[OWW-SC] 'Publishing' on Pre-print services like arXiv.org

[Drew Endy]

Hi Julius,

Thanks for leading this / taking things forward.

Here are some comments from my own perspective, starting selfishly  
with the community that I am based in and as a OWW user.

I am very keen to have a preprint server for the synthetic biology  
community.  I am also very keen to reduce (as close to zero as  
possible) the transaction costs associated with moving papers from OWW  
and a pre-print server to a peer-reviewed journal.  (as one point of  
reference, I am spending about 12 hours of my time dealing with a BMC  
journal trying to get a manuscript into the proofs stage).

So, I'd like to see arXiv.org set up a synthetic biology section.  I'd  
also like to see Nature Preceedings do the same (does anybody have a  
sense for how Preceedings is doing?).

Simultaneously, I'd like to see one or more journals commit to  
considering papers that have been published on pre-print servers.   
Specifically, for the synthetic biology community, I think that we  
should target Molecular Systems Biology, Journal of Biological  
Engineering (although they are BMC and I'm worried about transaction  
costs), and the relatively new IET journal that publishes the iGEM  
projects.

Moving to a more meta, OWW strategy level, if OWW can use an existing  
preprint server(s), and these preprint servers provide DOIs for their  
holdings, then OWW might not need to setup its own DOI server.  To  
feel like I have a clue though, I really need to understand what the  
preprint servers like arXiv are prepared to deal with.  For example,  
if we put a "button" on the top right of every OWW page that said  
(Publish!), which resulted in the current edit of the page being  
automatically submitted to the correct section of the correct preprint  
server (via a collection of toggle boxes that pop up after pushing the  
Publish! button, would arXiv and Preceedings be able to deal with  
this?  As I'm typing this out, my sense is that OWW needs to set up  
it's own DOI server, and that when somebody hits "Publish!" they have  
the option of sending it to arXiv.org, Preceedings, any other existing  
preprint server that exists and that wants to partner with us, but  
also a OWW preprint server (which is nothing more than our own DOI  
server).  This will let people DOI whatever they want, while also  
building the OWW publishing brand, and providing outlets to existing  
publishing channels (this association will also help the OWW  
publishing brand).

Finally,, while I am hopelessly biased, I think that the synthetic  
biology community provides a good launch community for using a  
preprint server in biological research.  The community is young,  
vibrant, and full of immigrants.  We can set the standards of practice  
within the culture now.  Other existing communities will have a harder  
time of this (i.e., if the paper is not published in Cell then it does  
not exist -- overstatement I know).

Best,
Drew

On Nov 28, 2007, at 10:55 AM, Julius B. Lucks wrote:

> Hi SC,
>
> Following up on last month's meeting, I would like to gather your  
> ideas on how the OWW community might like to use a pre-print service  
> such as arXiv.org or Nature Proceedings to 'publish' content  
> originally created on OWW.
>
> My first impression was that these pre-print services could be used  
> as a stepping-stone towards more traditional publication - i.e. an  
> article would be written with the OWW wiki, and when sufficiently  
> polished, sent off to arXiv as an official pre-print.  This would  
> provide a citeable uri for that version of the document, and would  
> be used as the basis to notify the community of the polished work,  
> as well as submit to a traditional peer-reviewed journal (if the  
> authors desire).
>
> In discussing this at the last SC meeting, Barry mentioned a very  
> interesting possibility of posting non-article content such as lab  
> protocols or reagent lists up on a pre-print archive.  I would like  
> to brainstorm with you possible uses of pre-print archives.  In  
> particular:
>
> * Would you consider using a pre-print archive as a way to turn a  
> wiki document into a journal article (wiki -> pre-print -> paper)?
> ** If so, are you ready to try this out, or do you know of anyone  
> that is ready?  I would like to walk whoever is ready through the  
> process with them and see how it goes.  I can also facilitate  
> submission to arXiv.org's quantitative biology section if that is  
> necessary.
>
> * What other types of documents do you imagine posting on a pre- 
> print archive?  (protocols, reagent lists, etc.)
> ** For each type of document, it would be great to know why the wiki  
> page is insufficient for your purposes.  For example, Barry  
> mentioned that reviewers were hesitant to honor a wiki link as a  
> citeable document.
>
> * What is the best way to ask the OWW community outside the SC these  
> questions?
>
> I would appreciate ALL of your comments.  I think arXiv.org is  
> already prepared to handle traditional journal-article-like  
> submissions, but might be more hesitant for other types of  
> submissions.  I would like to get a list of ideas to before I  
> discuss this with them.
>
> Thanks for your help,
>
> Cheers,
>
> Julius
>
>
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