Imperial College London

Henry Rzepa

In the two-publisher model [I
proposed](http://www.ch.imperial.ac.uk/rzepa/blog/?p=10998 "A two-publisher model for the scientific article: narrative+shared data."){target="_blank"}
a post or so back, I showed an example of how *data* can be incorporated
(transcluded) into the story narrative of a scientific article, with
both that story and the data each having their own independently citable
reference (using a doi for the citation). Here I take it a step further,
by publishing a functional procedure in a digital
repository\[cite\]10.6084/m9.figshare.811862\[/cite\] and assigned its
own
doi:[**10.6084/m9.figshare.811862**](http://doi.org/10.6084/m9.figshare.811862){target="_blank"}.

The following HTML

`<iframe src="http://wl.figshare.com/articles/811862/embed?show_title=1" height="443" width="500" frameborder="0"></iframe>`

can then be incorporated into any Web page, including this post, to
invoke the service. What does this do? It takes a pre-prepared
Gaussian-style cube file containing values of the electron density of a
molecule, and converts this into non-covalent-interaction (NCI)
isosurfaces\[cite\]10.1021/ja100936w\[/cite\] (as [described
here](http://www.ch.imperial.ac.uk/rzepa/blog/?p=2230 "Non-covalent interactions (NCI): revisiting  Pirkle"){target="_blank"}).
Two new two files, a **.xyz** coordinate file and a **.jvxl** isosurface
file ([see
here](http://www.ch.imperial.ac.uk/rzepa/blog/?p=8733){target="_blank"}
for an example of its application) are written to the user's local file
space. These files in turn can be integrated into an interactive data
presentation and this new object can have a *doi.*

So now we see how unique identifiers can be used with a digital
repository to:

1.  Publish a data calculation and assign it a *doi*
2.  A script or procedure (as a Web Service) to convert the preceding
    data can itself be published and assigned a *doi*
3.  Step two is then invoked using that doi, and the output(s) can be
    also be *raw* into a digital repository, or wrapped beforehand in
    some manner to produce a visual presentation of this new data before
    being assigned a *doi*
4.  All three components, if needed, can now be cited in a narrative
    article describing the science, and this too of course may (after
    peer review) also receive its own *doi*
5.  The first three components can, if needed, be transcluded into the
    fourth to create the final composite appearing in the journal (or
    blog post as here). 

So below is this service. You can either use it here, or simply resolve
the *doi* above into a separate web page. This version uses Java, and so
you have to be prepared to answer questions about security etc. An
alternative version not using Java (based on JSmol) is probably too
slow; sometimes the procedure has to convert 300+ Mbytes of Gaussian
cube, and take about 30 seconds to do so.

At any rate, if you have read any of my posts which show NCI
isosurfaces, and wondered how to do it for yourself, here is your
chance!

::: {.wp_orcid_field}
[https://orcid.org/0000-0002-8635-8390](https://orcid.org/0000-0002-8635-8390){target="_blank"
rel="author"}
:::


In the two-publisher model I proposed a post or so back, I showed an example of how
<em>
 data
</em>
can be incorporated (transcluded) into the story narrative of a scientific article, with both that story and the data each having their own independently citable reference (using a doi for the citation). Here I take it a step further, by publishing a functional procedure in a digital repository[cite]10.6084/m9.figshare.811862[/cite] and

Rogue Scholar Beiträge

Publishing a procedure with a doi.