Publishing on OpenWetWare
The Steering Committee has been talking about developing an alternative publishing system/model through openwetware. I wish I could give a more concrete definition of what we are trying to achieve, but we are still in a pretty active debate and nothing clear has emerged.
My personal opinion about it, is that the first thing to do is for OWW to build a publishing community by creating a free, open-access, moderated system to publish Synthetic Biology papers. These papers would not have to be strictly the same as traditional peer-reviewed papers, and could include descriptions of protocols, part characterizations/designs, etc. In addition these papers could use OWW url’s as citations, thus establishing a legitimate credit system for OWW contributions. Both of these are a little hard to achieve with current publishers, hence the need for our own channel. We would only start with synthetic biology because it is a small, young and vibrant crowd, and of course this would apply to all disciplines eventually - we just need to get on our feet.
Specifically, I am a strong advocate of trying out a model in which people write their papers/publishable bits on the OWW wiki. Once they are done (revised, commented on, etc.) we publish them to arXiv.org where the work is moderated and if accepted is then hosted there and in effect given a doi which is more citeable in conventional publication. From there it can be submitted wherever the author wishes.
To be specific, my particular reasons for wanting to use the arXiv are as follows:
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 has a flexible enough system so that we could have an arXiv-hosted OWW journal with essentially no backend cost. In fact, certain astro-physics and mathematics societies already do create their own ‘overlay’ journals on the arXiv.
OWW can easily create an arXiv ’skin’ that contains a commenting system overlaid on the backend content hosted by the arXiv, or whatever else we want to do.
To that end, I am trying out a little experiment. I am going to write a paper on the arXiv on a topic that would not normally be publishable in a peer-reviewed journal: about how I used the python programming language to perform all the computational work in a recent comparative genomics study. I will write the paper on OWW, send out the link to it for comments, and when I have revised it, I will submit it to the quantitative biology section of the arXiv.
Anyone that is interested, please see: Python - All a Scientist Needs. Leave a comment there, or here, and let me know what you think!
Posted: February 7th, 2008 under Publishing.
Comments: 11
Comments
Comment from Jason Kelly
Time: February 7, 2008, 8:07 pm
writing up this paper sounds like a great idea. Until we try to push some real stuff like this through we won’t know where the hurdles are going to be, good luck with it.
Comment from bill
Time: February 9, 2008, 3:30 pm
Great idea, very minor quibble: arXiv isn’t suitable for most biological research papers. So when looking to expand beyond Synth Biol/Quant Biol etc, maybe consider Nature Precedings?
Comment from Julius
Time: February 10, 2008, 1:58 pm
Hi Bill - Thanks for the comment. Nature Precedings is certainly a possiblity for this type of stuff. We’ll just have to see where the community wants to go with it. Baby steps first!
Comment from Julius
Time: February 10, 2008, 5:15 pm
Note that this post was picked up by Open Access News
http://www.earlham.edu/~peters/fos/2008/02/openwetware-looks-at-publishing.html
Thanks Jason for pointing this out.
Comment from Jean-Claude Bradley
Time: February 12, 2008, 6:50 am
I agree - Nature Precedings is a great vehicle that would do all the things you are trying to accomplish, with the Nature editors stamp of approval on top of it. That said, there is no reason to also submit to arXiv to see what happens and compare. As long as you don’t give away your copyright to a publisher you can experiment freely.
Comment from Alexander Wait Zaranek
Time: February 12, 2008, 5:19 pm
If we are worried that the ArXiv maintainers might reject certain types of articles, surely, we could investigate the procedure for adding that new aticle type? I think it’s great to be part of a larger scientific community that has been openly publishing their work for many years. –AWZ
Comment from Julius
Time: February 12, 2008, 5:53 pm
I’m actually biased in favor of the arXiv over Nature Precedings partly because I know the arXiv folks really well, and I continue to do some work for them (http://export.arxiv.org/api_help/) (just getting my biases out in the open), and partly because it is very well established, has a lot of things figured out and is already THE standard of ‘open’ publishing in so many fields.
The process for creating a new sub-arXiv is completely community driven. All we would have to do is 1.) demonstrate a need for another sub-arXiv to handle our submissions, 2.) present the case to the arXiv, and 3.) provide a list of people who would be willing to moderate the new sub-arXiv to screen submissions.
Number 1.) is the hardest, and I think the place to start is to submit everything to q-bio and just see how it goes. Since we have a personal connection, it should not be too hard to get them in.
All this is mainly to say that I am confident that an arXiv system could work if we got the community around it. They have been around since 1991 and practically started open access scientific publishing. They are also part of Cornell University Library which is determined to keep it going for a long time to come. The same could be true for Nature Precedings, but I just don’t know the same level of detail for it, and I’m not sure how long they will be around if the system is not working for them.
Comment from bill
Time: February 13, 2008, 3:52 am
The process for creating a new sub-arXiv is completely community driven.
Ah, I did not know that. In that case I think you should just ignore me, and go with the system you know best (and which has an incontestable track record). 
Worst case, we wind up with bio-arXiv(s) overlapping with Precedings — which is a good thing for long-term archiving anyway.
Comment from austen
Time: February 15, 2008, 1:36 am
First of all Fuck Nature Preeceedings. Are you kidding me?
Julius you’ve got the connections to make this happen if it’s not you making this happen it’s not going to get done. Let me know what I can do.
arXiv is needed for all the sciences. 1 addition that needs to be made is HTML formatting on aiXiv. I fucking hate pdf/postscript. Self archiving is better than nothing—but half the time I don’t even want to read them because they’re always in PDF format.
HTML lets us see the network of connections between papers much more easily. All the bullshit science citiation metrics could be thrown out and we could just use google scholar.
There are opensource solutions to make this happen.
Topaz http://plosone.org
Open Journal System: http://pkp.sfu.ca/?q=ojs
Rhaptos (runs Connexions): http://rhaptos.org/
CrossRef forward linking: http://crossref.org/02publishers/forwardlinkinghowto.html
THE DAYS OF PROFIT PUBLISHING ARE OVER.
JOIN THE FREE SCIENCE MOVEMENT
Comment from Alexander Wait Zaranek
Time: February 16, 2008, 3:05 pm
Harvard’s FAS has stepped toward Open Access. There’s an article about it at Nature News: http://www.nature.com/news/2008/080215/full/news.2008.605.html
“At Nature, for example, authors are encouraged to submit their own, unedited version of their paper to funding bodies and universities for public dissemination six months after publication, along with a reference to the official peer-reviewed version in Nature. The appearance of a preprint in an online archive, such as arXiv, does not automatically disqualify a work from publication.”
Comment from Hilary
Time: April 15, 2008, 4:53 pm
I’m a little late to the discussion… (Disclaimer: I work on Nature Precedings)
I understand Julius’s biases towards using ArXiv–they’ve got a great community of active users and their model is basically the model for anyone looking to establish a preprint server. We’ve really benefited from discussions about how to set up a preprint server with a number of people who worked on ArXiv, including Paul Ginsparg.
Precedings is a new site and I can appreciate that it’s unclear what might happen with the site. Part of the catch-22 is that people are hesitant to submit because they don’t know what will happen if the site isn’t a success, but obviously the site won’t work if no one submits. We are looking to set up mirrors of the site in the future to ensure redundancy and archiving with a couple of partner organizations. (Although, we use a CC-attribution license, so technically, anyone could set up an archive of the papers on Precedings as long as authorship information is available.)
One difference is that Precedings is designed for the biomedical sciences and tends to attract a more bio-oriented crowd. For subjects like biophysics, I’d suggest considering submitting to both sites–as Bill pointed out, this might be the best option if you want to ensure long-term availability.
Write a comment