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approaches to research and explicitly includes the making available of failed, less significant, and otherwise unpublished experiments; so called 'dark data'.[1] The practice of open notebook science, although not the norm in the academic community, has gained significant recent attention in the research[2][3] and general[1][4] 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[5] and draws on many of its ideas.

Open Notebook Science

History

The term "open-notebook science"[6] 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:[7]

... 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

Practitioners

Active

Experimental (alphabetical by last name)

"A team of groundbreaking scientists at SGC are now sharing their lab notebooks online".[11][12][13]

Theoretical

  • Tobias J. Osborne[22]
  • Carl Boettiger, Theory and computational modeling in ecology and evolution.[23][24]
  • Dror Bar-Natan[25]
  • Andrés G. Saravia,[26] physics Ph.D. student at Cinvestav-Mérida.
  • Daniel Himmelstein, who led Project Rephetio — a drug repuposing study that used GitHub and Thinklab for realtime open notebook science and collaboration.[27]

Archived (alphabetical by last name)

  • Brigette Black[28]), physics Ph.D. student in Koch lab at the University of New Mexico.
  • Jean-Claude Bradley[29]
  • Jeremiah Faith[30]
  • Nadiezda Fernandez-Oropeza,[31] Biomedical Engineering Ph.D. student in Koch lab at the University of New Mexico.
  • Mike Lawrence
  • Linh Le,[32] undergraduate physics major and alumnus of Koch lab at the University of New Mexico.
  • Andy Maloney,[33] postdoctoral researcher in Smyth lab at University of Texas. Ph.D. in Koch lab at the University of New Mexico (2011)[34][35]
  • Cameron Neylon[36]
  • Alejandro Tamayo[37]
  • Influenza Origins and Evolution[38]

Recurrent (Educational)

Partial/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.[40]

  • The Open Notebook Science Network [41] 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.[42]
  • 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[43]
  • OpenWetWare (hosts many laboratories and allows for selective sharing of information related to each research group)
  • Caleb Morse[44]
  • Gus Rosania[45]
  • Antony Garrett Lisi[46]
  • Rosie Redfield,[47] microbiologist at the University of British Columbia; all results discussed but raw experimental notebook is not exposed.
  • Martin Johnson,[48] marine chemist at the University of East Anglia.[49]
  • Greg Lang,[50] post doc in David Botstein's lab at Princeton University.[51] - 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,[52][53] three different batches of product are used in the characterization and each spectrum references the specific experiment where each batch was used: EXP099,[54] EXP203[55] and EXP206.[56] This work was subsequently published in the Journal of Visualized Experiments,[57] 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[58] or Partial[40] 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' 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[59][60] 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,[61] now directed towards reporting solubility measurements in non-aqueous solvent, has received sponsorship from Submeta,[62] Nature[63] and Sigma-Aldrich.[64] The first of ten winners of the contest for December 2008 was Jenny Hale.[65]

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".[66]

See also

References

  1. ^ a b Freeing the Dark Data of Failed Scientific Experiments, Goetz, T., Wired Magazine, Sept.25, 2007
  2. ^ Sanderson, K; Neylon, C (September 2008). "Data on display". Nature. 455 (7211): 273. doi:10.1038/455273a. PMID 18800097.
  3. ^ Singh, S. (April 2008). "Data on display". Cell. 133 (2): 201–3. doi:10.1016/j.cell.2008.04.003. PMID 18423188.
  4. ^ 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.
  5. ^ "Chemical & Engineering News - Serving the chemical, life sciences and laboratory worlds".
  6. ^ Bradley, J. C. (2007). "Open Notebook Science Using Blogs and Wikis". Nature Precedings. doi:10.1038/npre.2007.39.1.
  7. ^ Bradley, Jean-Claude (September 26, 2006). "Open Notebook Science". Drexel CoAS E-Learning.
  8. ^ "Open science: University of Toronto researchers to publish lab notes in real time". University of Toronto News. Retrieved 2018-01-21.
  9. ^ "Researcher is an Open Book: First to Share Lab Notes in Real Time". 26 February 2016. Archived from the original on 6 March 2016. Retrieved 6 March 2016.
  10. ^ Resnick, Brian (3 March 2016). "Science is too secretive and slow. So this researcher is live-blogging her work". Vox.com. Archived from the original on 4 March 2016. Retrieved 6 March 2016.
  11. ^ "Extreme Open Science at SGC – A team of groundbreaking scientists at SGC are now sharing their lab notebooks online". opennotebook.thesgc.org. Retrieved 2018-01-26.
  12. ^ SGC Channel (2018-01-24), Webcast: Open Lab Notebooks: An Extreme Open Science Initiative 19 Jan 2018, retrieved 2018-01-26
  13. ^ "About – Extreme Open Science at SGC". opennotebook.thesgc.org. Retrieved 2018-01-26.
  14. ^ "Nickolas J. LaSorte's Open Science Notebook".
  15. ^ "Tamara Maiuri". fhs.mcmaster.ca. Retrieved 2018-01-22.
  16. ^ ContentMine (2015-11-03), 2014 Lecture: Open Notebook Science by Peter Murray-Rust, retrieved 2018-01-21
  17. ^ "IheartAnthony's Research".
  18. ^ "Open Source Malaria". Archived from the original on 13 March 2016. Retrieved 7 May 2016.
  19. ^ "Our Experiment - Open Source Malaria". Archived from the original on 14 March 2016. Retrieved 7 May 2016.
  20. ^ Todd, Matthew (May 7, 2016). "Open source removes secrecy in drug research". The Science Show (Interview). Interviewed by Alice Williamson. Australian Broadcasting Corporation. Archived from the original on 7 May 2016.
  21. ^ "ONSchallenge - list of experiments".
  22. ^ "Tobias J. Osborne's research notes".
  23. ^ Carl Boettiger. "Lab Notebook".
  24. ^ "intro to notebook".
  25. ^ "Dror Bar-Natan: AcademicPensieve".
  26. ^ "Research Engine - Andres".
  27. ^ Himmelstein, Daniel; Lizee, Antoine; Khankhanian, Pouya; Brueggeman, Leo; Chen, Sabrina; Hadley, Dexter; Hessler, Chrissy; Baranzini, Sergio; Green, Ari (2015). "Rephetio: Repurposing drugs on a hetnet [project]". Thinklab. doi:10.15363/thinklab.4.
  28. ^ "User:Brigette D. Black/Notebook/Brigettes Notebook".
  29. ^ "UsefulChem - All Reactions".
  30. ^ notebook archived April 15, 2008
  31. ^ "User:Nadiezda Fernandez-Oropeza/Notebook/Notebook".
  32. ^ "User:Linh N Le/Notebook".
  33. ^ "Andy Maloney".
  34. ^ "User:Andy Maloney/Notebook/Lab Notebook of Andy Maloney/Table of Contents/Table of Contents".
  35. ^ "User:Andy Maloney/Preface to dissertation".
  36. ^ notebook
  37. ^ Fruit Computer Laboratory notebook, blog
  38. ^ "Molecular Evolution, Phylogenetics and Epidemiology".
  39. ^ "Physics307L".
  40. ^ a b Bradley, Jean-Claude Comment on Pseudo Open Notebook Science? from Quantum Pontiff June 27, 2008
  41. ^ "Open Notebook Science Network".
  42. ^ "Members". Open Notebook Science Network. 2014-07-18. Retrieved 2018-01-26.
  43. ^ notebook, needs login
  44. ^ "User:Cmorse/Notebook/MediaWiki for Open Science".
  45. ^ notebook
  46. ^ "Deferential Geometry -".
  47. ^ "RRResearch".
  48. ^ notebook)
  49. ^ Selective Content, Immediate Sharing
  50. ^ "Lang Lab Website".
  51. ^ All Content, Delayed Sharing
  52. ^ Bradley, Jean-Claude; Mirza, Khalid; Owens, Kevin; Osborne, Tom & Williams, Antony (August 2008). "Optimization of the Ugi reaction using parallel synthesis and automated liquid handling". Nature Precedings. hdl:10101/npre.2008.2237.1.
  53. ^ "UsefulChem - paper03".
  54. ^ "UsefulChem - EXP099".
  55. ^ "UsefulChem - EXP203".
  56. ^ "UsefulChem - EXP206".
  57. ^ Bradley, Jean-Claude; Mirza, Khalid; Owens, Kevin; Osborne, Tom & 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.
  58. ^ Bacon, David Pseudo Open Notebook Science? from Quantum Pontiff June 26, 2008
  59. ^ Woelfle, Michael; Seerden, Jean-Paul; de Gooijer, Jesse; Pouwer, Kees; Olliaro, Piero; Todd, Matthew H. (19 September 2011). Geary, Timothy G., ed. "Resolution of Praziquantel". PLoS Neglected Tropical Diseases. 5 (9): e1260. doi:10.1371/journal.pntd.0001260. PMC 3176743. PMID 21949890.
  60. ^ 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.
  61. ^ Open Notebook Science Challenge
  62. ^ "Useful Chemistry".
  63. ^ "Useful Chemistry".
  64. ^ "Useful Chemistry".
  65. ^ "Useful Chemistry".
  66. ^ The Open Notebook Science Claims Page
Antony Garrett Lisi

Antony Garrett Lisi (born January 24, 1968), known as Garrett Lisi, is an American theoretical physicist and adventure sports enthusiast. Lisi works as an independent researcher without an academic position. He is a strong proponent of balance in life, in his case between scientific research and enjoyment of the outdoors.Lisi is known for "An Exceptionally Simple Theory of Everything," a paper proposing a unified field theory based on the E8 Lie group, combining particle physics with Einstein's theory of gravitation. The theory is incomplete and not widely accepted by the physics community.

Antony John Williams

Antony John Williams is a British chemist and expert in the fields of both nuclear magnetic resonance (NMR) spectroscopy and cheminformatics at the United States Environmental Protection Agency. He is the founder of the ChemSpider website that was purchased by the Royal Society of Chemistry in May 2009. He is a science blogger, one of the hosts of the SciMobileApps wiki, a community-based wiki for Scientific Mobile Apps and an author.

Benzoic acid

Benzoic acid , C7H6O2 (or C6H5COOH), is a colorless crystalline solid and a simple aromatic carboxylic acid. The name is derived from gum benzoin, which was for a long time its only known source. Benzoic acid occurs naturally in many plants and serves as an intermediate in the biosynthesis of many secondary metabolites. Salts of benzoic acid are used as food preservatives and benzoic acid is an important precursor for the industrial synthesis of many other organic substances. The salts and esters of benzoic acid are known as benzoates .

Cinnamic acid

Cinnamic acid is an organic compound with the formula C6H5CH=CHCOOH. It is a white crystalline compound that is slightly soluble in water, and freely soluble in many organic solvents. Classified as an unsaturated carboxylic acid, it occurs naturally in a number of plants. It exists as both a cis and a trans isomer, although the latter is more common.

Governor General's Academic Medal

The Governor General's Academic Medal is awarded to the student graduating with the highest grade point average from a Canadian high school, college or university program. They are presented by the educational institution on behalf of the Governor General.

H.R. 5108 (113th Congress)

The bill H.R. 5108 would establish the Law School Clinic Certification Program of the United States Patent and Trademark Office (USPTO) to be available to accredited law schools for the 10-year period after enactment of this Act.H.R. 5108 was introduced into the United States House of Representatives during the 113th United States Congress.

Jean-Claude Bradley

Jean-Claude Bradley was a chemist who actively promoted Open Science in chemistry, including at the White House, for which he was awarded the Blue Obelisk award in 2007. He coined the term "Open Notebook science". He died in May 2014. A memorial symposium was held July 14, 2014 at Cambridge University, UK.One outcome of his Open Notebook work is the collection of physicochemical properties of organic compounds he was studying. All of this data he made available as Open data under the CCZero license. For example, in 2009 Bradley et al. published their work on making solubility data of organic compounds available as Open data. Later, the melting point data set he collaborated on with Andrew Lang and Antony Williams was published with Figshare. Both data sets were also made available as books via the Lulu.com self-publishing platform.He blogged extensively and contributed to at least 25 individual blogs. In an interview in 2008 with Bora Zivkovic titled "Doing Science Publicly", he spoke of his work and online presence. In 2010, he gave an extensive interview about the impact of Open Notebook science with Richard Poynder.

Lab notebook

A laboratory notebook (colloq. lab notebook or lab book) is a primary record of research. Researchers use a lab notebook to document their hypotheses, experiments and initial analysis or interpretation of these experiments. The notebook serves as an organizational tool, a memory aid, and can also have a role in protecting any intellectual property that comes from the research.

List of stationery topics

This is a list of stationery topics. Stationery has historically pertained to a wide gamut of materials: paper and office supplies, writing implements, greeting cards, glue, pencil cases and other similar items.

Open Notebook Science Challenge

The Open Notebook Science Challenge is a crowdsourcing research project which collects measurements of the non-aqueous solubility of organic compounds and publishes these as open data; findings are reported in an open notebook science manner. Although anyone may contribute research data, the competition is only open to post-secondary students in the USA and UK.

The challenge in turn forms part of the UsefulChem project, an ongoing open notebook science effort to synthesize and screen potential new anti-malarial drugs. Data from the Solubility Challenge will be used to build predictive computational models of solubility for use in optimising syntheses.The challenge began on September 28, 2008 and, as of February 2014, involves researchers and their students from at least 4 different institutions and has resulted in the acquisition of over 7672 solubility measurements.

Open data

Open data is the idea that some data should be freely available to everyone to use and republish as they wish, without restrictions from copyright, patents or other mechanisms of control. The goals of the open-source data movement are similar to those of other "open(-source)" movements such as open-source software, hardware, open content, open education, open educational resources, open government, open knowledge, open access, open science, and the open web. Paradoxically, the growth of the open data movement is paralleled by a rise in intellectual property rights. The philosophy behind open data has been long established (for example in the Mertonian tradition of science), but the term "open data" itself is recent, gaining popularity with the rise of the Internet and World Wide Web and, especially, with the launch of open-data government initiatives such as Data.gov, Data.gov.uk and Data.gov.in.

Open data, can also be linked data; when it is, it is linked open data. One of the most important forms of open data is open government data (OGD), which is a form of open data created by ruling government institutions. Open government data's importance is borne from it being a part of citizens' everyday lives, down to the most routine/mundane tasks that are seemingly far removed from government.

Open research

Open research is research conducted in the spirit of free and open-source software. Much like open-source schemes that are built around a source code that is made public, the central theme of open research is to make clear accounts of the methodology freely available via the internet, along with any data or results extracted or derived from them. This permits a massively distributed collaboration, and one in which anyone may participate at any level of the project.

Especially if the research is scientific in nature, it is frequently referred to as open science. Open research can also include social sciences, the humanities, mathematics, engineering and medicine.

Open science

Open science is the movement to make scientific research (including publications, data, physical samples, and software) and its dissemination accessible to all levels of an inquiring society, amateur or professional. Open science is transparent and accessible knowledge that is shared and developed through collaborative networks. It encompasses practices such as publishing open research, campaigning for open access, encouraging scientists to practice open notebook science, and generally making it easier to publish and communicate scientific knowledge.

Open Science can be seen as a continuation of, rather than a revolution in, practices begun in the 17th century with the advent of the academic journal, when the societal demand for access to scientific knowledge reached a point at which it became necessary for groups of scientists to share resources with each other so that they could collectively do their work. In modern times there is debate about the extent to which scientific information should be shared. The conflict that led to the Open Science movement is between the desire of scientists to have access to shared resources versus the desire of individual entities to profit when other entities partake of their resources. Additionally, the status of open access and resources that are available for its promotion are likely to differ from one field of academic inquiry to another.

Open source

Open source is a term denoting that a product includes permission to use its source code, design documents, or content. It most commonly refers to the open-source model, in which open-source software or other products are released under an open-source license as part of the open-source-software movement. Use of the term originated with software, but has expanded beyond the software sector to cover other open content and forms of open collaboration.

Trial registration

Trial registration is the practice of publishing the methodology of clinical trials before they begin. This reduces problems from publication bias and selective reporting (such as choosing the methodology after the results are known). Clinical trial registrations are now common and required by many funders and governments, and are increasingly being standardized. Trial registration is less common in other disciplines, but is part of the open science movement.

United States Patent and Trademark Office

The United States Patent and Trademark Office (USPTO) is an agency in the U.S. Department of Commerce that issues patents to inventors and businesses for their inventions, and trademark registration for product and intellectual property identification.

The USPTO is "unique among federal agencies because it operates solely on fees collected by its users, and not on taxpayer dollars". Its "operating structure is like a business in that it receives requests for services—applications for patents and trademark registrations—and charges fees projected to cover the cost of performing the services [it] provide[s]".The USPTO is based in Alexandria, Virginia, after a 2005 move from the Crystal City area of neighboring Arlington, Virginia. The offices under Patents and the Chief Information Officer that remained just outside the southern end of Crystal City completed moving to Randolph Square, a brand-new building in Shirlington Village, on April 27, 2009.

The current Under Secretary of Commerce for Intellectual Property and Director of the USPTO is Andrei Iancu. He began his role as Director on February 8, 2018. Iancu was nominated by President Trump in August 2017, and unanimously confirmed by the U.S. Senate. Prior to joining the USPTO, he was the Managing Partner at Irell & Manella LLP, where his practice focused on intellectual property litigation.The USPTO cooperates with the European Patent Office (EPO) and the Japan Patent Office (JPO) as one of the Trilateral Patent Offices. The USPTO is also a Receiving Office, an International Searching Authority and an International Preliminary Examination Authority for international patent applications filed in accordance with the Patent Cooperation Treaty.

Concepts and
practices
Organizations
Activists
Projects and
movements
Concepts
By location
Open data projects

This page is based on a Wikipedia article written by authors (here).
Text is available under the CC BY-SA 3.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.