Open notebook science
Open notebook science is the practice of making the entire primary record of a research project 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 approaches to research and explicitly includes the making available of failed, less significant, and otherwise unpublished experiments; so called 'dark data'. The practice of open notebookscience, although not the norm in the academic community, has gained significant recent attention in the research, 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, crowdsourcing data, and citizen science. It is inspired in part by the success of open-source software and draws on many of its ideas.
The term "open notebook science" was first used in a blog post by Jean-Claude Bradley, an Associate Professor of Chemistry at Drexel University. Bradley described open notebook science as follows:
... there is a URL to a laboratory notebook that is freely available and indexed on common search engines. It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world—Jean-Claude Bradley
- Jean-Claude Bradley
- Andrew S.I.D. Lang
- Cameron Neylon
- Open Notebook Science Challenge
- Raf Aerts
- Alejandro Tamayo
- Mike Lawrence
- Andy Maloney, postdoctoral researcher in Smyth lab at University of Texas. Ph.D. in Koch lab at the University of New Mexico (2011)
- Anthony Salvagno, physics Ph.D. student in Koch Lab at the University of New Mexico
- Matthew H. Todd, University of Sydney (Todd lab).
- Tobias J. Osborne
- Stephen McIntyre
- Carl Boettiger, Theory and computational modeling in ecology and evolution.
- Dror Bar-Natan
- Andrés G. Saravia, physics Ph.D. student at Cinvestav-Mérida.
- Jeremiah Faith
- Influenza Origins and Evolution
- Linh Le, undergraduate physics major and alumnus of Koch lab at the University of New Mexico.
- Brigette Black), physics Ph.D. student in Koch lab at the University of New Mexico.
- Nadiezda Fernandez-Oropeza, Biomedical Engineering Ph.D. student in Koch lab at the University of New Mexico.
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.
- Protocolpedia allows sharing and storage of lab protocols.
- Sci-Mate 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 East Anglia University.
- Greg Lang, post doc in David Botstein's lab at Princeton University. - shared on approximately a weekly basis
The aim of Open Notebook Science is to make the full record of scientific research available. This enables other scientists to obtain detailed descriptions of procedures, raw and analyzed data to either compare with their own work or to build on. Advocates argue that this can improve the communication of science, increase the rate at which research can progress, and reduce time lost due to the repetition of failed experiments. In particular advocates argue that it enables more effective collaboration and enables new forms of collaboration in which the collaborators are not necessarily known in advance. One of the goals of open notebook science is to "improve scientific communication".
In addition to the primary value of laboratory notebooks to scientists, there are several secondary values that warrant their archival preservation and public accessibility for the long-term. The preservation of laboratory notebooks and electronic laboratory notebooks (ELNs) as records of enduring value for the history and philosophy of science has been a topic discussed nationally and internationally by Shannon Bohle. Bohle discussed the use of laboratory notebooks as historical records documenting the process of discovery and patenting inventions in the US and the UK in her talk “Science Archives and History: Facilitating Discovery through Laboratory Notebooks” at the British Society for the History of Science conference held at the University of Oxford in 2008. In her presentation “Laboratory Notebooks,” in “Preserving Digital Research Data in the Health Sciences” section at Joint Annual Meeting of the Society of American Archivists and the Council of State Archivists held on August 14, 2009 in Austin, Texas, she emphasized how laboratory notebooks played a role in the "archives in the development of digital repositories for long-term retention and management of research data in electronic formats" and argued why archived laboratory notebooks are essential for "managing ethical and legally compliant options for access and use of the data." On October 31, 2012, Bohle spoke at the University of Cambridge on the role laboratory notebooks played in James D. Watson's cancer research and their relationship to his Nobel Prize on the occasion of the "50th Anniversary of the Awarding of the Nobel Prize in Physiology or Medicine for the Discovery of the Structure of DNA," along with a description of her archival project organizing, preserving, and describing this Nobel laureate's notebooks while employed at Cold Spring Harbor Laboratory from 2006-2007. As part of a three-part article series on Open Science and Open Data published in 2013 in association with Nature and Scientific American, she also argued that laboratory notebooks are part of e-Science, and as such, pubic accessibility to them are important in the name of transparency in order to redress "major questions addressing the process of scientific integrity and ethics" of an immediate or historical nature.
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, 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, 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 Pseudo or Partial have been used as qualifiers for the sharing of laboratory notebook information in a selective way or with a significant delay.
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' 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 behaviour, 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 and difficult to publish the results in the traditional peer reviewed 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 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.
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, now directed towards reporting solubility measurements in non-aqueous solvent, has received sponsorship from Submeta, Nature and Sigma-Aldrich. The first of ten winners of the contest for December 2008 was Jenny Hale.
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".
- Freeing the Dark Data of Failed Scientific Experiments, Goetz, T. , Wired Magazine, Sept.25, 2007
- Sanderson, K; Neylon, C (September 2008). "Data on display". Nature 455 (7211): 273. doi:10.1038/455273a. PMID 18800097.
- Singh, S. (April 2008). "Data on display". Cell 133 (2): 201–3. doi:10.1016/j.cell.2008.04.003. PMID 18423188.
- Williams, A. (2008). "Internet-based tools for communication and collaboration in chemistry". Drug Discovery Today 13 (11–12): 502–506. doi:10.1016/j.drudis.2008.03.015. PMID 18549976.
- Everts, S. Open Source Science, Chemical & Engineering News, July 2006, 84 (30) p. 34.
- Bradley, J. C. (2007). "Open Notebook Science Using Blogs and Wikis". Nature Precedings. doi:10.1038/npre.2007.39.1.
- Blog post
- Fruit Computer Laboratory notebook, blog
- Ph.D notebook
- Open PhD dissertation
- Schistosomiasis notebook
- Malaria notebook
- notebook on climate change
- intro to notebook
- notebook archived April 15, 2008
- Human/Swine A/H1N1 Influenza Origins and Evolution
- Bradley, Jean-Claude Comment on Pseudo Open Notebook Science? from Quantum Pontiff June 27, 2008
- notebook, needs login
- research blog
- Selective Content, Immediate Sharing
- All Content, Delayed Sharing
- Bradley, Jean-Claude Processing Drug Discovery raw data collaboratively and openly using Open Notebook Science, American Chemical Society National Fall Meeting, Aug 20, 2008. (Philadelphia)
- Bohle, Shannon. Science Archives and History: Facilitating Discovery through Laboratory Notebooks. Available from The British Society for the History of Science Sixth Three Societies Conference, Keble College, University of Oxford (Oxford, United Kingdom) <http://www.bshs.org.uk/wp-content/uploads/2008-3Societies-Prog.pdf> (Jul 4, 2008).
- Bohle, Shannon. “Laboratory Notebooks” in “Preserving Digital Research Data in the Health Sciences.” Available from Joint Annual Meeting of the Society of American Archivists and the Council of State Archivists conference, Austin, Texas <http://saa.archivists.org/Scripts/4Disapi.dll/4DCGI/events/eventdetail.html?Action=Events_Detail&Time=45281358&InvID_W=1064> (Aug 14, 2009).
- Bohle, Shannon. "James D. Watson and Cancer Research: 50th Anniversary of the Awarding of the Nobel Prize in Physiology or Medicine for the Discovery of the Structure of DNA." St. Edmund's College, University of Cambridge. <http://docs.google.com/file/d/0B4esZVCQ2yHNZXZuWWNrMnB1UzA/edit?usp=sharing> (Oct 31, 2012).
- Bohle, Shannon. "James D. Watson Collection, Record Group 2, Series 6: Laboratory and Course Notebooks, 1947-1951, 1958-1961." Available Cold Spring Harbor Laboratory. <http://libfe.cshl.edu/archives/archives/Watson_Archives/Series_6_Finding_Aid.pdf> (May 2006).
- Bohle, Shannon. “What is E-science and How Should it be Managed?.” Available from Scientific and Medical Libraries, Scilogs(published in association with Nature and Scientific American) <http://www.scilogs.com/scientific_and_medical_libraries/what-is-e-science-and-how-should-it-be-managed/> (12 June 2013).
- Bradley, Jean-Claude; Mirza, Khalid; Owens, Kevin; Osborne, Tom and Williams, Antony (August 2008). "Optimization of the Ugi reaction using parallel synthesis and automated liquid handling". Nature Precedings. hdl:10101/npre.2008.2237.1 .
- Bradley, Jean-Claude; Mirza, Khalid; Owens, Kevin; Osborne, Tom and Williams, Antony Optimization of the Ugi reaction using parallel synthesis and automated liquid handling (UsefulChem wiki version)
- Bradley, Jean-Claude and Mirza, Khalid UsefulChem EXP099
- Bradley, Jean-Claude and Mirza, Khalid UsefulChem EXP203
- Bradley, Jean-Claude and Mirza, Khalid UsefulChem EXP206
- Bradley, Jean-Claude; Mirza, Khalid; Owens, Kevin; Osborne, Tom and Williams, Antony (November 2008). "Optimization of the Ugi reaction using parallel synthesis and automated liquid handling". Journal of Visualized Experiments (21): 942. doi:10.3791/942. PMC 2762777. PMID 19066532.
- Bacon, David Pseudo Open Notebook Science? from Quantum Pontiff June 26, 2008
- Woelfle, Michael; Seerden, Jean-Paul, de Gooijer, Jesse, Pouwer, Kees, Olliaro, Piero, Todd, Matthew H., Geary, Timothy G. (19 September 2011). "Resolution of Praziquantel". In Geary, Timothy G. PLoS Neglected Tropical Diseases 5 (9): e1260. doi:10.1371/journal.pntd.0001260. PMC 3176743. PMID 21949890.
- Woelfle, Michael; Olliaro, Piero, Todd, Matthew H. (22 September 2011). "Open science is a research accelerator". Nature Chemistry 3 (10): 745–748. doi:10.1038/nchem.1149. PMID 21941234.
-  Open Notebook Science Challenge
- Bradley, J.-C. "Submeta Open Notebook Science Awards!" UsefulChem blog November 4, 2008
- Bradley, J.-C. "Nature Sponsors Open Notebook Science Challenge" UsefulChem blog November 20, 2008
- Bradley, J.-C. "Sigma-Aldrich First Official Sponsor of Open Notebook Science Challenge" UsefulChem blog September 30, 2008
- Bradley, J.-C. "First Submeta Open Notebook Science Award Winner" UsefulChem blog November 26, 2008
- The Open Notebook Science Claims Page