Please help define the requirements for a new publishing channel:

John Cumbers blogs: here are the initial requirements that we mentioned, please edit away here: , leave comments on the blog below…

From the Feb 6th publishing teleconference

1) Alternative channel for smaller publication units, e.g protocol publication, videos, wiki pages, not necessarily competing with traditional PDF type journals.

2 )ability to Publish OWW wiki pages

3) ability for community to give and get some type of reward

4) DOI given when community feels it is good enough

Old posting: What would be your top 5 priorities from a new style publishing system?

John Cumbers says:
I was charged with two tasks at the last steering committee meeting, the first was to stoke the fire of the steering committee blog, the second was to fire up the publishing group into action. With the steering committee teleconference this Thursday, I present both to you here for fear of being shamed:

We’ve been thinking about how OWW might shake up the publishing model for a while now, in July 06 there was an OWW retreat held at MIT, we had some great ideas for reddit, digg or slashdot style publishing systems but none were carried through (I take some of that responsibility, my idea was to launch a local version of digg (pligg) but it didn’t fly. Recently these ideas have surfaced again with Julius Lucks suggesting an OWW Arxiv style pre-print server and Drew Endy suggesting a Poww (Proceedings of Open Wetware journal) on the steering committee list serve. Now that OWW has more resources (staff, money..) there are calls to broach the subject once more.

It was suggested that the publishing needs of the synthetic biology community might be a good place to start this discussion as it was a young field, full of converts, and in need of a suitable low cost, fast publishing channel which was not currently being met. From emailing with Jim Haselhoff last year, editor of IET syn bio, I know that he already has plans for a free web based publishing model for foundational research in synthetic biology. It was also previously suggested that could work with publishers to provide incentives for sharing information that isn’t traditional peer-reviewed. On the traditional side, here is what is on offer so far:

Systems and Synthetic Biology published by Springer:

Molecular Systems Biology published by Nature

IET Synthetic Biology published by the IET

Journal of Biological Engineering published by the IBE/BMC

So I’ve probably missed some so please add any in the comments and I’ll edit them in, but there is a start to the discussion on what the community would want from a fast web based publishing channel and how it could be achieved, more importantly how could recognition be gained from this way of publishing.

I propose a discussion via the comments here first, followed by a teleconference for all those interested on Wed this week before the Thu main steering committee teleconference, please sign up if you’re interested, in the meantime: What would be your top 5 priorities from a new style publishing system, I start with mine:

1) Incremental publishing of open science, as it happens
2) commenting system, real names
3) A way to guide me through the information, down with the scroll bar
4) video, screen casts and beautifully laid out information
5) Something like RSS updates, without the feeling of being overloaded

Speak with you Wed/Thu I hope,



  1. Reshma’s avatar

    I think one area where OWW could make an impact is making the process of publishing easier. Writing papers is actually quite a painful process in terms of the effort that goes into formatting figures, the text, references etc. By constructing a publishing pipeline on OWW, could we somehow make this process easier? Reducing the barriers to publishing becomes especially critical if you want to encourage folks to publish not just major pieces of work (like research projects) but also smaller scale but no less important pieces of work like characterization of a part or device.


  2. Julius’s avatar

    I’ll add some comments about why I think the arXiv is a great place to focus OWW publishing efforts. (Sorry to repeat myself, but this is the first time everyone can see this discussion.)

    For those of you not familiar with, it is an e-print archiving and distribution system that was actually the first of its kind (1991), and represents the first real major electronic scientific publishing channel. It currently serves the communities of physics, math, computer science, statistics and quantitative biology.

    • The arXiv would be open to having an ‘oww’ or ‘synthetic biology’ section, much like it has condensed matter physics, high energy phyciscs sections. In fact it already has a section called ‘quantitative biology’ that we could submit to. The sections are weakly moderated for suitable content by people in the field.

    • The arXiv is an e-print system, and is often used as an intermediate step between research and publishing in a more peer-reviewed journal. There are also cases where the arXiv is the final resting place for a paper, including those in the PLoS One model where the science is good, but it is not ‘hot’ enough to get into a journal.

    • The arXiv is completely electronically based, and offers many services including ingest and digest APIs to create automatic submission tools, and include arXiv content inside websites (rss) and tools (like pubmed searching).

    • An arXiv article is assigned a unique identifier (not a standard doi though), that is citeable.

    • The arXiv uses latex as its type-setting system. What the author produces in latex on their computer is pretty much what shows up on the arXiv. In regards to Reshma’s comment above, it would not be inconcievable to have an automatic wiki to latex conversion tool that would facilitate the submission of papers written on OWW to the arXiv.

    • The arXiv has a flexible enough system so that we could have an arXiv-hosted POWW journal with essentially no backend cost. In fact, certain astro-physics and mathematics societies already do create their own ‘overlay’ journals on the arXiv.

    • The one drawback is that the arXiv is focused on the traditional publishing model of papers, and thus they would prefer to have only submissions that COULD be submitted to a peer-reviewed journal. As of yet, there is no mechanism for data deposition, protocol-only submissions, etc. However we could talk to them.

    • As John suggests above, there is no commenting system on the arXiv. However, this does not preclude OWW creating an arXiv ‘skin’ that contains a commenting system overlaid on the backend content hosted by the arXiv.


  3. johncumbers’s avatar

    So I’m still a fan of trying out an OWW version of digg/pligg and seeing how it goes. This idea wasn’t carried through before as people were skeptical that it would work due to the large number of Digg clones around and the lack of critical mass needed to actually digg things (I was going to use as an example, but it now looks like it is getting quite a few pliggs). However, there are a bunch of other cool features that pligg would offer, such as a nicer commenting system, ability to rank comments as well as articles, and also the ability to see what other people are pligging, for example, if I think Julius Lucks is cool and I’m often interested in the stuff that he’s interested in then I could click on his name and see all the stuff that he’s pligged. He’s a fairly ugly implementation of pligg, but you can click on each user and see what they submitted / pligged ni the past.

    So how does this relate to OWW publishing? We simply add a ‘pligg this’ button to every page and allow people to publish a page of their wiki and others to rank and comment on it.

    Just my 2 cents. Teleconference will be at 11am tomorrow, Wed, EST, please call USA +1 617 324 7374 to take part. Agenda will be:

    1) What does the community need as far as a publishing channel? What are the key requirements.
    2) is this met elsewhere, why/why not?
    3) should we set something up, what would be the scope?
    4) would we want to involve third parties, if so how? who?
    5) Logistics and time-line
    6) What to report to steering committee, and date of next meeting



  4. Ricardo Vidal’s avatar

    Although it is imperative to discuss the system where and how the data is kept, I find it far more important to discuss the form how the information is recorded.

    Within the wiki system, I consider the usability of the input interface of great importance. Easier, more straight forward ways of registering research information with different formats. Photos, video, screencasts, etc

    Even the way information is displayed is important. Excessive vertical scroll is a problem with long pages. Maybe a tab system can be implemented to provide more rich and complex pages.

    I wont list my top 5 since they coincide with some already mentioned, but I must repeat that usability is the most important factor to get research scientists, students and professors using OWW.


  5. David Bikard’s avatar

    Have a look at this:
    You’ll find here some great ideas !

    It would also be great to have the same kind af thing as:


  6. Reshma’s avatar

    First, off thanks John and Julius for kickstarting these conversations again. Based on today’s publishing group meeting, I think a few things crystallized for me based on people’s comments. (You capture most of these in your blog post but I thought I would expand on them more here.) I’ll largely try to keep these thoughts independent of the actual mechanism that we use to implement such a system (such as arXiv or a particular journal).

    1. We need to start with a particular research community. In order to gain traction with a new publishing channel. Since synthetic biology is still an emerging field, has a need for new kinds of publications and there are a core group of people from the field interested in publishing, synthetic biology is an attractive choice for an initial testbed community.

    2. We need to provide an outlet for new types of publications. Right now the primary way to get credit for research work is through publication of research papers. There need to be avenues for publishing other classes of work: standardized protocols, new BioBrick part designs, system specifications, device characterization datasheets etc. As Jason pointed out, these alternative publications don’t have a good outlet right now and thus OWW has an opportunity to fulfill a nascent need in the community.

    3. We need some form of peer review. The reward structures in biological research are largely centered around peer review. While informal review via a wiki or a pligg-like commenting system is useful, for the work to be taken seriously I think some sort of formal peer review of the work is needed.

    4. The new publication channel needs to support citeable objects. Right now there is a lack of clarity around whether OWW pages can be cited in “real” papers or now. Either through DOI’s or something else, we need to ensure that the published works are referenceable.

    I completely agree with John that we need to be able to publish things quickly and allow the review to happen post-publication. In some sense, OWW already tries to enable rapid publication and post-publication review (simply through revisions to the page and numbers of page views). Obviously, there is lots of room for improvement in this space. But I think we could benefit from another layer on top of OWW which takes content that has been vetted by the community (whether it be a protocol, wikireview, tutorial or something else) and “publish” it. Publishing would involve both a more formal peer review and turning the page into a referenceable object. One advantage we could offer is simply lower the barriers to publishing. As folks pointed out, right now people spend huge amounts of time formatting work for publication. If we could offer a streamlined process (which would be no small feat), an OWW publishing channel could attract a fair amount of interest.


  7. lorrie’s avatar

    Here are some notes I jotted down from our publishing teleconference on Feb. 6.

    The discussion centered around John’s first agenda question: “What does the community need and what are the requirements”, with forays into how the needs are (or are not) currently being met and how OpenWetWare might step up to meet them.

    One suggestion was to create publishing channels for various scientific areas with tools or platforms for that community to use. Synthetic biology is probably the best community (or channel) to start with, followed by personalized medicine. A key requirement for success of these publishing channels is figuring out the rewards scheme for participation. Discussion of whether OWW should follow the traditional peer review system or create something new followed.

    So what would OWW do in this publishing channel? All agreed that we would not follow the traditional channel of papers, but would rather focus on smaller units of publishable material such as protocols, specs of parts, reviews, etc.

    We also discussed how people would be credited for what they publish. Do we assign DOI numbers and if so, how and when? All agreed that some form of peer review is needed, as is the ability to cite work on OWW. How do we manage the process? John suggested using a Pligg-like system.

    Finally, what are the requirements for such a publishing channel? Since it’s an alternative channel, paper is not required. Work could begin on OWW and migrate to some form of publishable unit (still linking to background material or earlier versions stored on OWW).

    Another conference call will be scheduled in two weeks.


  8. Julius’s avatar

    I made a recent blog post about my personal views of where OWW should go on pubsishing. It mostly addresses Reshma’s 4 points above, but using the arXiv. I decided to go ahead and try it out myself – I’m going to write a paper using the OWW wiki, send out a request for comments with the link, collect comments and revise, then submit to the arXiv quantitative biology section. Note that the paper I am writing is NOT suitable for traditional publication – at least I don’t know of a journal that would touch it because it is about programming methods without any hypothesis/data.

    In any case, you can see the blog post from the link below. It should be an interesting experiment!


  9. Euan’s avatar

    (as a disclaimer: I work for Nature on web stuff. I’m a big fan of OWW.)

    Why not use Precedings instead of arXiv?

    It’s there to complement arXiv, you get a DOI, it’s mirrored by PubMedCentral (I think, could be wrong about that), all content is CC attribution, it’s free, yadda yadda.

    The problem with any sort of scientific Digg clone might be that there simply isn’t the critical mass of users to make them useful – Digg with only one or two votes per story wouldn’t be very interesting. There’ve been loads and they all suffer from this issue. :(



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