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Open-notebook science is the practice of making the entire primary record of a
research project Research is "creative and systematic work undertaken to increase the stock of knowledge". It involves the collection, organization and analysis of evidence to increase understanding of a topic, characterized by a particular attentiveness t ...
publicly available online as it is recorded. This involves placing the personal, or laboratory, notebook of the researcher online along with all raw and processed data, and any associated material, as this material is generated. The approach may be summed up by the slogan 'no insider information'. It is the logical extreme of
transparent Transparency, transparence or transparent most often refer to: * Transparency (optics), the physical property of allowing the transmission of light through a material They may also refer to: Literal uses * Transparency (photography), a still, ...
approaches to research and explicitly includes the making available of failed, less significant, and otherwise unpublished experiments; so called 'dark data'.Freeing the Dark Data of Failed Scientific Experiments
Goetz, T., Wired Magazine, Sept.25, 2007
The practice of open notebook science, although not the norm in the
academic An academy (Attic Greek: Ἀκαδήμεια; Koine Greek Ἀκαδημία) is an institution of secondary or tertiary higher learning (and generally also research or honorary membership). The name traces back to Plato's school of philosophy, ...
community, has gained significant recent attention in the research and general media as part of a general trend towards more open approaches in research practice and publishing. Open notebook science can therefore be described as part of a wider open science movement that includes the advocacy and adoption of open access publication,
open data Open data is data that is openly accessible, exploitable, editable and shared by anyone for any purpose. Open data is licensed under an open license. The goals of the open data movement are similar to those of other "open(-source)" movement ...
, crowdsourcing data, and citizen science. It is inspired in part by the success of
open-source software Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Op ...
and draws on many of its ideas.


History

The term "open-notebook science" was first used in 2006 in a blog post by Jean-Claude Bradley, an Associate Professor of Chemistry at Drexel University at the time. Bradley described open-notebook science as follows:


Practitioners


Active


Experimental (alphabetical by last name)

* Aled Edwards & colleagues, University of Toronto. * Rachel Harding, post-doctoral fellow with University of Toronto's (SGC) Structural Genomics Consortium. ** blog at http://labscribbles.com/ ** Twitte
@labscribbles
** Zenodo https://zenodo.org/search?f=author&p=Rachel%20Harding&ln=en ''"A team of groundbreaking scientists at SGC are now sharing their lab notebooks online"''. * Nickolas J. LaSorte, Postdoctoral Fellow at the FDA in the area of Wireless Coexistence. * Tamara Maiuri ** blog at https://raytruantlab.wordpress.com/ ** Twitte
@tam_maiuri
** Zenodo https://zenodo.org/search?page=1&size=20&q=maiuri *
Peter Murray-Rust Peter Murray-Rust (born 1941) is a chemist currently working at the University of Cambridge. As well as his work in chemistry, Murray-Rust is also known for his support of open access and open data. Education He was educated at Bootham School ...
, Cambridge, UK. * Anthony Salvagno, Ph.D., Director of Education of #SciFund Challenge. * Matthew H. Todd, Open Source Malaria,
University College London , mottoeng = Let all come who by merit deserve the most reward , established = , type = Public research university , endowment = £143 million (2020) , budget = ...
(Todd Group). * Open Notebook Science Challenge * The Digital Botanical Gardens Initiative (DBGI) observable at http://www.dbgi.org/dendron-dbgi/


Theoretical

* Tobias J. Osborne * Carl Boettiger, Theory and computational modeling in ecology and evolution. * Dror Bar-Natan * Andrés G. Saravia, physics Ph.D. student at Cinvestav-Mérida. * Daniel Himmelstein, who led Project Rephetio — a drug repurposing study that used GitHub and Thinklab for realtime open notebook science and collaboration.


Archived (alphabetical by last name)

* Brigette Black), physics Ph.D. student in Koch lab at the University of New Mexico. * Jean-Claude Bradley * Jeremiah Faith * Nadiezda Fernandez-Oropeza, Biomedical Engineering Ph.D. student in Koch lab at the University of New Mexico. * Mike Lawrence * Linh Le, undergraduate physics major and alumnus of Koch lab at the University of New Mexico. * Andy Maloney, postdoctoral researcher in Smyth lab at University of Texas. Ph.D. in Koch lab at the University of New Mexico (2011) * Cameron Neylon * Alejandro Tamayo * Influenza Origins and Evolution


Recurrent (educational)

* Junior Physics Lab (307L) at
University of New Mexico The University of New Mexico (UNM; es, Universidad de Nuevo México) is a public research university in Albuquerque, New Mexico. Founded in 1889, it is the state's flagship academic institution and the largest by enrollment, with over 25,400 ...


Partially open/pseudo-open notebooks

These are initiatives more open than traditional laboratory notebooks but lacking a key component for full Open Notebook Science. Usually either the notebook is only partially shared or shared with significant delay.Bradley, Jean-Claude Comment on Pseudo Open Notebook Science? from Quantum Pontiff June 27, 2008
/ref> * The Open Notebook Science Network is a WordPress blog network designed to be used to create and maintain individual/lab notebooks. As of January 2018, there are currently 126 active members of this group. * Protocolpedia allows sharing and storage of lab protocols. *
Sci-Mate Sci-Mate was a proposal for an open collaboration of scientists using Web 2.0 software to address well known challenges in academic publishing and technology transfer. The site provided free access to a collection of Web 2.0 software applications i ...
allows users to define access permissions, but can be used as an open notebook tool. * Vinod Scaria * OpenWetWare (hosts many laboratories and allows for selective sharing of information related to each research group) * Caleb Morse * Gus Rosania * Antony Garrett Lisi * Rosie Redfield, microbiologist at the University of British Columbia; all results discussed but raw experimental notebook is not exposed. * Martin Johnson, marine chemist at the
University of East Anglia The University of East Anglia (UEA) is a public research university in Norwich, England. Established in 1963 on a campus west of the city centre, the university has four faculties and 26 schools of study. The annual income of the institution f ...
. * Greg Lang, post doc in David Botstein's lab at Princeton University. - shared on approximately a weekly basis


Benefits

A public laboratory notebook makes it convenient to cite the exact instances of experiments used to support arguments in articles. For example, in a paper on the optimization of a
Ugi reaction The Ugi reaction is a multi-component reaction in organic chemistry involving a ketone or aldehyde, an amine, an isocyanide and a carboxylic acid to form a bis-amide. The reaction is named after Ivar Karl Ugi, who first reported this reaction in ...
, three different batches of product are used in the characterization and each spectrum references the specific experiment where each batch was used: EXP099, EXP203 and EXP206. This work was subsequently published in the
Journal of Visualized Experiments The ''Journal of Visualized Experiments'' (styled ''JoVE'') is a peer-reviewed scientific journal that publishes experimental methods in video format. The journal is based in Cambridge, MA and was established in December 2006. Moshe Pritsker is the ...
, demonstrating that the integrity data provenance can be maintained from lab notebook to final publication in a peer-reviewed journal. Without further qualifications, Open Notebook Science implies that the research is being reported on an ongoing basis without unreasonable delay or filter. This enables others to understand exactly how research actually happens within a field or a specific research group. Such information could be of value to collaborators, prospective students or future employers. Providing access to selective notebook pages or inserting an embargo period would be inconsistent with the meaning of the term "Open" in this context. Unless error corrections, failed experiments and ambiguous results are reported, it will not be possible for an outside observer to understand exactly how science is being done. Terms such as PseudoBacon, David Pseudo Open Notebook Science? from Quantum Pontiff June 26, 2008
/ref> or Partial have been used as qualifiers for the sharing of laboratory notebook information in a selective way or with a significant delay.


Drawbacks

The arguments against adopting open notebook science fall mainly into three categories which have differing importance in different fields of science. The primary concern, expressed particularly by biological and medical scientists is that of '
data theft Data theft is a growing phenomenon primarily caused by system administrators and office workers with access to technology such as database servers, desktop computers and a growing list of hand-held devices capable of storing digital information, s ...
' or 'being scooped'. While the degree to which research groups steal or adapt the results of others remains a subject of debate it is certainly the case that the fear of not being first to publish drives much behavior, particularly in some fields. This is related to the focus in these fields on the published peer reviewed paper as being the main metric of career success. The second argument advanced against open notebook science is that it constitutes prior publication, thus making it impossible to
patent A patent is a type of intellectual property that gives its owner the legal right to exclude others from making, using, or selling an invention for a limited period of time in exchange for publishing an enabling disclosure of the invention."A ...
and difficult to publish the results in the traditional
peer review Peer review is the evaluation of work by one or more people with similar competencies as the producers of the work ( peers). It functions as a form of self-regulation by qualified members of a profession within the relevant field. Peer revie ...
ed literature. With respect to patents, publication on the web is clearly classified as disclosure. Therefore, while there may be arguments over the value of patents, and approaches that get around this problem, it is clear that open notebook science is not appropriate for research for which patent protection is an expected and desired outcome. With respect to publication in the peer reviewed literature the case is less clear cut. Most publishers of scientific journals accept material that has previously been presented at a conference or in the form of a preprint. Those publishers that accept material that has been previously published in these forms have generally indicated informally that web publication of data, including open notebook science, falls into this category. Open notebook projects have been successfully published in high
impact factor The impact factor (IF) or journal impact factor (JIF) of an academic journal is a scientometric index calculated by Clarivate that reflects the yearly mean number of citations of articles published in the last two years in a given journal, as ...
peer reviewed journals but this has not been tested with a wide range of publishers. It is to be expected that those publishers that explicitly exclude these forms of pre-publication will not accept material previously disclosed in an open notebook. A third argument advanced against open notebook science is that it vitiates independence of competing research and hence may result in lack of all important independent verification of results. This is not the same as data-scooping, but the much more subtle possibility of allowing data that is co-evolving to influence each other. In traditional science large experimental collaborations often establish fire-wall rules preventing communication between members of competing collaborations to prevent not just data leakage but also influencing the methodology by which data is analyzed. The final argument relates to the problem of the 'data deluge'. If the current volume of the peer reviewed literature is too large for any one person to manage, then how can anyone be expected to cope with the huge quantity of non–peer-reviewed material that could potentially be available, especially when some, perhaps most, would be of poor quality? A related argument is that 'my notebook is too specific' for it to be of interest to anyone else. The question of how to discover high quality and relevant material is a related issue. The issue of curation and validating data and methodological quality is a serious issue and one that arguably has relevance beyond open notebook science but is a particular challenge here.


Funding and sponsorship

The Open Notebook Science Challenge,Open Notebook Science Challenge
/ref> now directed towards reporting solubility measurements in non-aqueous solvent, has received sponsorship fro
Submeta
Nature Nature, in the broadest sense, is the physical world or universe. "Nature" can refer to the phenomena of the physical world, and also to life in general. The study of nature is a large, if not the only, part of science. Although humans are ...
and Sigma-Aldrich. The first of ten winners of the contest for December 2008 was Jenny Hale.


Logos

Logos can be used on notebooks to indicate the conditions of sharing. Fully open notebooks are marked as "all content" and "immediate" access. Partially open notebooks can be marked as either "selected content" and/or "delayed".The Open Notebook Science Claims Page
/ref>


See also

*
Open access (publishing) Open access (OA) is a set of principles and a range of practices through which research outputs are distributed online, free of access charges or other barriers. With open access strictly defined (according to the 2001 definition), or libre op ...
*
Open data Open data is data that is openly accessible, exploitable, editable and shared by anyone for any purpose. Open data is licensed under an open license. The goals of the open data movement are similar to those of other "open(-source)" movement ...
*
Open research Open research is research that is openly accessible and modifiable by others. The central theme of open research is to make clear accounts of research methods freely available via the internet, along with any data or results extracted or derived ...
* Open content * Open science * Open source


References

{{Academic publishing Open data Notebooks Scientific method Open science