Henry Rzepa's Blog

In the two-publisher model I proposed 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.

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). Two new two files, a .xyz coordinate file and a .jvxl isosurface file (see here 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!

Tags: HTML, Java, separate web page

This entry was posted on Wednesday, October 2nd, 2013 at 2:38 pm and is filed under Chemical IT. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.