“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 Open notebook science makes the research process transparent and provides unsuccessful, not very significant, or unpublished outcomes (sometimes called “dark data”) to anyone interested (Goetz 2007).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 Negative data from unpublished research might additionally provide important insights (Mlinarić et al. 2017; Nimpf and Keays 2020).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/

Tullney, M. (2021). TIB becomes Major Development Partner of the Public Knowledge Project (PKP). https://blogs.tib.eu/wp/tib/2021/02/16/tib-and-pkp/

[W]e must be especially sensitive to the ways in which open science policies may actually worsen existing inequalities, and make efforts to mitigate these effects.

Read more:

Ross-Hellauer, T., Fessl, A., & Klebel, T. (29 December 2020). Can We Have Open Science Where No Scholar Is Left Behind? Social Science Space. https://www.socialsciencespace.com/2020/12/can-we-have-open-science-where-no-scholar-is-left-behind/

I propose that all journals should, in principle, try their best to have authors and institutions make their raw data open in a public database or on a journal web site upon the publication of the paper, in order to increase the reproducibility of published results and to strengthen public trust in science. Currently, the data sharing policy of Molecular Brain only ‘encourages’ all datasets on which the conclusions of the manuscript rely to be either deposited in publicly available repositories (where available and appropriate) or presented in the main paper or additional supporting files, in machine-readable format (such as spread sheets rather than PDFs) whenever possible. Building on our existing policy, we will require, in principle, deposition of the datasets on which the conclusions of the manuscript rely from 1 March 2020. Such datasets include quantified numerical values used for statistical analyses and graphs, images of tissue staining, and uncropped images of all blot and gel results.

In my own recent experience with journal editing, I can say that having the ability to access underlying data for any study would provide me with more confidence when considering the results discussed in a paper, regardless of discipline.

Miyakawa does recognize the need for more robust data infrastructures for supporting raw data provision by authors and calls for better infrastructures for this:

…institutions, funding agencies, and publishers should cooperate and try to support such a move by establishing data storage infrastructure to enable the securing and sharing of raw data, based on the understanding that ‘no raw data, no science.’

Read more:

Miyakawa, T. No raw data, no science: another possible source of the reproducibility crisis. Mol Brain 13, 24 (2020). https://doi.org/10.1186/s13041-020-0552-2

1. Co-editor for Evidence Summaries at Evidence Based Library and Information Practice, a fully open journal hosted by the University of Alberta (Canada)
2. Engaged in the IFLA Document Delivery and Resource Sharing (DDRS) committee and the organization of the 16th ILDS conference, which takes place every two years. As part of this involvement, program subcommittee members (including myself and NTK’s Sasha Skenderija) created a “light” peer review process for conference papers and decided to publish our conference proceedings openly as an eBook using the existing NTK infrastructure, including a pre-existing repository and creation of an official cataloging record to improve access to the document.

While at times daunting (finding EBLIP peer reviewers during the summer at times seemed like climbing Mount Everest! And who knew some Czech ISBN rules date back to the mid-90s!), both experiences have left me with a clear understanding of what fully moving to an open access environment can mean, when members of various academic communities take it seriously. It all boils down to a community’s rolling up its sleeves and being serious about defining and implementing what scholarly communications/output mean to that particular community plus utilizing (and pushing to expand and improve) existing technological infrastructures.

When this work is done, everyone involved in the process learns: the educational benefits of really engaging in working behind-the-scenes on an open access journal or eBook (in any role: author, publisher, peer reviewer, copy editor, editor) are tremendous, and anyone with an Internet connection interested in the community’s outputs (note: there are still serious Digital Divide hurdles to be solved in this regard) can engage in discussion about the published output.

Stepping back: defining (seriously) what scholarly communications means to a community

I can understand why metrics defining what is considered to be “scholarly output” were developed (funders—including universities and not just grant funding agencies—must have fair and transparent guidelines for academic promotion and distribution of limited grant funding), but I know I’m not alone in feeling that such standards can be misinterpreted, can be overly inflexible, and can be “gamed” by certain players. In the end, each academic community defines its rules.

In terms of contributing to open access movements, it’s up to each academic community to do its soul-searching. Do we want everyone in the world to be able to access our efforts? Why do our journals charge article processing charges (APCs), if they charge them? Are the APCs fair? Will reducing APCs impact quality (or not)? If there’s money involved, where does all the money go?

If it’s hard for your community to answer such questions, it’s maybe time for the community to ask itself why.

Taking advantage of (and pushing to expand and improve) existing technological infrastructures

In thinking about APCs, if a community decides to handle behind-the-scenes work with volunteers (“paid” by learning to be better writers, reviewers, and editors; by gaining academic service activities to put on CVs and to talk about in annual reviews; fame and glory [j/k]), the only “cost” to providing open journal access is the technological infrastructure. EBLIP works with the Open Journal Systems (OJS), a Public Knowledge project, hosted by University of Alberta Libraries; for the ILDS eBook, we used a pre-existing library repository.

Many of these kinds of individual initiatives, at individual institutions or libraries, have sprung up over the past decade. They’re there for members of academic communities to take advantage of, but are often forgotten and/or limited to members of an individual institution. Sometimes, maybe too often, commercial solutions are more user friendly and have broader reach. If we’re serious about open access—and long-term access to information we can trust—maybe it’s time researchers and libraries start asking themselves better questions about solutions which already exist. Why does “Commercial Solution X” work better than our repositories? Are we fast enough to deliver new solutions that can compete with commercial ones? If we’re too slow, why is this the case? How can we do better?

Then there are the even bigger questions: What can we do to change the common issues we face—not just at our institution, but across our global academic community as a whole? How can we share resources to make our efforts accessible to all? How can we serve a greater good better? 

Such questions are easy to lose sight of in the day-to-day sea of academic activities. I’d argue it’s maybe time to stop getting jostled by the waves and to put our hands on the rudder.

This is a story about more than subscription fees. It’s about how a private industry has come to dominate the institutions of science, and how librarians, academics, and even pirates are trying to regain control.

Full story:

Resnick, B. & Belluz, J. (2019). “The war to free science: How librarians, pirates, and funders are liberating the world’s academic research from paywalls.” Vox. Retrieved from https://www.vox.com/the-highlight/2019/6/3/18271538/open-access-elsevier-california-sci-hub-academic-paywalls

There will be a shakedown in the business. Some journals will lose out. Publishing is not a static business — the advent of the preprint server has really changed things, for example. Journals are going to change, and Plan S could have a strong influence.

Else, H. (22 Feburary 2019). Open-access pioneer Randy Schekman on Plan S and disrupting scientific publishing, Nature News Q&A. Available at:  https://www.nature.com/articles/d41586-019-00595-y?utm_source=twt_nnc&utm_medium=social&utm_campaign=naturenews&sf208184622=1

There is enthusiasm and support for the overall goals of Plan S; however, there is also a great deal of concern about the implementation guidance and the very real possibility of negative unintended effects.

Hinchliffe, L. J. (2019). “Taking Stock of the Feedback on Plan S Implementation Guidance,” The Scholarly Kitchen. https://scholarlykitchen.sspnet.org/2019/02/11/with-thousand-of-pages-of-feedback-on-the-plans-s-implementation-guidance-what-themes-emerged-that-might-guide-next-steps/

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.