[open-science] Inside view to the story of an high impact publication

Fri Oct 5 08:55:59 UTC 2012

On Fri, Oct 5, 2012 at 9:49 AM, Mike Taylor <mike at indexdata.com> wrote:

> Lots of interesting stuff here.
>
> As a practical matter, if I were a mathematician or physicist, and so
> I and my collaborators wrote my papers in the text-based LaTeX format,
> I would routinely use github as the collaboration point. Perfect
> version control, good and widely understood public UI.
>

Indeed. Would it be publicly visible or would it need a private
subscription. And presumably it could be opened later.
Github is so much more attractive for scholarly manuscripts than DSpace,
etc. (which are primarily dead archives)

>
> Unfortunately, in palaeo we all use MS-Word (or, more recently,
> OpenOffice or one of its many derivatives), and binary formats like
> this are less suitable for github. It could still be done, maybe.
>
> -- Mike.
>
>
>
>
> On 5 October 2012 09:42, Peter Murray-Rust <pm286 at cam.ac.uk> wrote:
> >
> >
> > On Fri, Oct 5, 2012 at 5:50 AM, Susi Toma <toma.susi at aalto.fi> wrote:
> >>
> >> Dear open-science readers,
> >>
> >> You might be interested to read a longish blog post I wrote about a
> recent
> >> high impact research article (alas, not open access; let me know if you
> want
> >> to read it and don't have access) I co-authored with Jani Kotakoski. It
> >> contains some interesting statistics of the email correspondence as
> well as
> >> inside details of the process, somewhat along the ideals of open
> science.
> >>
> >> http://mostlyphysics.wordpress.com/2012/10/04/the-story-of-an-article/
> >>
> >
> > This is a carefully detailed account of collaboration in authoring a
> > conventional closed access paper. I think many may find it useful.  I
> think
> > it stresses collaboration, the problems of refereeing and editors, but it
> > isn't similar to open science. So my comments are primarily about that...
> > Please take them as constructive.
> >
> > In a full open science process the major part of the research would have
> > been posted openly and would potentially have been available to people
> > outside the research group both for reading and comment.
> >
> > If the open process is restricted to authoring then the manuscripts would
> > have been posted openly. You mention a large  number of emails and
> > Googledocs. Googledocs is a relatively poor vehicle for scientific
> > manuscripts as it has poor version/control and poor reference management.
> > Indeed this is an area where I would like to see open offerings that
> address
> > these points.
> >
> > You have submitted to journals (ACS) which will refuse to publish if
> *any*
> > of the work has appeared in public anywhere. For example, in the distant
> > days when I published with ACS, we published a paper on the CML schema.
> > (This is in the field of cheminformatics and ACS was the only publisher
> > anywhere who would accept papers on this topic - we now have Open Access
> > alternatives.) I asked the editor if we could post the schema for public
> > comment and this was refused. Nowadays I would simply do it. The ACS does
> > not allow Green archival of any sort except in dark archives with large
> > embargo times (probably decades).
> >
> > Your initial paper - on which I can't comment as there is no public
> record
> > of it was required by the journals to be bounced around different
> > publishers. It was both too long for some and too short for others and
> looks
> > like your original paper has been split into two by the journal system.
> The
> > first, as I understand it, is 4 pages and contains little useful
> > experimental detail - this will be published separately. Is this the best
> > way to publish the science? I don't know since none of the versions are
> > publicly accessible.
> >
> > The message I take from this is that the journal system puts serious
> > pressures on where and how to publish. In open-science we don't have this
> > problem. We publish to the world and record everything. We (or someone
> > else!) can write narratives on the data.
> >
> > If we limit this to open-access (i.e. do the science closed but publish
> > openly in conventional journals) this emphasizes the need for a versioned
> > record of the publication. All significant versions should be available
> for
> > public view and comment. It may be that you would find public support for
> > your original manuscript or you may find there were significant flaws.
> >
> > This has been a useful example and my suggestion is that this list
> > (open-access) should think about open authoring tools. It's clear that a
> > huge amount of wasted effort is created by the re-authoring process -
> > reformatting, re-doing the reference labels, etc. In OKF we have an
> emerging
> > toolkit that will address some of these points.
> >
> >>
> >
> >
> >
> > --
> > Peter Murray-Rust
> > Reader in Molecular Informatics
> > Unilever Centre, Dep. Of Chemistry
> > University of Cambridge
> > CB2 1EW, UK
> > +44-1223-763069
> >
> > _______________________________________________
> > open-science mailing list
> > open-science at lists.okfn.org
> > http://lists.okfn.org/mailman/listinfo/open-science
> >
>

-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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