A review of Open Notebook Science in the biomedical informatics domain
An incomplete Zero Draft, assembled by Heather Piwowar


Motivation

• "Too often when errors or cases of fraud occur in science, the lab data required to reconstruct what happened have gone astray. And too often, the co-authors failed to exert due scrutiny on their colleagues' activities in order to prevent such misfortunes. The damage to personal and institutional reputations can be severe and, in rare high-profile cases, public trust can be eroded."  [Nature e-Notebook Editorial]
• "e-notebooks allow the sharing of data, to the immediate benefit of collaborators (for examples, see Nature 436, 20; 2005)"  [Nature e-Notebook Editorial]
• "just knowing that a notebook is available to others in the lab, and archived for the future, should compel the keeping of better records."  [Nature e-Notebook Editorial]
• "one can and should go further. Electronic notebooks can be archived by researchers' employers, with a number of attendant benefits. If each notebook (or subset of it) is allocated a unique identifying code — a permanent alphanumeric string containing information about provenance, creation dates and digital location — it can be cited in journals as a confirmation that the data are safely stored, ultimately available and sharable (with due regard for the rights of the researchers involved)."  [Nature e-Notebook Editorial]
• "confirms that the original data can be retrieved in the case of errors or accusations of fraud. No longer would claims of lost notebooks be brought up in misconduct investigations."  [Nature e-Notebook Editorial]
• "additional benefit is that the data may have a value not only to the researchers who produced them but to others too, independently of the publications that report them. That value can be recognized explicitly by citation of the identifying code, enabling due credit to be given to the researchers who produced them."  [Nature e-Notebook Editorial]
• "Funding agencies also need to recognize that, by providing such support, some of the concerns over the loss of data can be assuaged, and the rigour and transparency of publicly funded research will be improved."  [Nature e-Notebook Editorial]
• Ibanez et al. put it this way: "Limiting access to scientific information hinders innovation, complicates validation, and wastes valuable socio-economic resources. Open Science is an effective way of overcoming the nearsightedness of the contemporary obsession with intellectual property."
• "We live in an age when google provides us all with more than 2 gigabytes worth of storage for free to store and "never delete" our email.
  There is absolutely no excuse for all of public science to archive its data in paper and pen books that die the moment the page is turned.
  It is about time for public organizations to talk about open frameworks to collect and store data generated in all NIH/NSF funded labs. All data can be archived, especially data of the unpublished kind in a mega NIH/NSF/ managed public archive."   Posted by: Hari Jayaram | May 9, 2007 04:45 AM at http://blogs.nature.com/nautilus/2007/05/share_your_lab_notes.html
• "Which situation would you rather be in if a case of plagiarism needed to be settled? Can you imagine how embarrassing it would be to get caught doing that?"  [http://usefulchem.blogspot.com/2007/05/totally-retrosynthetic.html]
• "The reader, who has the most invested in assessing the validity of the work, is really in the best position to act as a reviewer." ... "Thus, in the Google Age, the most important criterion for the usability of a document is immediate online availability. Articles and information sources that are not immediately available will only be pursued as a second choice, even if the vehicle is reputable."  "With the advent of easy to use, free and hosted social software like blogs and wikis, and extremely efficient indexing by major databases such as Google, publication costs and learning curves are essentially zero. It is now possible to connect a researcher providing information with a researcher looking for that information very quickly with minimal technological obstacles.
  
  Keeping the actual laboratory notebook of a research group in real time on a public wiki and holding discussions on a public blog is the natural extension of the openness concept leveraging today's technologies and global infrastructure. Operating with such transparency and demonstrating that science can be accomplished in this type of an environment is at the core of the UsefulChem project."  [http://usefulchem.blogspot.com/2007/04/funding-usefulchem.html]
  

Definition

• "To clear up confusion, I will use the term Open Notebook Science, which has not yet suffered meme mutation. "  [Bradley JC, "Open Notebook Science" at Drexel COaS E-Learning 9/26/2006]
• "It seems to me that Access and Data are crucial by definition; you could do Open Science which relied on proprietary software, provided you made the raw data and your publications openly accessible.  It is, of course, more efficient to use software that is available to everyone without intellectual property or cost barriers.  Similarly, open standards and open licensing might not be fundamental to the practice of Open Science, but both make possible such vast increases in efficiency that I would argue for their inclusion in any comprehensive definition or declaration."  [Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]
• "Open (Access + Data + Source + Standards + Licensing) = Open Science."  [Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]
• "A formal definition will have to wait for future conferences at which scientists and their allies can hammer out the Open Science equivalent of the BBB Declarations"  [Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]
• "I think the Wikipedia Open Science stub has the right idea in propounding a sort of meta-definition: "a general term representing the application of various Open approaches... to scientific endeavour""  [Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]
• "Andrés Guadamuz González ventures "the application of open source licensing principles and clauses to protect and distribute the fruits of scientific research""
• Ibanez et al. put it this way: "The practice of Open Science is based on three pillars: Open Access, Open Data, and Open Source."  [Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]
• "publishing day-to-day results (including all raw data) in an online lab notebook"    [Hooker B, "The Future of Science is Open, Part 3: An Open Science World" at 3quarksdaily 1/22/2007]

Completeness

• "no insider information" [Bradley JC, "Open Notebook Science" at Drexel COaS E-Learning 9/26/2006]
• "If research is ONS you should show absolutely everything (including failed attempts) in your official laboratory notebook and linked raw data."  [Bradley JC, Comment on ResearchRemix 7/19/2007] 
• "The question of including ideas, future projects and other forms of communication extends the concept of sharing to something I usually refer to as Completely Transparent Science. With humans this is an ideal that cannot be reached realistically - you would have to include every conversation and every unrecorded thought. There are logistical problems with that and some difficulty with respecting privacy issues."  [Bradley JC, Comment on ResearchRemix 7/19/2007] f
• I do my best to record these thoughts (hypotheses, milestones, etc.) on our main blog and link back to the laboratory notebook for access to the raw data:
  http://usefulchem.blogspot.com
  I have found recently that the use of a mailing list can keep a fairly good record of the small details that don’t show up on the blog or wiki, especially with external collaborations:
  http://groups.google.com/group/usefulchem
  "  [Bradley JC, Comment on ResearchRemix 7/19/2007] 
• "Electronic notebooks, like their paper cousins, record the daily thoughts and experiments of bench scientists. Ideally, they contain data that flow automatically from lab instruments and can be read by all lab members. Pages are date- and time-stamped, and all changes tracked and signed. Earlier versions can be reconstructed."  [Nature e-Notebook Editorial]
• "in the meantime all of his research output is captured and made available to the world.  Importantly, this includes information which would never otherwise have been published -- negative results, inconclusive results, things which simply don't fit into the narrative of any manuscript he prepares, and so on"   [Hooker B, "The Future of Science is Open, Part 3: An Open Science World" at 3quarksdaily 1/22/2007]
  
• "They are, to begin with, the perfect place for things like negative results, odd observations and small side-projects -- research results for which the risk of having an idea stolen is greatly outweighed by both the possibility of picking up a collaboration and the importance of having made available to the research community information which would never surface in a traditional journal. "   [Hooker B, "The Future of Science is Open, Part 3: An Open Science World" at 3quarksdaily 1/22/2007]
• "I'm still not sure what makes sense in this space - thoughtful blog postings and pre-prints are certainly useful.  Very raw information such as we might get with "open notebook science" I'm not so convinced about." [http://scilib.typepad.com/science_library_pad/2007/06/thinking-about-.html]

Availability

• indexed on common search engines  [Bradley JC, "Open Notebook Science" at Drexel COaS E-Learning 9/26/2006]
• freely available [Bradley JC, "Open Notebook Science" at Drexel COaS E-Learning 9/26/2006]
• "The access to the notebook must be completely open to humans and machines (no login for example)."   [Bradley JC, Comment on ResearchRemix 7/19/2007] f

Timeliness

• " The timeliness is a very good point. The policy in my lab is that all of the Log sections of experiments have to be updated at the very latest by the end of that day. "  [Bradley JC, Comment on ResearchRemix 7/19/2007] 
• Results, Discussion and Conclusion can be done later as we process the raw data and consult the literature. I think that is pretty common for any laboratory notebook, paper or electronic.  "  [Bradley JC, Comment on ResearchRemix 7/19/2007] 
• "If the lab had a private notebook updated immediately then a public one with different content or released at a later time I would not consider that ONS."  [Bradley JC, Comment on ResearchRemix 7/19/2007] 

Format:

• " I mean that there is a URL to a laboratory notebook (like this)" [Bradley JC, "Open Notebook Science" at Drexel COaS E-Learning 9/26/2006]
• "There are numerous e-notebook products available, but none dominates in all sectors. The pharmaceutical industry, which is well accustomed to regulation, has adopted company-wide solutions, and the US Food and Drug Administration has determined that the use of electronic notebooks is acceptable in drug filings. This high degree of usage is in stark contrast to academia."  [Nature e-Notebook Editorial]
• "There will be challenges with respect to maintenance of the archives and the standardization of software"  [Nature e-Notebook Editorial]
• "Being on a third-party hosted wiki, the notebook entries have time and date stamps which can establish priority if that should be necessary; version tracking provides another layer of authentication."  [Hooker B, "The Future of Science is Open, Part 3: An Open Science World" at 3quarksdaily 1/22/2007]
• wiki and blogs for writing theses [http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=353]
• "pm286 Says:
  June 9th, 2007 at 9:02 pm

  (3)
  I completely agree. Wikis and HTML are not the best ways of managing data-rich projects - it needs XML and/or RDF to manage the structure. On the other hand XML is harder for communal projects than HTML/Wikis. Is there a way of dumping the particular Wiki as XML?

  Is there any way the data should be kept in a structured form that is downloadable."  [http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=353]
  

• "Although there are several software packages created specifically to function as electronic notebooks, what we have found is that a simple wiki is really well suited for this purpose. A hosted and free service, like Wikispaces, is simple to use, has excellent version control, built-in RSS capabilities and is indexed very quickly by Google. And because it is hosted by an agency not connected to the laboratory, the third-party time stamps should hold up well to prove who knew and did what when."  Posted by: Jean-Claude Bradley | May 3, 2007 08:24 PM on http://blogs.nature.com/nautilus/2007/05/share_your_lab_notes.html
• "In the paper that we are currently writing, we will use links to the experiment pages in the wiki as formal references. We'll see if publishers will accept that."  Posted by: Jean-Claude Bradley | May 3, 2007 08:24 PM on http://blogs.nature.com/nautilus/2007/05/share_your_lab_notes.html
• "The document is made in latex (specifically pdflatex on a mac). I've posted a simple example electronic lab notebook in latex with the commands and functions that I frequently use. sample.tex is the main file; see this file to determine if you need to install any latex libraries. sample.pdf is the compiled document. If you don't know how to use latex, do a google search for The Not So Short Introduction to Latex."  [http://www.jeremiahfaith.com/open_notebook_science/]
  

• "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"  [Bradley JC, "Open Notebook Science" at Drexel COaS E-Learning 9/26/2006]
• "The wiki records details of experiments (effectively serving mainly as the group laboratory notebook) and the blog serves to highlight milestones and key problems.
  But the day to day interaction between the collaborators is lost in the email system that currently serves as our workhorse for getting things done.  This mailing list should help capture that process and everyone who is comfortable discussing in the open is welcome to contribute."  [http://usefulchem.blogspot.com/2007/07/usefulchem-mailing-list_04.html]
• "But now, as we move to the manipulation of tens of thousands (and soon to millions) of molecules, we need to transition to a true database."  [http://usefulchem.blogspot.com/2007/06/inchimatic-chemspider-and-usefulchem.html]
• "But there are some advantages to the wiki over the blog. Since every version of every page is archived, it is possible to view the evolution of the thesis over time. Also, as Alicia's supervisor, my comments are tracked - as well as her responses. One member of her thesis committee also agreed to provide feedback via the wiki."  ... "Another important feature of Alicia's thesis is that she linked back to experiment pages on UsefulChem, where all the raw data is housed. She was thus able to provide the ultimate citation to her own work as well as selected experiments from her co-workers to make a point, while being extremely clear about everyone's contribution.   For this reason, I think that wikis will be used increasingly as part of a scientist's porfolio to demonstrate special skills or writing ability. In our current system, all we know is that an individual was a co-author on a certain number of articles and we have to glean their contribution mainly from letters of recommendation. Wouldn't it have more impact for a potential employer to be shown the number and type of experiments done by an individual, the equipment they used and the observations they made?"  [http://usefulchem.blogspot.com/2007/06/thesis-on-wiki-interest.html]

Adoption:

• "Any change that requires adjustments to the way scientists go about their daily work meets with resistance and, for many researchers, lab notebooks are wrongly considered to be private property."  [Nature e-Notebook Editorial]
• "Academic acceptance of e-notebooks will not improve unless universities promote their use and recognize that e-notebooks can help them fulfil their responsibilities as the owners of most grant-funded data."  [Nature e-Notebook Editorial]
• "Institutions therefore need to show leadership in this area, and funding agencies should provide additional infrastructure support earmarked for the development and upkeep of electronic notebook systems"  [Nature e-Notebook Editorial]
• "Doing research in public, instead of in secret, is a new and somewhat unnerving idea for most scientists; early adopters like Jeremiah are essential to take the edge off that unfamiliarity."  http://www.sennoma.net/main/archives/2007/07/giving_open_notebook_science_a.php
• "In times of ever more limited funding and more and more competition, open science will not emerge. Researchers now have to fight not only for scientific results, but for their own livelihoods and that of their families.The more funding gets cut, the more it needs to be restricted on topics deemed important. More researchers will accumulate in such "hot areas", making them even more important. Nothing will be shared in such a situation, but instead you will see a rise in scientific misconduct"  [Bjorn comment at http://scienceblogs.com/clock/2007/05/open_notebook_science.php]

Opportunities

• "A good example of re-purposing is using some results and observations from a failed experiment in a way that was never intended by the original researcher. This just doesn't happen regularly in science because failed experiments are almost never included in publications."  [Bradley JC, "Open Notebook Science" at Drexel COaS E-Learning 9/26/2006]
• "It's also, to be honest, just plain fun to snoop around in someone else's lab notes! I was amused to note that Jeremiah talks to and about himself in his notebook, the same way I do -- "if I weren't so stupid I'd...", "next time load the control first, doofus", etc. I wonder if everyone does that?"  http://www.sennoma.net/main/archives/2007/07/giving_open_notebook_science_a.php
• "I think this is a good example of the integration of research and teaching. This is a real spectrum taken strictly for research then re-purposed for an educational objective. And because the data are open and indexed on popular search engines, this integration was possible between people who did not have a prior collaboration.  This also makes a really good case for the value of Open Notebook Science and the availability of raw NMR data in JCAMP format, especially using a browser-based viewer like JSpecView. This type of information (the full spectrum of a starting material) would likely not have been included in a traditional publication, even in the supplementary information section."  [http://usefulchem.blogspot.com/2007/07/spectral-deconvolution-with-usefulchem.html]

Overcoming issues:

• "aguy said "have their work "data mined" and cannibalised without acknowledgement."

  I think arXiv deals with this danger brilliantly. It puts an indelible time-stamp on EVERY version of the manuscript you submit. One can submit newer versions forever. By the same token, older versions cannot be removed; they remain accessible to the public forever.

  Posted by: rrtucci | Oct 30, 2006 9:34:40 AM"  [http://3quarksdaily.blogs.com/3quarksdaily/2006/10/the_future_of_s_1.html]

• "Secretiveness in a scientist is a disfigurement, to be sure, but it has its comic side; one of the most comically endearing traits of a young research worker is the illusion that everyone else is eager to hurry off to do his research before he can. In reality, his colleagues want to do their own research, not his. A scientist who is too cagey or suspicious to tell his colleagues anything will soon find that he himself learns nothing in return. G.F. Kettering, the well-known inventor (antiknock gasoline additives) and co-founder of General Motors, is said to have remarked that anyone who shuts his door keeps out more than he lets out. The agreed house rule of the little group of close colleagues I have always worked with has always been "Tell everyone everything you know"; and I don't know anyone who came to any harm by falling in with it.
  
  P.B. Medawar, Advice to a Young Scientist" via http://www.jeremiahfaith.com/open_notebook_science/
• "The ability to do science in a fully transparent and open format may be one of the most important functions of tenure at this time in scientific history."  [http://usefulchem.blogspot.com/2007/05/more-talk-on-open-notebooks.html]
• "With the idea of creating an infrastructure that can be quickly and cheaply duplicated by other researchers, UsefulChem uses free and hosted services like Blogger (blogs), Wikispaces (wikis), YouTube (video), Google Video (video) and ManyEyes (data visualization). However, funding is still needed to purchase chemicals, equipment and support students.
  
  One of the attractive features of funding Open Notebook Science is the built-in transparency of how resources are spent. Just like the rest of the world, a funding source has access to the daily work of the laboratory group and their collaborators and is free to provide feedback at any time."  [http://usefulchem.blogspot.com/2007/04/funding-usefulchem.html]
• "The experiment will consist in seeing which chemistry publishers will accept a paper written on a public wiki and the use of links to experiment pages on a laboratory notebook wiki as valid references. As I learned from a talk by one our librarians Jane Bryan a few weeks ago, publishers are really becoming tolerant of pre-prints hosted on institutional repositories. This is really not that different.
  
  Who knows - it might even work for an ACS journal. We'll see."  [http://usefulchem.blogspot.com/2007/04/wiki-paper-experiment-started.html]
• "One of the concerns expressed about Open Notebook Science is that scientists would not want their raw data available to others without their interpretations.
  
  I am used to dealing with questions of intellectual property rights, priority and impeding the ability to publish in prestigious journals. But the idea that it may be useless (or even perceived as irresponsible) to publish raw data without full analysis by the head scientist of a group is probably also an important barrier to the adoption of Open Notebook Science, or at least more open forms of science.
• When my group publishes experiments on UsefulChem, the general order is typically: the experimental plan, the log, the results as raw data, observations then conclusions. Error correction based on feedback occurs at all points in the process.
  
  So by default we almost always have much our raw data available without interpretation for long periods. And probably most of that information will never get interpreted (at least by us) because we don't need it to meet the narrow objectives of our experiments now or in the future.
  
  But it is essential for these raw data to be available openly to humans and automated agents if we want Science2.0 to explode. (The data also need to be tagged and formatted properly to truly leverage automation - but more on that later)
  
  The evolution of an experiment page is messy. Doing science is messy. There are errors to correct and faulty assumptions to confront and remove as we get more information and analyze an experiment.
  
  I think that learning about science almost exclusively through polished journal articles can be discouraging, especially to new students. Like attorneys, scientists tend to write papers (at least the good ones) with arguments using selective evidence to support a clear point. There is nothing wrong with this, and I think that humans need this type of format much of the time to process new information. However, this approach leaves a lot out about how science actually gets done.
  
  For example, if a chemist has developed a new reaction, the typical way to publish it is to try the reaction under different conditions and with different reactants. In principle this is very simple: do the reactions, fill in a table with yields then publish. In practice, at least in the organic chemistry labs where I have done my time, it does not work that way usually. Yields will vary between people and sometimes the reaction just won't work for a reason that never gets elucidated.
  
  So what is the actual yield that will be reported? The best one? The worst one? The average? If you use the average, do remove outliers? If some of the product was spilled, do you still take that yield into consideration or completely scrap that run?
  
  Every scientist who has written a paper has had to make a decision about what to do with the ambiguity of raw scientific information. And every day that the paper is not written and submitted because of ambiguity, the world doesn't know about it.
  
  When we report our raw laboratory logs and data, we are not concerned about a number that will show up in a table (eventually hopefully) in a printed journal. We are concerned about truthfully reporting what we did, observed and thought at that time. There is no carpet under which to sweep ambiguity. All scientists should be doing that in their laboratory notebook. By sharing it in real time the world can benefit immediately."    [http://usefulchem.blogspot.com/2007/03/npr-interview-on-open-notebook-science.html]
• "The typical issues came up: intellectual property, recognition, archiving and getting scooped."  [http://usefulchem.blogspot.com/2007/01/back-from-nc-science-blogging.html]

Current state

• "J-C: as you point out, examples with actual data are still few and far between, which is why I say Open Science is "in its infancy"."  comment by Bill at http://3quarksdaily.blogs.com/3quarksdaily/2006/11/the_future_of_s.html
  
• ""When I was using that term on general search engines to build up our own collection of examples (at the bottom of our main page), I was frustrated by the difficulty in finding links to actual data."  Posted by: Jean-Claude Bradley | Nov 27, 2006 6:20:18 AM at http://3quarksdaily.blogs.com/3quarksdaily/2006/11/the_future_of_s.html

Examples

• "I know it's possible because Jean-Claude Bradley is doing it; he calls it Open Notebook Science.  His lab's shared notebook is the UsefulChem wiki, which is supplemented by the UsefulChem blog for project discussion and the UsefulChem Molecules blog, a database of molecules related to their work. "  [Hooker B, "The Future of Science is Open, Part 3: An Open Science World" at 3quarksdaily 1/22/2007]
• "I know of a few blog posts in this category.  This and this from Bora Zivkovic are, I think, the first instances of original data on a blog. This series from Sandra Porter is earlier but involves bioinformatic analysis (that is, original experimentation, but no original data), as do this and this from Pedro Beltrao.  Egon Willighagen blogs working software/scripts for cheminformatics, and Rosie Redfield and her students blog hypotheses, thinking-out-loud and even data.  Blogs are also good for sharing protocols, like the syntheses posted by the anonymous proprietor of Org Prep Daily."  [Hooker B, "The Future of Science is Open, Part 3: An Open Science World" at 3quarksdaily 1/22/2007]
• "One of the things that Open Science advocates most sorely lack is concrete examples."  http://www.sennoma.net/main/archives/2007/07/giving_open_notebook_science_a.php
• "Jeremiah Faith, a Boston U graduate student in bioinformatics, has put his lab notes online"
• "The fact that Alicia’s masters thesis “Synthesis of Diketopiperazines, Possible Malaria Enoyl Reducatase Inhibitors Using Open Source Science” is being written on a wiki was noted by Pharyngula, A Blog around the Clock and Pimm - Partial Immortalization. I am particularly happy that Attila from Pimm has obtained permission from his supervisor to write at least part of his thesis on his blog. Outside of the sciences, I recall Mark Wagner doing something similar for his thesis on educational gaming. Also see Laura Blankenship’s thesis on blogging in the classroom"  [http://usefulchem.blogspot.com/2007/06/thesis-on-wiki-interest.html]
• "Jean-Claude Bradley calls his approach to electronic lab notes Open Notebook Science, and is already putting together his first fully-open paper. His lab's shared notbook is made up of the UsefulChem wiki and blog. " [comment by Bill Hooker at http://blogs.nature.com/nautilus/2007/05/share_your_lab_notes.html]
• "Shiva has created a wiki and blog:
  My Research Proposals at http://myresearchproposals.wikispaces.com/
  Totally Retrosynthetic at http://totallyretrosynthetic.blogspot.com/
  
  He tells me that he will continue to post his ideas there and, when he is in a position to do it, his research results. If he does, this is exactly what I had in mind when creating UsefulChem: a completely free and hosted model to carry out Open Science that can be replicated by anyone, anywhere, overnight."  [http://usefulchem.blogspot.com/2007/05/totally-retrosynthetic.html]

Relationship to Open Science

• "Anything less than this may still be a form of Open Science but is not ONS"  [Bradley JC, Comment on ResearchRemix 7/19/2007]
  
• "In a 2003 essay, Stephen Maurer noted that:  "Open science is variously defined, but tends to connote (a) full, frank, and timely publication of results, (b) absence of intellectual property restrictions, and (c) radically increased pre- and post-publication transparency of data, activities, and deliberations within research groups."  "

Relationship to Open Source Science and other terms.   Also contains some "historical context"
Additional information in "terms" section of Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007

• "In Open Source Software, the code is made available to anyone to modify and repurpose. What we have been trying to do with UsefulChem is to provide the analogous entity for chemical research, which is raw experimental data along with the researcher's interpretation in a format that anyone can easily re-analyze, re-interpret and re-purpose."  [Bradley JC, "Open Notebook Science" at Drexel COaS E-Learning 9/26/2006]
• "Unfortunately, in addition to the confusion with Open Source Software, others are using the term Open Source Science to mean discussions about pre-prints of regular journal articles."  [Bradley JC, "Open Notebook Science" at Drexel COaS E-Learning 9/26/2006] 
  
• "One thing that might be worth thinking about is the fact that Open Science is a term that excludes many projects in the humanities and social sciences. I think Open Research might be a good alternative. If you're interested check out http://en.wikipedia.org/wiki/Open_research

  All the best,
  Matthias

  Posted by: Matthias Röder | Jul 21, 2007 11:01:33 AM"  [Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]

• "When I was using that term on general search engines to build up our own collection of examples (at the bottom of our main page), I was frustrated by the difficulty in finding links to actual data. After all, by definition, there should be links to scientific data in the context of discussing Open Science or Open Source Science. Those were assumptions that I had to revise and led me to create the term Open Notebook Science to make those assumptions explicit."  Posted by: Jean-Claude Bradley | Nov 27, 2006 6:20:18 AM at http://3quarksdaily.blogs.com/3quarksdaily/2006/11/the_future_of_s.html
• "I think "Open Science" stands the best chance of becoming a useful "brand""  comment by Bill at [Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]
• "There have to be some boundaries - I think Open ScienceData (though crude) roughly delineates the area. There are aspects of Open Data (e.g. maps) which don't fit, but I suspect that we may need to draw the line.
  

  Posted by: Peter Murray-Rust | Nov 27, 2006 6:47:12 PM" at http://3quarksdaily.blogs.com/3quarksdaily/2006/11/the_future_of_s.html

• "the problem with "crude", that is, ugly or unwieldy, handles is that no one wants to grab them. Following on from some of your comments about Blue Obelisk, I think Open Science (viz. openness in science) could use a "banner" under which to rally troops. It seems to me that the way to get one is to find an appropriate (if perhaps not perfect) term that will stick in minds, and commandeer it. Look at the FS/OSS split; I have no dog in that fight, but I'd like to avoid a similar one between OS/OSScience/OD/whatever.

  Posted by: Bill | Nov 27, 2006 7:19:33 PM"  from http://3quarksdaily.blogs.com/3quarksdaily/2006/11/the_future_of_s.html

• "I think "Open Science" is the banner under which the various Open X clans might most profitably assemble.  It is punchy, fairly self-explanatory and does not carry any of the potential confusion with related movements in software that might plague "Open Source Science".  (Nor, for that matter, will it give rise to daft analogies about what exactly is science's "source code".)  Moreover, it seems a natural counterpart to the established term Open Access, and is apparently the term of choice for Science Commons/iCommons, which puts the considerable weight of the Creative Commons behind it. "  [Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]

Relationship to Open Standards:

• "In his introduction to the chemistry-focused Blue Obelisk (group? movement?), Peter Murray-Rust refers to Open Standards as "visible community mechanisms which act as agreed protocols for communicating information".   What he is talking about is metadata and a semantic web for science. "  [Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]
• "Examples abound: the Proteomics Standards Initiative, MIAPE, MIAME, Flow Cytometry Standards, SBML, CML, another CML, the Open Microscopy Environment and dozens of others. "[Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]
• "Science commons makes the point using the tumor suppressor TP53:[Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]

  There are 39,136 papers in PubMed on P53. There are almost 9,000 gene sequences [...] 3,800 protein sequences [and] 68,000 data sets available. This is just too much for any one human brain to comprehend."

Relationship to Open Data:
Great examples and history for sequence data, text mining, bibliometrics here: 

Hooker B, "The Future of Science is Open, Part 3: An Open Science World" at 3quarksdaily 1/22/2007

• "In the same way that Open Access accelerates the research cycle and facilitates collaboration, so too does Open Data -- and Open Standards is the infrastructure that makes it possible." [Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]

Relationship to Open Source:

• "Open science means that every step in the development process is open, where is many chemoinformatics programs are dumped into the open source sphere at the end. That is not the way it should be."  [Willighagen E.  "The Open Notebook 10 years ago" at chem-bla-ics 7/16/2007]

Relationship to Open Discourse:
Lots of info here:  http://3quarksdaily.blogs.com/3quarksdaily/2007/01/the_future_of_s.html


Licensing and Relationship to Open Licensing
See links at the bottom
Also see lengthy summary here http://3quarksdaily.blogs.com/3quarksdaily/2006/11/the_future_of_s.html

• "Open Licensing also provides a kind of infrastructure -- in this case, for dealing with intellectual property issues.  It's fine to simply put your product on the web and let the world do as it will, but many people prefer (or, depending on where they work, are legally required) to retain some control over what others do with their work.  In particular, if you are concerned with openness you may want to ensure that the original and all derivative works remain part of the commons (e.g. copyleft rather than copyright). That means reserving at least some rights, which is where licensing comes in. " ...   [Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007]
  

Open Notebook Science in Informatics and Computational fields

• "when I use the term Open Notebook Science I generally refer to physical experiments done in a laboratory. We try to do the same for completely electronic "experiments" (like docking) but it has proven to be difficult to do as well. This may be because it is much easier to run "experiments" than in a physical lab and a lot of tweaking happens quickly without formally going through an objective, procedure, results, discussion and conclusion. This may be why it works better to track using a mailing list."  Jean-Claude Bradley in comments at [Willighagen E.  "The Open Notebook 10 years ago" at chem-bla-ics 7/16/2007]
• In cheminformatics:  "what did the OSN look like almost ten years ago?
  
  It looked like the early open source chemoinformatics projects, such as CompChem and JMDraw set up by Christoph (the SourceForge projects have, unfortunately, been deleted; so I cannot link to the original project pages). JChemPaint and Jmol also originate from those years.
  
  These projects were OSNs avant le lettre: an experiment in chemoinformatics is the definition of a new (or reformulation of an old) algorithm, writing down the experiment (source code in this code), uploaded into a repository (Open Science!) for everyone to comment on, possible sent around an announcement for discussion to mailing list, and reporting the outcome (preferable in a peer-reviewed journal). While I am ranting^Wtalking about the issues, chemoinformatics is in the luxurious situation that reproducibility of a procedure is much easier, except for the missing data part.
  
  Just wanted to say that OSN is really nothing new, not to chemistry anyway. Maybe for lab chemists. Jean-Claude has shown to be very successful in promoting these open science ideas among lab chemists"  [Willighagen E.  "The Open Notebook 10 years ago" at chem-bla-ics 7/16/2007]
• "I think also BioPerl has started a long time ago in producing code in the open, not just a dump after development. Still, there is quite a difference from software development and knowledge discovery."  Pedro Beltrão in comments at [Willighagen E.  "The Open Notebook 10 years ago" at chem-bla-ics 7/16/2007]
• "Pedro, I agree that those working with computers have a clearer advantage of exchanging software and data; just look the the easy copying of music and movies. I do want to stress, though, that a lot of open science chemo-/bioinformatics is not true open science, and Jean-Claude is showing how this is done.
  
  The open notebook science is to me allowing others to look up all parameters settings and optimizations needed to reproduce what I did. I do not see much difference in what I am doing right now, as what I was doing when in synthetic organic chemistry. (Yes, I used to be a lab chemist myself.)" in comments by Egon Willighagen at [Willighagen E.  "The Open Notebook 10 years ago" at chem-bla-ics 7/16/2007]

Digging into an example
http://usefulchem.wikispaces.com/First+100+Targets
Has a todo list
A page that lists all experiments
A mailing list (readable by everyone)
A list of references
Paper drafts
Helpful snippets (isolated compounds)
Best practice reminders
Wiki, so can have discussions (need to create free login), see recent changes.  Content protected from edits.
A page that shows all recent changes to the site
A link to site hit statistics
Ads by Google
"Contributions to http://usefulchem.wikispaces.com are licensed under a Creative Commons Attribution Share-Alike 2.5 License.
Portions not contributed by visitors are Copyright 2007 Tangient LLC."
Entries contain some experiment writeups, script code, screenshots, links to excel sheets
Questions to themselves in bold
"The UsefulChem project was started in the summer of 2005 by Jean-Claude Bradley, associate professor of chemistry at Drexel University. Initially, the project consisted of a single blog, UsefulChem.blogspot.com, with the objective of carrying out chemistry research in areas that could benefit most from an Open Science model. In a process that was documented in the blog, the synthesis of anti-malarial compounds was identified as a worthwhile objective. Synthetic approaches were discussed and developed, and with new graduate and undergraduate students, lab work was started and recorded online from February 2006. Since then the project evolved to three graduate and three undergraduate students.

One of the graduate students is responsible for developing the automation components of the system. As often repeated by Peter Murray-Rust, a long time champion of Open Science in chemistry, cheminformatics still lags significantly behind bioinformatics, especially when comparing with the quantity and quality of open data in areas such as genomics. By representing molecules, reactions and results in a way that can be universally accessed and understood by machines as well as humans, there is great potential for accelerating progress in chemical research. This is especially true if "failed experiments" are routinely reported since they still provide valuable information to other researchers in designing their next experiments.

With the idea of creating an infrastructure that can be quickly and cheaply duplicated by other researchers, UsefulChem uses free and hosted services like Blogger (blogs), Wikispaces (wikis), YouTube (video), Google Video (video) and ManyEyes (data visualization). However, funding is still needed to purchase chemicals, equipment and support students. "  [http://usefulchem.blogspot.com/2007/04/funding-usefulchem.html]


Digging into another example

• Useful Chemistry blog:  "This is an open source science project in chemistry. Post specific problems in chemistry that need to be solved. Post specific partial solutions to these problems. Or execute a suggested step. NOTE: ANYTHING POSTED HERE IS SUBJECT TO A SHARE-ALIKE WITH ATTRIBUTION CREATIVE COMMONS LICENSE (see bottom of page for link)"  [http://usefulchem.blogspot.com/]
• Has list of contributors

And another example
Jeremiah Faith's lab notebook... downloading.

References

Bradley JC, Comment on ResearchRemix 7/19/2007

Bradley JC, "Open Notebook Science" at Drexel COaS E-Learning 9/26/2006

Hooker B, "The Future of Science is Open, Part 2: Open Science" at 3quarksdaily 11/27/2007

Hooker B, "The Future of Science is Open, Part 3: An Open Science World" at 3quarksdaily 1/22/2007

Willighagen E.  "The Open Notebook 10 years ago" at chem-bla-ics 7/16/2007

Nature e-Notebook Editorial 5/3/2007
Nature 447, 1-2 (3 May 2007) | doi:10.1038/447001b; Published online 2 May 2007



More resources for me to look into
Links at the bottom of this post:  http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html
All the open links in my browser!
JC Bradley Nature Precedings submission
http://wiki.nodalpoint.org/open_science

Here, as promised, a bunch of papers/articles for background on Open Licensing (warning, lots of pdfs, some subscription-only) from http://3quarksdaily.blogs.com/3quarksdaily/2006/11/the_future_of_s.html
Open Science: Open Source Licenses in Scientific Research
The Economic Logic of “Open Science” and the Balance between Private Property Rights and the Public Domain in Scientific Data and Information: A Primer
Commons-Based Strategies and the Problems of Patents
New Institutions for Doing Science: From Databases to Open Source Biology
The Science Commons in Life Science Research: Structure, Function, and Value of Access to Genetic Diversity.
Is Copyright undermining Biodiversity Research and Conservation?
Can ‘Open Science’ be Protected from the Evolving Regime of IPR Protections?
The Market Economy, and the Scientific Commons