Posts Tagged ‘Java’

3D-rendered molecular models on this blog: an update.

Thursday, January 16th, 2014

So much to do, so little time to do it. That is my excuse at least. Right from my first post on this blog in 2008 I have tried to enhance it using Jmol, a Java-based applet (normally indicated with the caption Click for 3D). This has been pretty stable for some five years now, but a recent spate of security-based releases of the JRE (Java runtime environment) for desktop computers has impacted, the latest of which was released yesterday (Java 7, V 51).  Put simply, when I started, an unsigned applet was fine. Now to run, it can only be a properly signed applet. Fortunately, there are two solutions:


Publishing a procedure with a doi.

Wednesday, October 2nd, 2013

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[1] and assigned its own doi:10.6084/m9.figshare.811862.



  1. Henry S. Rzepa., "Script for creating an NCI surface as a JVXL compressed file from a (Gaussian) cube of total electron density", 2013.

The blog post as a scientific article: citation management

Monday, February 27th, 2012

Sometimes, as a break from describing chemistry, I take to describing the (chemical/scientific) creations behind the (WordPress) blog system. It is fascinating how there do seem increasing signs of convergence between the blog post and the journal article. Perhaps prompted by transclusion of tools such as Jmol and LaTex into Wikis and blogs, I list the following interesting developments in both genres.


Mobile-friendly solutions for viewing (WordPress) Blogs with embedded 3D molecular coordinates.

Sunday, December 11th, 2011

My very first post on this blog, in 2008, was to describe how Jmol could be used to illustrate chemical themes by adding 3D models to posts. Many of my subsequent efforts have indeed invoked Jmol. I thought I might review progress since then, with a particular focus on using the new generations of mobile device that have subsequently emerged.


Science publishers (and authors) please take note.

Monday, October 24th, 2011

I have for perhaps the last 25 years been urging publishers to recognise how science publishing could and should change. My latest thoughts are published in an article entitled “The past, present and future of Scientific discourse” (DOI: 10.1186/1758-2946-3-46). Here I take two articles, one published 58 years ago and one published last year, and attempt to reinvent some aspects. You can see the result for yourself (since this journal is laudably open access, and you will not need a subscription). The article is part of a special issue, arising from a one day symposium held in January 2011 entitled “Visions of a Semantic Molecular Future” in celebration of Peter Murray-Rust’s contributions over that period (go read all 15 articles on that theme in fact!).


Embedding molecules in blogs: ChemDoodle, WebGL and SVG

Friday, December 24th, 2010

If you get a small rotatable molecule below, then ChemDoodle/HTML5/WebGL is working. Why might this be important? Well, the future is mobile, in other words, devices that rely on batteries or other sources of built-in power. This means the power guzzling GPU cards of the past (some reach ~400 Watts!) cannot be used. Rather than using e.g. a full power OpenGL library, one will use Web-based graphics libraries, which (to quote Wikipedia) extends the capability of the JavaScript programming language to allow it to generate interactive 3D graphics within any compatible web browser. A typical target device might be for example Apple’s iPad (for which the redoubtable Jmol, which is based on Java, is unlikely to ever work).