open-notebook science

The term "open-notebook science"{{Cite journal | last1 = Bradley | first1 = J. C. | doi = 10.1038/npre.2007.39.1 | title = Open Notebook Science Using Blogs and Wikis | journal = Nature Precedings | year = 2007 | doi-access = free }} 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:{{cite web|url=http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html |title=Open Notebook Science |work=Drexel CoAS E-Learning |first =Jean-Claude |last=Bradley |author-link=Jean-Claude Bradley |date=September 26, 2006}}

{{Quote|... 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}}

• Aled Edwards & colleagues, University of Toronto.{{Cite web|url=https://www.utoronto.ca/news/open-science-university-toronto-researchers-publish-lab-notes-real-time|title=Open science: University of Toronto researchers to publish lab notes in real time|website=University of Toronto News|language=en|access-date=2018-01-21}}
• Rachel Harding,{{cite web | url=http://medicine.utoronto.ca/news/researcher-open-book-first-share-lab-notes-real-time | title=Researcher is an Open Book: First to Share Lab Notes in Real Time | date=26 February 2016 | access-date=6 March 2016 | archive-url=https://web.archive.org/web/20160306121820/http://medicine.utoronto.ca/news/researcher-open-book-first-share-lab-notes-real-time | archive-date=6 March 2016 | url-status=live }}{{cite news | last=Resnick | first=Brian | url=https://www.vox.com/2016/3/3/11148452/science-blog | title=Science is too secretive and slow. So this researcher is live-blogging her work. | website=Vox.com | date=3 March 2016 | access-date=6 March 2016 | archive-url=https://web.archive.org/web/20160304101611/http://www.vox.com/2016/3/3/11148452/science-blog | archive-date=4 March 2016 | url-status=live }} post-doctoral fellow with University of Toronto's (SGC) Structural Genomics Consortium.
• blog at http://labscribbles.com/
• Twitter [https://twitter.com/LabScribbles @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".{{Cite web|url=https://opennotebook.thesgc.org/|title=Extreme Open Science at SGC – A team of groundbreaking scientists at SGC are now sharing their lab notebooks online|website=opennotebook.thesgc.org|language=en-GB|access-date=2018-01-26}}{{Citation|last=SGC Channel|title=Webcast: Open Lab Notebooks: An Extreme Open Science Initiative 19 Jan 2018|date=2018-01-24|url=https://www.youtube.com/watch?v=vxoxKVUWsUY|access-date=2018-01-26}}{{Cite web|url=https://opennotebook.thesgc.org/about/|title=About – Extreme Open Science at SGC|website=opennotebook.thesgc.org|language=en-GB|access-date=2018-01-26}}

• Nickolas J. LaSorte,{{cite web|url=http://nicklasorte.wordpress.com/|title=Nickolas J. LaSorte's Open Science Notebook}} Postdoctoral Fellow at the FDA in the area of Wireless Coexistence.
• Tamara Maiuri{{Cite web|url=https://fhs.mcmaster.ca/biochem/maiuri_tamara.html|title=Tamara Maiuri|website=fhs.mcmaster.ca|language=en-CA|access-date=2018-01-22}}
• blog at https://raytruantlab.wordpress.com/
• Twitter [https://twitter.com/tam_maiuri @tam_maiuri]
• Zenodo https://zenodo.org/search?page=1&size=20&q=maiuri
• Peter Murray-Rust,{{Citation|last=ContentMine|title=2014 Lecture: Open Notebook Science by Peter Murray-Rust|date=2015-11-03|url=https://www.youtube.com/watch?v=-wPYkJJ1PqQ|access-date=2018-01-21}} Cambridge, UK.
• Anthony Salvagno,{{cite web|url=http://research.iheartanthony.com/|title=IheartAnthony's Research}} Ph.D., Director of Education of #SciFund Challenge.
• Matthew H. Todd, Open Source Malaria,{{cite web | url=http://opensourcemalaria.org/ | title=Open Source Malaria | access-date = 7 May 2016 | archive-url=https://web.archive.org/web/20160313044704/http://opensourcemalaria.org/ | archive-date=13 March 2016 | url-status=live }}{{cite web | url=http://malaria.ourexperiment.org | title=Our Experiment - Open Source Malaria | access-date=7 May 2016 | archive-url=https://web.archive.org/web/20160314111312/http://malaria.ourexperiment.org/ | archive-date=14 March 2016 | url-status=live }}{{cite interview |last=Todd |first=Matthew |interviewer=Alice Williamson |title=Open source removes secrecy in drug research |work=The Science Show |publisher=Australian Broadcasting Corporation |date=May 7, 2016 | url=http://www.abc.net.au/radionational/programs/scienceshow/open-source-removes-the-secrecy-in-drug-research/7390322 | archive-url=https://web.archive.org/web/20160507111332/http://www.abc.net.au/radionational/programs/scienceshow/open-source-removes-the-secrecy-in-drug-research/7390322 | archive-date=7 May 2016 | url-status=live }} University College London (Todd Group).
• Open Notebook Science Challenge{{cite web|url=http://onschallenge.wikispaces.com/list+of+experiments|title=ONSchallenge - list of experiments}}
• The Digital Botanical Gardens Initiative (DBGI) observable at http://www.dbgi.org/dendron-dbgi/

• Tobias J. Osborne{{cite web|url=http://tjoresearchnotes.wordpress.com|title=Tobias J. Osborne's research notes}}
• Carl Boettiger, Theory and computational modeling in ecology and evolution.{{cite web|url=http://www.carlboettiger.info/lab-notebook.html|title=Lab Notebook|author=Carl Boettiger}}{{cite web|url=http://www.carlboettiger.info/archives/211|title=intro to notebook}}
• Dror Bar-Natan{{cite web|url=http://drorbn.net/AcademicPensieve/|title=Dror Bar-Natan: AcademicPensieve}}
• Andrés G. Saravia,{{cite web|url=https://research-engine.appspot.com/andres|title=Research Engine - Andres}} 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.{{Cite journal|last1=Himmelstein|first1=Daniel|last2=Lizee|first2=Antoine|last3=Khankhanian|first3=Pouya|last4=Brueggeman|first4=Leo|last5=Chen|first5=Sabrina|last6=Hadley|first6=Dexter|last7=Hessler|first7=Chrissy|last8=Baranzini|first8=Sergio|last9=Green|first9=Ari|title=Rephetio: Repurposing drugs on a hetnet [project]|journal=Thinklab|url=http://thinklab.com/p/rephetio|doi=10.15363/thinklab.4|year=2015|doi-access=free}}

• Brigette Black{{cite web|url=http://openwetware.org/wiki/User:Brigette_D._Black/Notebook/Brigettes_Notebook|title=User:Brigette D. Black/Notebook/Brigettes Notebook}}), physics Ph.D. student in Koch lab at the University of New Mexico.
• Jean-Claude Bradley{{cite web|url=http://usefulchem.wikispaces.com/All+Reactions|title=UsefulChem - All Reactions}}
• Jeremiah Faith[http://www.jeremiahfaith.com/open_notebook_science/jeremiah_faith_lab_notebook.pdf notebook archived April 15, 2008]
• Nadiezda Fernandez-Oropeza,{{cite web|url=http://openwetware.org/wiki/User:Nadiezda_Fernandez-Oropeza/Notebook/Notebook|title=User:Nadiezda Fernandez-Oropeza/Notebook/Notebook}} Biomedical Engineering Ph.D. student in Koch lab at the University of New Mexico.
• Mike Lawrence
• Linh Le,{{cite web|url=http://openwetware.org/wiki/User:Linh_N_Le/Notebook|title=User:Linh N Le/Notebook}} undergraduate physics major and alumnus of Koch lab at the University of New Mexico.
• Andy Maloney,{{cite web|url=http://andymaloney.wordpress.com/|title=Andy Maloney}} postdoctoral researcher in Smyth lab at University of Texas. Ph.D. in Koch lab at the University of New Mexico (2011){{cite web|url=http://openwetware.org/wiki/User:Andy_Maloney/Notebook/Lab_Notebook_of_Andy_Maloney/Table_of_Contents/Table_of_Contents|title=User:Andy Maloney/Notebook/Lab Notebook of Andy Maloney/Table of Contents/Table of Contents}}{{cite web|url=http://openwetware.org/wiki/User:Andy_Maloney/Preface_to_dissertation|title=User:Andy Maloney/Preface to dissertation}}
• Cameron Neylon[http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/blog_id/5 notebook]
• Alejandro Tamayo[http://wiki.medialab-prado.es/index.php/Fruit_Computer_Laboratory Fruit Computer Laboratory] [http://figshare.com/figures/index.php/Fruit_Computer_openlab_experiments notebook], [http://computadordefrutas.wordpress.com/ blog]
• Influenza Origins and Evolution{{cite web|url=http://influenza.bio.ed.ac.uk/|title=Molecular Evolution, Phylogenetics and Epidemiology}}

• Junior Physics Lab (307L) at University of New Mexico{{cite web|url=http://openwetware.org/wiki/Physics307L|title=Physics307L}}

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.[http://scienceblogs.com/pontiff/2008/06/pseudo_open_notebook_science.php#comment-952367 Bradley, Jean-Claude Comment on Pseudo Open Notebook Science? from Quantum Pontiff June 27, 2008]

• The Open Notebook Science Network {{cite web|url=http://onsnetwork.org|title=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.{{Cite news|url=http://onsnetwork.org/members/|title=Members|date=2014-07-18|work=Open Notebook Science Network|access-date=2018-01-26|language=en-US}}
• 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{{Cite web |url=http://sysborgtb.osdd.net/ |title=notebook, needs login |access-date=2020-04-25 |archive-url=https://web.archive.org/web/20081101072644/http://sysborgtb.osdd.net/ |archive-date=2008-11-01 |url-status=dead }}
• OpenWetWare (hosts many laboratories and allows for selective sharing of information related to each research group)
• Caleb Morse{{cite web|url=http://openwetware.org/wiki/User:Cmorse/Notebook/MediaWiki_for_Open_Science|title=User:Cmorse/Notebook/MediaWiki for Open Science}}
• Gus Rosania[http://1cellpk.wikispaces.com/ notebook]
• Antony Garrett Lisi{{cite web|url=http://www.deferentialgeometry.org|title=Deferential Geometry -}}
• Rosie Redfield,{{cite web|url=http://rrresearch.blogspot.com/|title=RRResearch}} microbiologist at the University of British Columbia; all results discussed but raw experimental notebook is not exposed.
• Martin Johnson,[http://www.uea.ac.uk/ notebook)] marine chemist at the University of East Anglia.{{Cite web |url=http://onsclaims.wikispaces.com/ |title=Selective Content, Immediate Sharing |access-date=2009-02-26 |archive-url=https://web.archive.org/web/20120528194741/http://onsclaims.wikispaces.com/ |archive-date=2012-05-28 |url-status=dead }}
• Greg Lang,{{cite web|url=http://www.genomics.princeton.edu/glang/notebooks.htm|title=Lang Lab Website}} post doc in David Botstein's lab at Princeton University.{{Cite web |url=http://onsclaims.wikispaces.com/ |title=All Content, Delayed Sharing |access-date=2009-02-26 |archive-url=https://web.archive.org/web/20120528194741/http://onsclaims.wikispaces.com/ |archive-date=2012-05-28 |url-status=dead }} - shared on approximately a weekly basis

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,{{cite journal |author1=Bradley, Jean-Claude |author2=Mirza, Khalid |author3=Owens, Kevin |author4=Osborne, Tom |author5=Williams, Antony |name-list-style=amp |title=Optimization of the Ugi reaction using parallel synthesis and automated liquid handling |journal=Nature Precedings|date=August 2008 |doi=10.1038/npre.2008.2237.1 |hdl=10101/npre.2008.2237.1 |doi-access=free }}{{cite web|url=http://usefulchem.wikispaces.com/paper03|title=UsefulChem - paper03}} three different batches of product are used in the characterization and each spectrum references the specific experiment where each batch was used: EXP099,{{cite web|url=http://usefulchem.wikispaces.com/EXP099|title=UsefulChem - EXP099}} EXP203{{cite web|url=http://usefulchem.wikispaces.com/EXP203|title=UsefulChem - EXP203}} and EXP206.{{cite web|url=http://usefulchem.wikispaces.com/EXP206|title=UsefulChem - EXP206}} This work was subsequently published in the Journal of Visualized Experiments,{{cite journal |author1=Bradley, Jean-Claude |author2=Mirza, Khalid |author3=Owens, Kevin |author4=Osborne, Tom |author5=Williams, Antony |name-list-style=amp |title=Optimization of the Ugi reaction using parallel synthesis and automated liquid handling |journal=Journal of Visualized Experiments|date=November 2008 |url=http://www.jove.com/index/details.stp?ID=942|doi=10.3791/942 |pmid=19066532 |issue=21 |pmc=2762777 |pages=942}} 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[http://scienceblogs.com/pontiff/2008/06/pseudo_open_notebook_science.php Bacon, David Pseudo Open Notebook Science? from Quantum Pontiff June 26, 2008] 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 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 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{{cite journal|last1=Woelfle|first1=Michael|last2=Seerden |first2=Jean-Paul |last3=de Gooijer |first3=Jesse |last4=Pouwer |first4=Kees |last5=Olliaro |first5=Piero |last6=Todd |first6=Matthew H.|title=Resolution of Praziquantel|journal=PLOS Neglected Tropical Diseases|date=19 September 2011|volume=5|issue=9|pages=e1260|doi=10.1371/journal.pntd.0001260|pmid=21949890|pmc=3176743|editor1-last=Geary|editor1-first=Timothy G. |doi-access=free }}{{cite journal|last=Woelfle|first=Michael |author2=Olliaro, Piero |author3=Todd, Matthew H.|title=Open science is a research accelerator|journal=Nature Chemistry|date=22 September 2011|volume=3|issue=10|pages=745–748|doi=10.1038/nchem.1149|pmid=21941234|bibcode=2011NatCh...3..745W |doi-access=free}} 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.

The Open Notebook Science Challenge,[http://onschallenge.wikispaces.com/ Open Notebook Science Challenge] now directed towards reporting solubility measurements in non-aqueous solvent, has received sponsorship from [http://www.submeta.org/ Submeta],{{cite web|url=http://usefulchem.blogspot.com/2008/11/submeta-open-notebook-science-awards.html|title=Useful Chemistry}} Nature{{cite web|url=http://usefulchem.blogspot.com/2008/11/nature-sponsors-open-notebook-science.html|title=Useful Chemistry}} and Sigma-Aldrich.{{cite web|url=http://usefulchem.blogspot.com/2008/09/sigma-aldrich-first-official-sponsor-of.html|title=Useful Chemistry}} The first of ten winners of the contest for December 2008 was Jenny Hale.{{cite web|url=http://usefulchem.blogspot.com/2008/11/first-submeta-open-notebook-science.html|title=Useful Chemistry}}

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".[https://www.slideshare.net/jcbradley/nasa-open-notebook-science-talk The Open Notebook Science Claims Page]

• Open access (publishing)
• Open data
• Open research
• Open content
• Open science
• Open source

{{reflist|2}}

{{Open navbox}}

{{Open data navbox}}

{{Academic publishing}}

Category:Open data

Category:Notebooks

Category:Scientific method

Category:Open science