You are currently browsing the archive for the Publishing category.

To lookup an article using a document object identifier, there’s a cheap and cheerful way to do it based upon the work we did earlier to add access to pubget.

Without it, you can always resolve a DOI. Here’s a simplest example: Let’s say the DOI is 10.1021/ac7018574. This is an article by Cameron Neyland. If you want to redirect t the document, you can use an open DOI like this:

You can therefore represent a DOI  in OpenWetWare like this:

[ doi:10.1021/ac7018574]

That would display the string, doi:10.1021/ac7018574. Clicking on the link would bring you to the paper. This won’t provide any information about the document. Clicking on it will redirect your browser to the paper.

In addition to PubMed lookup, Pubget also includes a DOI resolver. You can access it via an RSS feed within OpenWetWare.

I’ve added a page including a set of examples and instructions to OpenWetWare to illustrate how this can be done as well as how the previous examples. You can look at the list of examples (and, please, add more!) here:

The result is that the title of the doc and a link to allow you to read the document are displayed. There’s currently no way to format these string directly but it’s coming. Look at the page to see an example. I’ll simplify this to allow an even shorter syntax to display it.

Just as pubget uses information about a university to determine what periodicals you have access to, the DOI system uses a ‘resolver’ to map a DOI into a reference to the periodical and the document described.

Biblio, the reference/citation extension in OpenWetWare currently does not support DOI’s. There is limited support for importing the metadata such as periodical, edition, authors, and even title, to do this withougt a bit of hacking. Let me know if anyone is interested in seeing this support added.

If anyone has questions about the use of a feature like this, please let me know. As I mentioned, don’t hold back on adding examples to the page in OWW.


Hello!  Is this thing on?  The last 12 months have seen significant life changes (seemingly successful) for many of the people within and around the OWW community.  Because OWW is a community (of researchers) we are past due for an update on how we are doing and open discussions of where we might want to be heading.

First, a few of the changes:

  • All of the founding researchers who created and obtained funding in support of OWW managed to  earn their PhDs from MIT.  Many of these folks have successfully launched a new company, Ginkgo BioWorks, in order to help make biology easy to engineer.  Indeed!
  • Lorrie LeJeune, who was our Managing Director was lured away to become a Senior Editor at Nature Education, which is an incredible opportunity for her to impact the lives of many learners.  Good luck Lorrie!
  • The Endy Lab wound down at MIT and has been reborn at Stanford.  Personally, I’ve moved twice, sold one condo, bought one house, helped to design and manage the construction of a new laboratory, and have been assembling a new research team.  Phew.

Second, what’s not changed:

  • Bill Flanagan remains gainfully employed at MIT, working to make OWW better and helping to put out the fires that flare up.  Simply put, Bill is an incredible resource for OWW and we are ridiculously lucky to have somebody at his skill level and with his strategic perspective at the heart of OWW.
  • We currently maintain funding from the US National Science Foundation in support of OWW.  To clarify one point in the recent and fantastic article by Jakob Sukale, the NSF grant expires 30 April 2010.  This grant currently pays for Bill’s salary and our server costs.  We are currently underspending on this grant and I will likely ask for a no-cost extension which, if granted, could extend our existing funding runway to April 2011.

Third, who is OWW?

  • I’ve found it very useful to understand who is actually using OWW.  I’d suspected that some people tend to talk about OWW and openness in research but that fewer folks are actually living the dream, so to speak.  Well, turns out that thanks to Bill, OWW maintains a statistics page here.  There are ~6000 registered OWW users (roughly doubling over the past year).  About 50 different users make edits to OWW pages on any given day.  About 500 unique users make edits each month.  Over 100,000 unique visitors browse OWW each month. This is incredible!
  • From a different perspective, OWW is incredibly small.  We also represent a broader experiment in changing the process of research that is very much in a fragile intermediate stage of its development.  Michael Nielsen did a good job of capturing some of the issues in his recent article, “Doing Science in the Open.”  Stated differently and from a personal perspective, I would currently be hard pressed to make a successful argument that supporting and using OWW has made the research in my own laboratory significantly better, as judged by our traditionally published results.  On the one hand, we had a great experience using OWW as a platform for developing a shared reference standard for measuring promoter activity in vivo. On the other hand, using OWW as it exists today has led to increased frustration with the slow inanities to be found within the conventional research publication process, while simultaneously and naively reducing the pressure to publish more formally and enabling others outside the (v. small) OWW community to “borrow” results without giving credit.  Perhaps this shouldn’t be surprising. All said, I’m more invested in OWW than ever before, and am convinced that we are figuring out a new way to do research.  We just have a lot of work to do in order to make the transition complete.

So fourth, what’s happening in terms of thinking about where we might go?

  • Lorrie LeJeune and Jason Kelly did a tremendous job exploring the entire process of research, from brainstorming ideas to promulgating results.  Some of these ideas are summarized here.  Many interesting questions and debates arise from considering this framing.  For example, is OWW about the information and knowledge maintained on our servers, or is it about the community of researchers that produces this content?  (personally, I think that the answer is both).  Stated  differently, should OWW support the process of research or should we focus on the capture and promulgation of research results?  (again, I’d vote both).  As a different example, does OWW exist primarily in order to stand as a shining beacon of openness in research, or are we simply trying to make the research process better which, given today’s information and communication technology platforms, tends to select for doing many more things in the open? (more on this third example below).
  • Bill Flanagan and I have been churning through the exciting opportunities that seem to continuously emerge given ongoing advances in information and communication technologies.  Some people refer to OWW as a wiki.  This makes me cringe.  Wikis are great but we likely need to transcend this framing in order to best realize solutions that could be developed in service of our community and our work.  You can find many early examples of this, such as Bill’s pilot efforts to integrate OWW with online document systems (e.g., Google Docs).

So, where should we go?  My own sense is that we should go meta and support the integration of many web-based tools and communities in support of making the research process better.  We will end up doing many more things in the open as a result.  We also need to partner more effectively with existing modes and channels of peer review and recognition.  But this is just my sense, so please chime in with your two cents, either via our Google discussion group, in the comments below, or by editing the appropriate OWW page.  We need to hear from the people who are depending on OWW, or who would use OWW if <blank> happened.  Also, for those of us for whom OWW is an essential part of our research existence, please participate in discussions about how to best guarantee the future funding of our operation.  We have time to work through different models, but need to start doing so now. Our Discussion list is
just a click away

Cheers, Drew

According to Scientific American, the not-so-open-access publisher Springer has just acquired the very open access pioneer site BioMed Central.

Regarding if BioMed Central will continue to be open access:

Those in the open access movement had watched BioMed Central with keen interest. Founded in 2000, it was the first for-profit open access publisher and advocates feared that when the company was sold, its approach might change. But Cockerill assured editors that a BMC board of trustees “will continue to safeguard BioMed Central’s open access policy in the future.” Springer “has been notable…for its willingness to experiment with open access publishing,” Cockerill said in a release circulated with the email to editors.

No information yet as to how much this acquisition cost.

What do you think about this? Will Springer just “experiment” with open access publishing for a while and then close the gates? Or is this a genuine attempt to join the OA movement?

The Journal of Visual Experiments (JoVE), a video-publication for biological research based in Sommerville, MA has recently been accepted for indexing in the hugely accessed PubMed and MEDLINE.

JoVE was founded in late 2006 as the first video-publication for biological research. With an editorial board including 20 scientists from leading academic institutions such as Harvard and Princeton. The online journal has grown to include over 200 video-protocols in fields such as immunology, neuroscience, microbiology and many others.

The National Library of Medicine (NLM) advisory board decided to include what is now the first and only video-publication in their large publication database and by doing so demonstrates openness to new and innovative ways of sharing science.

Moshe Pritsker, Ph.D., co-founder of JoVE in an email sent to us states:

“Inclusion in PubMed/MEDLINE is a big milestone for JoVE, and for the scientific publishing in general. It demonstrates the official acceptance of new approaches to science communication, such as video online, by the scientific community. Overall, it will increase the interest of the scientists to communicate their findings in video, making biological sciences more transparent and efficient.”

PLoSJust a few days ago, an article by Declan Butler was published in Nature regarding PLoS‘ open-access publishing model. This article was not well accepted by various open access advocates and science bloggers in general.

Johnathan Eisen from The Tree of Life was the first (that I noticed) to responde to the article and then many others followed along the same line.

Shortly after, Timo Hannay posted a “take two” at Nature’s Nascent that seemed to settle things down.

What I find to be the most notorious aspect in this whole string of events is that there is quite a large community of science bloggers that are ready to offer their “peer-review” in situations such as these. Is this a good thing? I would like to believe so…

Anyhow, I’ve only mentioned a few of the reactions. You can find plenty more reactions over at Bora’s Blog Around the Clock.

by [Julius B. Lucks](

The SC has been talking about how OWW can be used as a repository for Supplementary Material – click [here]( for a recent experiment on how this might work.

by [Julius B. Lucks](

![Oww Badges](

_OpenWetWare publication badges are a way to notify the community that an OWW page has appeared in a journal or at a conference. Pages that have these badges are in a state suitable for publication, and can also be actively maintained with minor changes._

Did you ever wonder if your favorite OWW page has appeared somewhere else, say in a journal or at a conference? Or did you ever wonder if the OWW page you are looking at is finished, or if it is still being actively edited? I certainly have, which is why I have been playing around with OWW publication badges lately.

Recently I wrote a paper on OWW entitled [Python - All A Scientist Needs]( When the paper was done, I decided to submit it to the [arXiv]( I wanted to notify the community that the article was in a final form, and to create a cite-able version that was in an easy-to-read and downloadable PDF format. In other words, I wanted to turn my OWW article into something similar to a journal article. The reason why I chose the arXiv was that it provided me with the facilities that I wanted (arXiv ID for citation, PDF downloads, an established community of readers, free), without all the hassles of a traditional journal, none of which would have taken this article in the first place.

So now I have an OWW paper, and an arXiv paper, but how do I let the community know that they are linked? Here is where the OWW publication badges come in. I simply inserted a line into my OWW article that looks like

{{publishbox_arxiv | your_arxiv_id | list_of_author_names}}

and voila!, a link is created on the page to my original arXiv post (see above image of the publication box). If you visit the [arXiv page for the article](, you will notice in the comments section below the abstract that this article is ‘Regularly maintained at this http URL’ (where the ‘http URL’ is a link to the OWW page.) That is put there to let everyone finding the article on the arXiv know that if they want to see the latest version, they should check out the original OWW article.

But why stop at articles, why not include conference presentations as well? The beauty of these badges is that they are completely extensible. I’ve already created a badge for letting everyone know that you have presented this work, and to use it, just put this at the top of your page

{{presentationbox| link_to_the_conference | link_to_the_slides }}

Publication badges are easy to use, and a great way to let people know that all that hard work of yours is being appreciated through publications and presentations.

Got any more ideas about how to use publication badges, leave a comment, or go out and use them!