influencing results).
• “Data deluge”: flooding the information space with a large amount of non-peer-reviewed material.
• Can be difficult without a smooth process: maintaining an open notebook should be executed effectively to avoid wasting too much time (as with a regular lab notebook).

What are the necessary characteristics of open notebooks? Harding (2019, p. 2) notes she designed her notebook “to be discoverable, accessible, clear, and detailed in its presentation, and to permit dialogue between readers and me, and to pave the way for collaborations.”

Examples of platforms for open notebooks:

Picking the right open notebook platform can be daunting. Every scientific field has a different environment with different data collection requirements and different data types (e.g., code, images, equations, value). Several open notebook options are listed below; you may wish to ask your mentor if they have a preference for a particular tool. One could additionally create a blog for an open notebook.

• https://openlabnotebooks.org/

To create an open notebook, contact the coordinator. Data are uploaded and stored on zenodo.org (maintained by CERN as a part of the OpenAIRE initiative). You can also link zenodo files to your ORCID profile.

• https://github.com/

Used by many open sourced software developers, among others. A code repository that allows parallel code editing.

• https://openwetware.org/

Join via a web form. Designated for biology and biological engineering.

• https://jupyter.org/

Free software, open standards, and web services for interactive computing across all programming languages.

Various interfaces (lab book, notebook, hub, Voilá) for sharing outputs.

Use https://nbviewer.org/ to make a jupyter notebook publicly shareable.

• https://open-neuroscience.com/

Open database for neuroscience projects.

If your research, for any reason, cannot be made public, another option for organisation and cooperating/sharing with other researchers or within teams, or managing protocols is the use of electronic laboratory notebooks. There are many options to choose from such as: https://rmarkdown.rstudio.com/, https://www.labarchives.com/, https://www.benchling.com/, and https://www.elabftw.net/ (among others).

Openly published protocols: If you do not wish to share your process but would like to publish and share a protocol which you have designed, a tool like https://www.protocols.io can be considered. After publishing a protocol on protocols.io you obtain a digital object identifier (DOI). A DOI can be used in a manuscript so that it can, if the article is approved for publication in a scientific journal, be published (automatically, if a DOI is used upon article submission) at a later date.

Resources:

Bradley, Jean-Claude. (2007). Open notebook science using blogs and wikis. Nature Precedings. https://doi.org/10.1038/npre.2007.39.1

Goetz, Thomas. (2007). Freeing the dark data of failed scientific experiments. Wired, 15(10). Available from: https://www.wired.com/2007/09/st-essay-3/ 

Harding, Rachel J. (2019) Open notebook science can maximize impact for rare disease projects. PLoS Biol, 17(1). https://doi.org/10.1371/journal.pbio.3000120

Mliarić, Ana, Horvat, Martina. & Šupak Smolčić, Vesna. (2017). Dealing with the positive publication bias: Why you should really publish your negative results. Biochem Med, 27(3). https://doi.org/10.11613/BM.2017.030201

Nature. (2016). Reality check on reproducibility. Nature, 533(7604), 437-437. https://doi.org/10.1038/533437a

Nimpf, Simon & Keays David A. (2020). Why (and how) we should publish negative data. EMBO Rep., 21(1). https://doi.org/10.15252/embr.201949775

Powell, Kendall. (2016). Does it take too long to publish research? Nature, 530, 148-151. https://doi.org/10.1038/530148a

Sanderson, Katherine. (2008). Data on display. Nature, 455(18), 273. https://doi.org/10.1038/455273a

Schapira, Matthieu. (2018). Open lab notebooks to increase impact and accelerate discovery . Springer Nature. Available at: https://researchdata.springernature.com/posts/29655-open-lab-notebooks-to-increase-impact-and-accelerate-discovery

Schapira, Matthieu & Rachel J Harding. (2019). Open laboratory notebooks: good for science, good for society, good for scientists. F1000Res, 8(87). https://doi.org/10.12688/f1000research.17710.2

Wallach, Joshua D, Boyack, Kevin W. & John P. A. Ioannidis. (2018) Reproducible research practices, transparency, and open access data in the biomedical literature, 2015-2017. PLoS Biology, 16. https://doi.org/10.1371/journal.pbio.2006930

Zirnask, Mart. (2014). Are open notebooks the future of science? UT Blog. Available at: https://blog.ut.ee/are-open-notebooks-the-future-of-science/

Full video of presentation available at:

Krueger, S. (2022). Resource discovery: Use cases in the academic field. https://youtu.be/C1clHHYtPPg

The Office has also made public a recent presentation of the UC strategy to its leadership (link, with video, below).

• University of California Office of Scholarly Communications (2019). Negotiating with scholarly journal publishers: A toolkit from the University of California. Retrieved from https://osc.universityofcalifornia.edu/open-access-at-uc/publisher-negotiations/negotiating-with-scholarly-journal-publishers-a-toolkit/
• Waibel, Günter (2019). Update on open access and academic journal contracts: a presentation to the UC Board of Regents’ Academic and Student Affairs Committee. Retrieved from https://osc.universityofcalifornia.edu/2019/07/update-on-open-access-and-academic-journal-contracts/

…California, through its cancellation, has nevertheless maintained its position unambiguously. It does not need ongoing journal subscriptions through ScienceDirect. Put another way: A major customer’s perceived value in the product offering has declined. Elsevier apparently no longer has the pricing power it once could assert.

Leakage

The source of the value decline is no mystery. Joe Esposito argued more than a year ago that ‘Sci-Hub is an unacknowledged reserve army prepared to enter the battle with publishers,’ noting elsewhere in the piece that time “is not on Elsevier’s side.”

But Sci-Hub is not alone. Sci-Hub is one of a series of services through which content is ‘leaking’ out of publisher sites through to users. While some of these sites are illicit and pirate, others like SSRN and institutional repositories are accepted parts of the ecosystem, and still others are like ResearchGate, whose intentions vary by observer.

Read more at: Schonfeld, R. (2019). Is the Value of the Big Deal in Decline? The Scholarly Kitchen. https://scholarlykitchen.sspnet.org/2019/03/07/value-big-deal-leakage/

• Full press release

John Wiley & Sons, Inc. (NYSE: JW-A and JW – B), a global leader in research and education, announced today a countrywide partnership agreement with Projekt DEAL, a representative of nearly 700 academic institutions in Germany. Under an annual fee, this transformative three-year agreement … [means] researchers at Projekt DEAL institutions can publish articles open access in Wiley’s journals. The partnership will better support institutions and researchers in advancing open science, driving discovery, and developing and disseminating knowledge.

But many of us in the library community worry about the accessibility of such tools to institutions without the funds to purchase them in terms of making more pressure on libraries to provide such services – pressure on institutions which may already be falling behind the wealthy institutions because of budgetary pressures due to subscription journal increases and other factors, expanding the effects of the digital divide. What would stop people in such cases from continuing to use P2P servers to access content their libraries cannot purchase or which are not available via open access? I cannot imagine that, in these cases, such libraries will be able to “disrupt the disrupters,” as promoted in the webinar follow-up email. AA will need critical subscription mass.

It can also mean, for wealthy institutions, that once the “lock” happens, subscription to the tool becomes difficult to discontinue in the future. And if there are only one or two good players in this space (and not a fully competitive marketplace, as currently appears to be the case), this always opens up the door to steep future fee increases and, at some point, threats to a long-term funding model, on the library side. But of course, the end users might not care about such worries. Should they?

It’s not just librarians who are concerned about big mergers and marketplace “consolidation”; smaller academic society publishers, too, are facing similar issues, as seen in an article by Angela Cochran from the American Society of Civil Engineers in The Scholarly Kitchen:

I am concerned about what I will call ‘lock out.’ As some librarians are concerned about their faculty, students, and institutions being ‘locked in’ to one particular publisher’s services, I am concerned about society and small publishers being ‘locked out’ of critical technology services.

She discusses these issues in relation to Wiley and Elsevier:

Many of us on the Atypon platform were varying degrees of concerned about the sale to Wiley. The concerns were entirely about a publisher owning the platform that housed the content of many other publishers. We are faced with the same situation now that Elsevier has bought Aries Systems. A publisher that competes with many of Aries Systems’ customers, now owns the submission and production system used by these publishers.

For some of us, like my organization (American Society of Civil Engineers), it’s a double-whammy. Our platform with all of its content and user data is owned by Wiley. Our submission system with all of our author and editorial data is owned by Elsevier.

Read the full article, “Clowns to the Left of Me…Jokers to the Right,” at: https://scholarlykitchen.sspnet.org/2018/08/06/clowns-left-jokers-right-independent-publisher-age-mergers-acquisitions/

• Press Release

I will have someone on staff attend one of the upcoming webinars about the service and report more here in the coming weeks.

It has become increasingly clear that the problem of rising journal costs in the context of a widespread movement toward open access can only be addressed by tackling the subscription system itself.

Read more:

Championing Change in Journal Negotiations