Open Notebook Science
Introduction to Open Science
Open Notebook Science
Incentives for being an open notebook scientist
The Effect of ONS on Intellectual Property
Open Notebook Platforms
Maintaining a Useful Open Notebook
Can ONS Replace the Traditional Publication System?
The Future of Open Notebook Science
Open science is the philosophy that scientific information be made accessible broadly to all levels of society. It is an umbrella term for multiple approaches to the dissemination of scientific information and includes the practices of citizen science, science outreach and science blogging, open notebook science, open data sharing, and open access to scholarly work among other things.
Most of the open science push is a result of the push for open access to peer reviewed literature. As scientific journals began hosting literature on the web, access to the articles was more viable. Despite publication to the web being a relatively low cost outlet, subscription prices have increased steadily and above the rate of inflation.
For perspective my own website is maintained for $70 a year, but the cost for subscription for Science (digital content only) is $146 per person per year. Granted there are other costs associated with publication, but you can see that the cost per person per journal would add up to insurmountable funds for most individuals. Institutions do receive a “group” discount, but ultimately not every university can afford to subscribe to every journal.
Because of this issue, open access journals have become more prevalent. Publishers like PLoS put the burden of publication cost on scientists who wish to publish with the platform. But even this mechanism has it’s drawbacks, as the cost per paper is costly. To combat this, even newer publishers like PeerJ, have simplified the costing and charged authors a low subscription to publish fee that is good for life.
As open access publication has gained steam, so have other open scientific endeavors. To supplement open access to publications, open access data and video repositories have emerged to give anyone access to hard scientific information. For example, figshare is an open data repository that gives scientists a permanent DOI (digital object identifier) and the ability for their shared data to be cited. On the other hand, BenchFly, a digital video repository much like YouTube, allows scientists to document their methods and provide open access to those protocols.
Other endeavors take open science to a new level. Citizen science projects allow anyone to partake in the scientific process. Galaxy Zoo allows anyone on the planet with a connection to the web to categorize objects photographed via the Sloan Digital Sky Survey. While various ecological projects like NestWatch, allow amateur and professional bird watchers to collect data on bird nesting habits and submit it to a database for analysis. Many of these endeavors have led to startling discoveries and contributed peer reviewed work.
Even scientific outreach has pushed the boundaries of open science. The emergence of science blogs and scientific blogging has helped expand science literacy of the public. Many blogs are maintained by real scientists reporting on either their own research, or digesting the research of peers. Several endeavors have emerged to bring more scientists into the mix. The #SciFund Challenge was developed as a crowdfunding opportunity to encourage researchers to share their science in hopes of attracting donors to contribute to their projects (See Appendix X).
It is very apparent that open science is still developing conceptually and in practice, and can grow to encompass much more. While I have been a part, in some way, with many of the programs mentioned above, I have mainly focused my efforts on the development of open notebook science (ONS) and ONS policy and philosophy. Ideally, open notebook science can act as a transition between a lot of these open science endeavors, and can even bridge traditional science with open science practices.
Open notebook science is simply the practice of making your entire research project available online as it is recorded. This online location is known as an open notebook and is the online analog to the paper notebook most scientists keep in their lab. It is the storage center for project plans, experimental protocols and setups, raw data, and even unfiltered interpretations. An open notebook can be any kind of website, as long as it suits the needs of the scientist and is available publicly (for useful notebook platforms see section XX)
Open notebook science was first coined in 2006 by Jean-Claude Bradley (Drexel University), to clarify a subdivision of open science (which at the time was known as open source science) and to avoid confusion with the term open sourced software. The term itself is an umbrella for several types of notebooks that are classified by publication time, from immediate to delayed posting, and content, ranging from all research content to some content.
Ideally, every scientist would maintain an open notebook in real-time which would encompass all aspects of their research. But many fears about dealing with complete open access, conflicts with intellectual property and publications, and online data overload hamper this movement. To combat this, practitioners encourage any form of open notebook science, even if that means uploading some information for a project from many years ago that never saw the light of day.
The goal of this practice is to enhance the scientific process. Through open notebooks, scientists would no longer need to repeat experimental errors made by colleagues. Access to raw data and published analyzed data would be provided. There would be no need to search through old handwritten notes from past lab members or past projects.
The benefits of ONS are numerous, not just personally but professionally as well. What’s more, many of the fears and drawbacks are actually misconceptions and don’t interfere with traditional scientific culture. In the coming sections, I will detail the incentives for open notebook science, discuss the role of intellectual property, present useful platforms, and describe the principles of keeping an open notebook. I will also present a thought experiment for using ONS as a potential replacement for current publication practices. Finally I will describe the future progression of open notebook science.
The scientific culture has become an incentivized one. Grant money is frequently awarded to scientists who have the most clout, the highest number of publications, and the publications with the highest impact and citations. Future career positions are also based on these numbers. So it makes sense that good work receives good rewards.
Unfortunately, it is a common misconception that open research is a system where academic creativity and labor are simply given away with no reward. Given the state of the traditional system, the rewards for practicing ONS seem low. However, there are plenty of tools in development that provide incentive to practicing scientists. Not only is there professional recognition opportunities, but there are many personal incentives for maintaining an open notebook.
Open notebook science can enhance your academic prowess through two main mechanisms: (1) experimental errors, shortcuts, and falsification will be reduced and (2) personal research efficiency will increase.
The best open notebook platforms (section XX) have features that allow easy organization and searching mechanisms. Maintaining a well organized notebook is a essential to any research project for future lab members and for personal development and reference. By keeping an electronic record, the time to maintain the notebook, and reference past projects and experiments is minimized. As the technology improves, many of these processes can be automated further widening the gap between the capabilities of electronic and open notebooks over traditional paper notebooks.
By maintaining an open record, the scientific process becomes transparent. Mistakes made in the lab become costly to the scientific reputation of the experimenter. If the error persists through publication, the chance for the flaw to be discovered is increased, and publication retraction may be required. Through open notebook science, experimental errors may be noticed sooner in the research process, not just by the experimenter, but by other lab members, collaborators, and other researchers independent of the lab.
Scientists may also feel immediate pressure from online exposure. This pressure could limit mistakes in the lab, which may be brought on by shortcuts in the experiment procedure, data acquisition, and analysis. The psychological effects of having to share protocols and results in full detail and in real-time could prevent shortcuts from having a negative effect on the research. To add to this, inconsistencies in the experiment (caused by non-thorough reporting) could be discovered, impacting the reputation of the lab and the experimenter.
Ultimately publishing openly in real time, forces an examiner to be careful, thorough, and explicit. Any errors made in an experiment could be remedied immediately, instead of down the line. Immediate fixes will have much less impact on a research project, which will save a research time, the lab money, and everyone some humility. No one will be able to question the integrity of the research, because the entire record will be available to anyone.
Open notebook science can increase the efficiency of all scientific research in a manner similar to the enhancement of the individual scientist. In this sense, the scale of benefit is much larger and can impact entire fields of science in addition to individuals and groups.
As experiments are peer reviewed and published, colleagues can follow the work of their peers through literature updates. Unfortunately, the peer review process can be time consuming and preeminent work could be delayed because of a variety of processes. ONS could provide an immediate workaround for the time delay of the peer review process. As research is published in real-time, or as near real-time as possible, colleagues could stay up-to-date with the latest research. Science would be operating at the forefront of thought instead of lagging behind.
Additionally, experimental procedure would benefit. As all research is published, experimenters would have access to detailed protocols, both failed and operational. This would decrease the time to start an experiment or even repeat an experiment from another lab. In the case of repeatability, the time to ensure the viability of an experiment would be dramatically decreased. No longer would an experiment be subject to interpretational error.
In addition to providing scientific methods, raw data could be used and reused in ways that were previously impossible. The internet is a huge loosely connected network of information, and can be at times disconnected. Tools have emerged and will continue to develop to make sense of all the new data being created daily. Tools like Dryad and DataOne provide data hosting, archiving, and searching (among other tools) to connect scientists from around the world to data from taken in distant locations. By providing access to data, new discoveries can be made that are only possible via electronic methods. For example, Google scientists partnered with the Center for Disease control to show that influenza outbreaks could be detected through local search queries.
Previously it is mentioned that the publication process is time consuming, but this isn’t to say that open notebook science would replace the peer review publication model (but I’ll discuss how that could be possible in section xx). Instead, I would argue that it could greatly supplement it. Open notebook science could hypothetically result in a data deluge (not unlike the current internet system). Scientists may feel overwhelmed with having to read every protocol or data set created by every lab they wish to follow. In this scenario, the current methods would be more than suitable. However, having access to the open notebook account of the experiments documented in a publication would provide deeper insight into the experimental record.
Open notebook science can provide new measures to a scientific career. Traditionally, a scientific career is evaluated based on several criteria: (1) grant awards, (2) peer reviewed publications, and (3) citations. When evaluating scientific merit, the number of publications and citations play the largest role.
As data becomes more accessible, and thus usable, there has arisen a need for the data to be credited. As such, many tools have emerged that allow scientists to organize, use, and reuse data and be credited for sharing data and to credit others for using data. Many of these tools have been developed specifically for scientific use (see figshare and ImpactStory).
While there are tools specifically designed to provide alternative metric analysis (altmetrics) of scientific data, many traditional web analysis tools can also be useful and are freely available. Web analytics software, for instance, can track user information for visitors to an open notebook. The value of an open notebook can be measured by analysing the pages that are most frequently visited, the duration of the visit, and where the visit led (to another post in the experiment perhaps).
Many website commenting systems like Disqus, provide link tracking capabilities (linkback counting) and social media propagation. Mostly, the purpose is to aggregate the entire conversation relating to a post in one location. This can, however, serve a dual purpose and provide an alternative take on the traditional meaning for citations. Standard web etiquette is such that users can directly link to other websites instead of through a traditional citation, as a means of providing credit for work and for pointing users directly to a source. This same practice exists in social media because of various limits imposed on users. While counting linkbacks isn’t meant to supplant citation merits, it could be used to provide a more complete account of scientific documentation and use.
Providing full, real-time access to research can have many benefits for the scientific community as a whole. Aside from the measurable impacts listed previously, there can be many more unknown benefits. Personally speaking, I’ve had several career milestones because of an online random encounter. I’ve made many personal and career network connections because my research is openly accessible. As such, it is my personal opinion that research should be made available, simply because one can never know what good may come because of the availability of information.
One of the biggest arguments I hear against open research is the fear about not being able to protect your intellectual property, also known as the fear of being scooped. The biggest oversight in that argument is that IP violations occur in traditional scientific culture both accidentally and maliciously. In an open environment, however, there is a greater risk of attracting this behavior if only because scientific research is made publicly available. With that said, there is nothing about being open that is any more inviting of harmful activity than in the traditional system. In fact, because of the current US legal system, being open may be more beneficial to protecting scientific information.
With regards to the US legal system, there are two primary protections available to scientists: (1) copyright law would protect recorded scientific information, for example data and ideas, while (2) patent law would protect scientific processes, production, procedures, etc.
Despite what is commonly believed, in no way does open notebook science prevent either protection from applying to scientific intellectual property. Open notebook science can actually stake your claim on IP and provide immediate protection. For patent law, patent protection is granted for one year once a work is publicly disclosed. If a patent is not filed, the IP becomes public domain and a patent can never be filed. In the case of copyright law, copyright applies from the moment of fixation (the moment scientific information is documented). In both cases, open notebook science can be used either as a defensive tactic to protect IP, or as an offensive tactic to prevent others from profiting from scientific IP.
Note: The contained information pertains strictly to the US legal system, and is based on information I alone researched. I am in no way a lawyer and offer no legal advice, but thought it would be foolish to not share basic copyright and patent law policy for scientific consideration.
Copyright law is essentially very simple, and has been made increasingly simple since it was originally expanded upon in the US Constitution. The most recent addendum to this statute came about in the 1976 Copyright Act, which defined rights to copyright holders (exclusive rights), how copyright is achieved, and even what does/does not constitute infringement (fair use).
While the law is simple in principle, copyright infringement is not necessarily black and white. In some instances it is questionable as to what is even copyrightable. In others, the matter of fair use is debatable. Even when there is infringement, it can be tough to prove because there are varying degrees of copying or "borrowing."
The bare-essential rules of copyright law can be seen in Table XX :
For a more thorough understanding of copyright law, please refer to my notebook entry on copyright law.
Rule 2 from table XX may reveal that copyright law doesn’t apply to most of science intellectual property, because it is fact based and process driven. Patent law was developed for this very reason. While there are no statutes against having dual protection in the form of patents and copyrights, it is not likely to receive copyright protection if there is patent protection since the copyright lasts much longer than the patent. But that's not to say none of science is copyrightable.
In fact, journal articles are in fact copyrighted. It can be interpreted that there is creative expression in organizing scientific discoveries (which are fact based) and that would make them copyrightable. Journals hold the copyrights for publications and have exclusive right to copy and distribute the articles any any material contained within. And there are cases where they've tried to enforce it.
In that link, the author tries to distribute (via publishing in her blog) figures from a publication and receives a cease and desist letter. Unfortunately it will never be known if there was a violation because the infringement never went to trial. She made an argument for fair use, which probably has some grounds, but skirted around the issue by recreating the figures using the original data (which is NOT copyrightable), thus making her own original figures which are therefore copyrightable. There is a chance that she has no fair use argument since her reuse (even through attribution) is a clear violation of distribution rights and can be viewed as falling within the same scope of the original publication.
In the case of publications, scientists waive their copyright upon submission and acceptance for publication and dissemination, and grant that copyright to the journal. Not all scientific output is formatted for publication, or released at all. In that case, it would greatly benefit scientists to publish their figures via an open notebook to provide copyright protection for their research (if that is in fact the goal).
With regards to the traditional science system, scientists are offered protection from the moment they record their data and create figures based on that data. They are even protected at conferences where they present their research (either via an oral or poster format). This is specifically useful in the case of scientific scooping, which isn't as rampant as we make it out to be but is still a major fear in the community. If there is a case of potential copyright infringement, you have the right to file suit (once you apply for copyright). If you can prove there was access to your research findings and there is substantial copying you may even win your case.
If you are an open scientist, in that you publish your research findings online before peer reviewed publication, you may be in an even better position. You are granted the same rights as a traditional scientist. In the open case, however, the proof of access is much easier to prove since a simple Google search can turn up your findings. The burden is then that you prove there is evidence of copying, which is hard enough as it is.
Because of all the possible interpretations of copyright application to science, I highly advocate the use of the Creative Commons licenses. The CC0 (public domain), CC-BY (use with attribution), and CC-BY-SA (use with attribution and share alike) afford the copyright owner the ability to share their research findings with the community and in turn allow the community to share, use, and reuse those findings without fear of retaliation. It is incredibly important to note that using the CC licenses (with the exception of the CC0) does NOT waive all exclusive rights as a copyright holder. They allow you to waive your rights as long as the reuser of the original work attributes, shares, etc (per terms of the license) in turn. If those stipulations are infringed, you are free to take action. In fact, there is legal precedence of such action.
The licenses provide a means for others to use information and data without worrying about moral ambiguities, legal issues, and in turn promote a culture of sharing and attribution. With the CC licenses there will be more societal pressure to do the right thing. When credibility is involved social pressure can work wonders.
For more information, please refer to the US Copyright Office website.
The America Invents Act was initiated in 2011 and institutes some new changes to patent law. The newest inclusion to the law is that now patents are given based on a first-to-file system, whereas previously they were given through a first-to-invent system. This change was implemented on March 16, 2013 as a way to conform to international policy, but also to decrease the burden of the US Patent Office in identifying first-inventor which can be extremely complicated and arduous.
In a first-to-file system, a patent will be granted to the first person to file a patent for a given invention. While the system is as simple as it sounds, it tends to give advantages to larger entities with the resources and efficiency to file patents for every invention conceived. It is outside the scope of this writing to argue the merits of a first-to-file or first-to-invent system, but this is mentioned because there are a couple of workarounds to the first-to-file mandate. The first is through the filing of a provisional application, and the second is through public disclosure. In both cases, there is a one-year grace period under which a patent must be filed lest it become public domain.
The provisional application is a low cost option that grants an inventor protection from competitive patent filings. The fee is $125 for small entity inventors, such as individuals, and $250 for large entities like corporations. The intellectual property remains a secret during the provisional period until patent. Public disclosure is a free alternative to the provisional patent, in the sense that there is nothing to file with the patent office. With this method, the details of an invention becomes public information, but no competitor may file a patent.
Scientifically speaking, patentable items include processes, designs, and technology of all sort (although computer programs are hard to patent or copyright). It is usually advantageous to maintain secrecy when dealing with intellectual property, and this culture is especially prevalent in science. As such many universities and institutions have legal services that aid scientists in patent filings. In an effort to maintain confidentiality, it is highly suggested by these services to file provisional applications for all inventions.
Much like copyright, the ultimate goal of a patent is to prevent competitors from stealing and reproducing a work without the inventor benefitting. It is little known fact that patents become public information after filing, generally 18 months after the earliest filing date. It is entirely possible for competitors to analyze a patent and create a “non-obvious”derivation of the work that can then be patented. In this scenario the benefit of the patent application is essentially lost.
Open notebook science can be a major benefit to the new patent process. Since it does cost money to file a provisional application, ONS (or other web disclosure) would provide a free alternative to the provisional application. The only difference between the two routes is that through ONS, the patent is immediately public information, while the provisional application maintains invention secrecy. Because the patent will eventually be public domain, the incentive to innovate is delayed a bit through the provisional process.
While ONS publicly discloses a scientific creation and encourages potential modification, it does not promote/encourage stealing the idea. Scientists are still protected from patent infringement. Now, if a competitor sees the notebook entries and makes non-obvious changes to the idea, then they can be granted a new patent, if filed. That is no different from how the patent process currently operates, it simply speeds up the process.
Filing a provision for every idea ever produced and paying $125 every time is a waste of money and resources. It is highly unlikely that every idea/invention will come to fruition. It also gives the US patent office a lot of unnecessary paperwork, and could actually stifle innovation and creativity. ONS would in turn allow a researcher to disseminate their ideas and protect the best ones for the original creator. Resources could be better used to fight for the best ideas and allow others to develop the ideas that won’t necessarily get the same level of attention or ever be produced.
In this way ONS could be used as a defensive tactic to protect a scientist from losing his/her best ideas. It is also possible for open notebook science to be used as an offensive tactic. In this maneuver, the documentation of ideas born from discussions or other endeavors creates prior art (which is essentially the same as public disclosure). An invention disclosed in prior art is exempt from patent protection. So in the case of public disclosure via ONS inventions would be blocked from filing for patent. Hypothetically, a researcher could publish any and all ideas, techniques, or technologies and prevent all competitors (and peers) from filing for patent.
In the interest of sharing research information, open notebook science may be the best protection against impediments in the scientific process.
The open notebook should ideally be the online representation of a standard lab notebook. Everyone has a different style, need, storage requirement and ultimately the open notebook should reflect this. To make all scientists adapt to one tool makes very little sense and would be a major discouragement to open notebook science. Software engineers take notes in their code, biologists need to take pictures, and mathematicians need any medium that can contain pages of equations.
There are a wide variety of electronic note taking applications available for consumer use both paid and free to use. In particular, I’ve discovered many applications that weren’t designed as electronic notebook platforms, but serve that purpose well. These platforms also have the distinction of being freely available tools and, in some cases, are products of the open source community. The platforms described here have the capability of being the most widely accepted and useful applications. As technology changes, I expect many new and useful tools to emerge and eventually supplant these platforms.
Originally developed as a blogging platform, Wordpress has become much more than that. It is the go to Content Management System (CMS) in web design and is used for online shopping, blogs, artistic portfolios, personal websites, and even open notebooks. Personally speaking, Wordpress is the most versatile platform for open notebooks and should be the model that open notebook scientists look toward.
Wordpress has a very intuitive interface both on the front- and backend. Creating new content requires a couple mouse clicks and the ability to type. The tagging/categorization system keeps your notebook organized and allows for easy navigation. Posts are automatically organized reverse chronologically (like a blog). And editing posts is very easy with several options for bulk editing, saving drafts, revision histories, scheduled publishing, and much more. There is even the capability of creating static pages, where content is sparsely altered (think “About” pages on websites).
As a CMS you can upload images and videos quite easily, but unfortunately you won’t be able to upload all file types (.pdf, .doc, etc) without messing with the website architecture. There is a lot of support from Automattic (makers of Wordpress), and the community of third-party developers is huge with an impressive array of free plug-ins and themes that enable you to tailor the platform to meet your needs. And the comment system allows you to create a community centered around your research, ideal for collaboration,project planning, and even real-time peer review..
Unfortunately many of the features and plug-ins are limited to those who self host (have their own website), but even using a Wordpress.com site has a decent amount of features and is ideal for those who want to get started in open notebook science, have limited technological prowess, or want something that works immediately.
IheartAnthony’s Research is a self-hosted Wordpress blog.
Almost everyone is familiar with MediaWiki because it is the backbone of Wikipedia. It is an open sourced application that is free to download and install on any public/private server. There are even some websites that allow users to register and begin using their customized version for use. OpenWetWare.org is one such site that is built around sharing scientific research and even has an open notebook setup tool.
With MediaWiki, the possibilities are endless. You can do nearly anything you want: create pages, categories, upload just about any file you want, and so much more. One of the largest advantages of MediaWiki over other platforms is that versioning is very intuitive. The revision history of pages is specially marked on every created page by default and allows visitors to see changes to any page.
However, most of these capabilities require at least a basic knowledge of HTML/CSS and some basic web scripting/coding may be necessary. There are plenty of sites that have tutorials and getting started won’t take very long, but the initial learning curve is a bit more than Wordpress, for instance. Other drawbacks include lack of automated organization or navigation features, which makes finding old notes very difficult. There are several capabilities within MediaWiki that can make this a little easier.
My original open notebook is hosted on the OpenWetWare.org wiki.
Open sourced software developers primarily use GitHub. It is a code repository that makes parallel code editing simple and is probably the most comprehensive tool for sharing and distributing code. It even has social media capabilities built into the site, which makes collaboration incredibly simple.
While not intended to be an open notebook platform, it has several features that make it perfect for the practice. It is possible to upload any file to the repository either online or directly from the command prompt of your PC/Mac. Collaborators and even strangers can copy your code/files and edit them as they see fit without affecting your version. If you allow it, those same collaborators can contribute back to your work directly by combining their work with yours. These features are built into the site structure, so GitHub does this all seamlessly.
GitHub even has a wiki associated with each individual repository, which makes it especially useful for open notebook science. Even if you aren’t a software developer, the use of the wiki combined with the ability to upload any file to your repository allows for a very powerful and dynamic notebook. It doesn’t have many of the features available in MediaWiki, but that doesn’t make it any less useful.
The social media-like capabilities allow you to follow other repositories, comment, contribute, share, etc. Other site architecture adds the support of a blog-like platform within GitHub. This capability isn’t all that user-friendly, but has the potential to make GitHub even more robust and attractive as an ONS platform. While GitHub is a very powerful technology, many of its drawbacks are of the user-friendly sort. Since it was developed with software developers in mind, less tech savvy users may become frustrated with the site interface.
Physics Junior Lab 308-L (Spring 2012) open notebooks, software, and labs are hosted on GitHub. For more information see Appendix XX
Google Drive is a cloud-based office package similar to the Microsoft Office suite of tools. It provides word processing, spreadsheet creation, presentation development, online form hosting, and even a drawing tool. In fact, this document was created in Google Drive. Drive “documents” support basic text formatting, some html, and can host images in-line in documents. Recently, Drive has added the functionality of full file hosting capabilities, similar to Dropbox. It can even convert .pdf and MS Office files into Drive documents for editing.
Google Drive is one of the best and easiest ways to collaborate on the web. Drive allows users to share documents with collaborators for viewing and editing. The most impressive feature is simultaneous editing. Users can interact through inline commenting, or through a chat window within the document. The collaboration features are perfect for joint publication creation, review, and editing. Potentially, it has the power to provide real-time in-document peer review capabilities.
Documents are private by default, but making them public is a simple process. Documents can even be embedded in other websites, for enhanced functionality. The organizational features of Drive work much like the file system in PC or Mac environments. Folders within Drive can even have public sharing or collaborator specific sharing. Any documents placed within shared folders are automatically given the same attributes as the parent folder.
Drive office tools are limited in fuctionality beyond collaboration, publication, and basic editing capabilities. Many features available in other notebook platforms are unavailable in Drive, but it does serve a useful purpose. It even provides a revision history that tracks changes and can revert documents to past states.
Many protocols in this publication are hosted publicly in Google Drive.
Evernote was designed as a private notebook type of service. It has just about everything you’d want in a notebook except that the upload features are limited to just pictures and videos. You can organize work in notebooks, and updating a notebook creates a new note. There are tools for smartphones and computers that allow you to work without needing to be on a web browser, and using the system is pretty straight forward since it was developed for the general public. It also has optical character recognition capabilities so images of handwritten words or pdf documents are scoured for text allowing all documents to be searchable within the platform.
By default your notes are private, so if you don’t like the idea of being open this may be the tool for you. There is the option to make your notes public, but the mechanism isn’t all the intuitive and public notes may not be search indexed (which makes it hard for others to find your useful protocols).
There are too many tools on the internet to for any one person to keep track of, but if another mechanism is desired, here are some useful and still freely available tools:
The most important aspect of open notebook science is to find a tool quickly that suits most of your needs. Many of the platforms can be supplemented using other tools that have embed capabilities. IheartAnthony’s Research is a notebook that incorporates Google Drive, SlideShare, Scribd, Google Maps, Youtube, BenchFly, figshare, Mindmeister, and others into the Wordpress structure.
The most approachable platform may be Wordpress since it is very intuitive, has a low learning curve, is very robust, incorporates plug-ins and a variety of themes for customization, features a strong and large user and developer base, and is easy to organize and search. For any scientist wishing to get started in ONS, Wordpress is the place to begin.
An open notebook is supposed to enhance the workflow of the researcher maintaining the record and provide the complete record of an experiment for others to follow and verify. Ideally, an open notebook would read like a well run blog: updated regularly, easy to follow, and contain a focused theme. Presented here are some aspects of open notebook science that should be kept in mind while notebooking.
Section XX contains a list of the most versatile web platforms that would make a powerful open notebook. It is erroneous to believe that any single technology will be self-contained and supporting system. My notebook contains a lot of supplemental information stored on different web platforms like Google Drive, figshare, SlideShare, and BenchFly for example. As such, the open notebook needs to be a versatile platform capable of changing functions as research needs arise. While it is difficult to predict what future needs will arise, ensure the ONS platform can be as flexible as possible. It is frustrating and time consuming to have to switch notebook platforms, start from scratch, reorganize, and potentially learn a new technology or at least become familiar with a new workflow.
Keeping an open/electronic notebook shouldn’t be time consuming, but don’t expect it to not require any time and attention. Most scientists keep a paper notebook with them in the lab and should maintain a detailed record of their experiments. No one ever complains about the time commitment involved in that. The issue is that potential open notebook scientists feel the need to maintain the open notebook in addition to the traditional paper notebook. A lot of time can be saved by developing a new workflow to be completely electronic, or as electronic as possible. Carry a laptop, tablet, or smartphone around and keep real-time notes via those mechanisms. Get used to documenting in the open notebook immediately, while the information is still sharp. It is imperative to do whatever is necessary to minimize the time spent maintaining a notebook, just keep it complete, readable, and up to date.
The most important feature of an open notebook is accessibility. The notebook must be accessible to the primary scientist (the one maintaining the record) and secondly should be accessible to others. This means that you should be able to access the information whenever and wherever you are so make sure you have a reliable hosting service. Accessibility is more than just being able to log onto a computer with internet. There is also the responsibility to ensure the information is easy to find as well. For this you will need to maintain an organized notebook and enable search indexing.
Most web platforms have an internal search feature, but the search feature is never as good as companies that focus strictly on search (see Google). By ensuring the notebook is search engine indexed you will help yourself and others in the long run. Personally speaking, I use Google to search my own notebook more frequently than I use my own notebook’s search feature.
Organizing a notebook goes hand in hand with searching. If a notebook is unorganized then it will be difficult to access important information. Platforms that support the tagging or categorization of notebook entries help a lot, and ones that list posts chronologically can help even more (blogging platforms). Organization is not strictly self-serving.
In web design, studies show that visitors will leave a site if relevant information is not found within a few seconds. The purpose of open notebook science is to provide relevant information to visitors. The goal is to get visitors to surf the notebook because it contains valuable scientific information that can increase the speed and efficiency of their research. If visitors cannot access that information, they will leave and the notebook will have failed its purpose.
Organization, and search indexing are not the only means to accessibility. The open notebook needs to be thorough and contain all information that goes into an experiment or project. Writing in shorthand may save a little time and effort, but in the long run it won’t serve anyone. Make sure that everything is documented as best as possible. The time required isn’t much longer, and it will turn out that time is saved later because the notebook is thoroughly organized and complete.
The ability to document audience engagement in real-time as experiments are undertaken is the edge that open notebook science has over all other forms of scientific communication. Make sure the platform you choose has the ability to converse with others. Wikis have talk pages, blogs have commenting systems, and if notes are published via social media, the mechanisms for communication are native. Having access to criticism, support, questions, and comments in real-time can tremendously improve research. It’s not enough to provide access to conversation, you also need to actually engage in conversation. If there is no response to communiques, then there is no incentive for the community to participate.
Scientists sacrifice time and repsonsibility to peer review an article in consideration for publication. They do this without financial compensation, and they do this anonymously. Publishers receive free labor during the most time consuming step of the publication process. With the low cost of electronic publication (and in some cases free), what exactly are universities, scientists, and the public paying for? This isn’t to say there are no costs for journals to cover, because there are. This is merely an argument to suggest that if scientists can freely and easily publish and disseminate their research, then what purpose do journals serve?
In order to publish via traditional methods one needs: (1) a publishing platform, (2) peer reviewers, and (3) a distribution mechanism. In an ideal system, there would also be some sort of formatting process and a copy editor to check the article for style, theme, and voice.
For the purposes of this discussion, the open notebook shall serve as the publication platform. All components necessary for simple publication are contained in many open notebook platforms. The ONS software makes the article accessible by publishing to the web and providing access to web crawlers for search engine indexing. It also archives the document for the lifetime of the website. In this regard, publishers are more likely to stand the test of time, but technology like Google Drive and Wordpress.com sites are equally likely to survive.
The distribution mechanism for open notebooks is essentially the same for publishers as it is for individual scientists. Since print material is not the goal, subscribers are not necessary. In this case, social media distribution is sufficient. The intended audience will likely be competitors, collaborators, colleagues, and others in the field. Most likely this audience is already following the research being reported and will be notified of the publication immediately. Occasionally someone outside the field will be interested in the published topic, and will come across the work by chance.
It is the peer review process that presents a challenge. As previously mentioned, scientists donate their time to review an article. The purpose of a publisher in this case is merely to connect an article with reviewers. It is in this step that publishers fail. Too frequently reviews are submitted that offer no feedback, are not thorough, or outside the scope of the purpose of peer review. The issue here is that reviewers are provided anonymity, which acts as a courage boost to reply with any comment. If this is the nature of feedback that scientists are pursuing, then there is no reason this cannot be attained through their own channels.
Using the commenting system of any notebook platform, allows researchers to receive valuable feedback and show credibility for the work. By sharing criticisms publically (whether anonymously or identified, but preferably identified), readers can be assured that the work has been reviewed and is considered valid research. The most difficult aspect of this part of the publication process is to find willing reviewers and to get them to agree to public review.
Finding peer reviewers could be as simple as sending out a request through the writer’s social network, online communities in the field of research, or even personal colleagues. Once three to five willing reviewers are identified, some ground rules should be detailed. The review process should be performed in a timely manner; feedback can be positive or negative as long as it is constructive; feedback should be complete. The review should also be judged on the scientific credibility and is not to be judged on potential impact or political factors. If these simple rules can be followed, there is no reason that anyone would need to post anonymously.
Once reviews are posted, feedback is accepted, and edits are made (or the process begins again) the article can be published in it’s new final form to the web. If the peer review process is linked to the final article, there is no reason to discount the credibility of the publication. To go the extra mile, the authors may request acceptance into Google Scholar, PubMed, or other scholarly search engine.
The point of the peer review process is to disseminate credible scientific information, but currently this is not the case. It is time consuming, costly, and overly complicated. Worse is that some peer reviewers aren’t held accountable for poor feedback. Through open notebook science, authors may be able to circumvent the issues surrounding the flaws in the publication process. They may even promote a faster publication system that provides high integrity research and credibility.
There are a lot of potential directions to pursue in open notebook science. The biggest need is an educational system built around open science initiatives and the use of open notebook science as a research practice.
I co-wrote an NSF grant for an Integrative Graduate Education and Research Traineeship (IGERT) program that was centered around open science initiatives and the data management needs of that system. The grant was written collaboratively in Google Drive and made publicly available. It was also highly supported by the open science community with featured support from figshare, BenchFly, and PLoS among other institutions. Unfortunately the grant was declined.
Recently I was introduced to a Creative Commons endeavor to create online courses for open research education. I am currently working with that program to develop educational resources for pursuing open research and providing open access.
The community efforts of open science and open notebook science are the most important aspects for changing the scientific culture. In order to enhance the sense of community, an open notebook network needs to be created and maintained. Initially the community of open notebook practitioners was small and most scientists knew each other. The community grows every day, and having access to scientists in specific fields of research is becoming increasingly important.
In order to keep that community growing, it is imperative to share all of the benefits of open notebook science. As such, a location to share ONS success stories should be curated. Once contributors are obtained, this curation is relatively simple. Many online forums are self maintained by community members and it should be no different for open scientists. In fact many open science endeavors are self-curated, as is typical in the open science community.
Overall, the best mechanism to spread open notebook science is through the practice of open notebook science. Ideally, an entire record of every research project that every scientist is a part of should be documented and provided. However, it isn’t necessary to follow that path. In order to complete the paradigm shift, small measures must be taken coinciding with the large ones. I have chosen to share all of my research in real-time to demonstrate the complete and ideal model of open notebook science.
Any researcher can select a few aspects of their research to share. As they become more comfortable with the system, they can select more to share. In time, other members of the scientific community will join in and convince other scientists to join. Shortly thereafter, other disciplines will undertake the effort. Open notebook science isn’t meant strictly for STEM fields. Humanities disciplines could benefit from the open documentation of their research. Even businesses could benefit from open practice.
Through documentation, promotion, use, reuse, and attribution others will begin to see the value in the open system both to scientific culture and individuals. Eventually, those who refuse the new system will be left behind. This is the future of science.