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open notebook scienceOpen Notebook Science (ONS) is slowly making a splash in the scientific community. By publishing all experiments in online notebooks via blogs and wikis, scientists are bypassing the lengthy patent process and working toward creating faster solutions to world problems.

Open Notebook Science (ONS) is “the practice of making a researcher’s laboratory notebook, and all associated supporting data, public in as close to real time as possible,” says Dr. Jean-Claude Bradley, Associate Professor of Chemistry at Drexel University in Pennsylvania and pioneer of ONS.


The first ONS research project was Bradley’s UsefulChem project.  He opened the walls of his lab to make all data open to the public through a wiki and blog mashup. By doing so, his experimental data can be indexed and harvested by both human and computational agents.

open notebook science

While his open approach is not the standard for science (especially in Chemistry), ONS is gaining rippled momentum in the scientific community as more and more scientists are seeing the value in collaborating on lab experiments.

What is the Difference Between ONS and Open Access?

Open Access (OA) and ONS are similar in that data is shared freely.  Open Access means there is no charge to the reader when the article is published.  Typically, a library has to pay for journal subscriptions, but Open Access journals are made free via the web.

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The main differences between OA and ONS are timing and detail.  In ONS, the scientists are working and documenting their research live. Both successes and failures are published.  This is not the standard for science where only successes are published (even in OA).

In OA, the articles are polished and can happen any time after an experiments concludes.  The publication is not live, and all of the failed experiments are removed.

open notebook science

Nature is an Open Access scientific journal devoted to environmental biology.  Their material is made free to the public, but it is polished work and not the raw types of work found in Open Notebook science.

Some OA journals are peer reviewed and some are not.  The OA Librarian has awesome resources on the topic if you would like to learn more.

What are the Benefits and Risks of ONS?

While losing the right to a patent can be financially devastating, the effects of producing faster research can help cure world killers.  Bradley estimates that we can cut down the time it takes to go from lab to medicine by 10-15 years with Open Notebook Science.

While pre-tenured faculty and research scientists need peer reviewed publications and patents to advance in their fields, many tenured scientists are able to contribute to the body of knowledge without much risk.

Time will tell is Bradley’s predictions are right, but, in the meantime, here are some tools for getting started.

How to get started

If you want to be start an Open Notebook for your scientific experiments, you need a few simple tools and a commitment to publishing successes and failures in real time.

Tools:

  1. A Blog with RSS Feed
  2. A Wiki
  3. An RSS Reader
  4. A Social Network
  5. A digital still camera
  6. A digital video camera

Methods:

  1. Keep a computer in the lab
  2. Document all steps, materials, and findings (good and bad) as they happen on your wiki notebook
  3. When possible, take pictures or video of experiments
  4. Write a summary for the blog BEFORE you leave the lab.
  5. Publish your blog so that it gets pinged by your RSS feedburner.
  6. During down time, keep current with other similar experiments using your social networks and RSS reader.

A Good Blog and Wiki Mix (Bliki)

Dr. Bradley uses Blogger and Wikispaces to create his Bliki environment, but any blog or wiki platform will work.  If you would like to explore and compare wikis, try wikimatrix.

You can learn more about wikimatrix from our article here. While Blogger is super powerful because it is owned by Google, there are lots of other blogging platforms out there.

Timely publishing is the key to ONS, and experiments should be documented in as near real time as possible. When possible, pictures and videos should be included in the bliki.  It is crucial to make sure that you connect your blog and wiki so they are seamless.

A Good RSS Reader

Open Notebook Science requires that a scientist keeps up to date with the experiments of others.  For example, in the Bradley Lab at Drexel, undergrad and grad students are working on a inhibitor to Enoyl Reductase, the root cause of malaria.

It is important for scientists to report their findings immediately while the details are fresh, so that others around the world can duplicate or enhance an experiment in their own labs.  Likewise, it is imperative for scientists to read the work of others so they can add to the body of knowledge.
RSS readers are a dime a dozen, but Google Reader is one of the best.  The students can write collect notes from other online notebooks, create notes in text, save and share notes, email notes to other team members, and organize materials very easily.

Open Notebook Science is about sharing data consistently in real time.  Bradley predicts that, in the future, humans won’t be needed to aggregate data.  But, for now, we have to collect and disseminate data the old fashioned way…by talking about it! Social networks like Facebook and Twitter allow for instant sharing, and Bradley uses FriendFeed to collect it all in one location.

The Wrap

Will Open Notebook Science change the nature of the scientific community? Probably not.  But, if more people share their data in real time, we can help people around the world combat disease.

Do you share your scientific data in real time?  Why or why not?

  1. Beth Ritter-Guth
    March 13, 2010 at 7:41 pm

    Jean-Claude Bradley wrote a nice follow up on his blog:

    http://usefulchem.blogspot.com/2010/03/open-notebook-science-tips.html

  2. Beth Ritter-Guth
    March 14, 2010 at 4:41 am

    Jean-Claude Bradley wrote a nice follow up on his blog:

    http://usefulchem.blogspot.com...

  3. Jean-Claude Bradley
    March 10, 2010 at 1:28 pm

    Beth - I think it is easier to format in an email compared to an RSS feed. Usually I don't even have to go to the wiki to clearly see the changes that a student made to a page the way it is formatted in email. Also if there are 20 changes to a wiki page Gmail keeps them all in the same conversation so it doesn't clutter up my inbox too much.

  4. Jean-Claude Bradley
    March 10, 2010 at 8:09 am

    Thanks for the thoughtful review Beth!
    Concerning RSS feeds, we find that they work fine for blogs but don't work that well for wikis. At least with Wikispaces, email alerts are much easier to follow.
    Also students don't tend to use the blog - at least in our environment. There should be enough information about their experiments on the wiki itself. They sometimes use FriendFeed though for participating in discussions.

    • Beth Ritter-Guth
      March 10, 2010 at 9:31 am

      Thanks, Jean-Claude! The work you are doing is amazing! Do you think there will be a better way to subscribe to wiki RSS in the future?

  5. SteveW
    March 8, 2010 at 12:38 pm

    While Nature is not Open Access, The Directory of Open Access Journals does list journals in a variety of fields which are open access: http://www.doaj.org/

    • Beth Ritter-Guth
      March 8, 2010 at 12:40 pm

      Thank you for the link, Steve!

  6. SteveW
    March 8, 2010 at 9:38 pm

    While Nature is not Open Access, The Directory of Open Access Journals does list journals in a variety of fields which are open access: http://www.doaj.org/

  7. Ord
    March 8, 2010 at 10:24 am

    1. Nature is NOT open access.
    2. Nature publishes papers in all areas of science - not only biology.

    • Beth Ritter-Guth
      March 8, 2010 at 12:42 pm

      Thank you, Ord, for the correction. While there are many free science related materials and resources on their site, most of their journals are not open access.

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