Hi, everybody!
I have followed this topic, JMOL, because the tool seems to be nice.
However, I am not a chemist or a biologist, but an experienced computer
engineer, who recently got a PhD with a topic of software reverse
engineering.
I am interested in using JMOL because* the atomistic model as a metaphor
of my research with its software atoms*, has several identical features
with concrete atoms.
If anybody is interested, please look at my book here:
http://dissertations.jyu.fi/studcomp/9789513932527.pdf. The cover
illustrates my principal metaphor.
*My elementary question to the JMOL-society is*: Could JMOL be used in
visualizating typical abstract concepts, e.g. typical method calls,
where methods are abstract "atoms", which only have a small kernel and
some links to other atoms? In the metaphor I thought that the links are
like electrons of an atom.
In computer simulations, which I specify for Java, the calling atom asks
information from the callees and creates new links between them. By
using this dynamic information (contents of links), it is possible for
the maintainer to trace program behaviour better than by using
traditional methods.
_*An example*: the method /main /calls methods A and B and method A
calls methods A1 and A2, and B calls some BX. /What kind of data format
would you use in presenting these invocations in JMOL?/
_
In my thesis I used the tool Graphviz (ATT) for making graphs. It is two
dimensional, but it can automatically create positions for the nodes (a
nice feature).
*Motivation*: If we could find a good way to present source code items
in JMOL, it could be a multidisciplinary opening to connect biological
information and computer science information further. There is some
research for that.
PS. My final contribution in the disseration is to connect GrammarWare
(presentations), ModelWare (modeling), SimulationWare (simulation for
Java and others) and KnowledgeWare (capturing knowledge). This
methodology is general and open to be extended into other disciplines,
too. These four technology spaces work excellently in program
comprehension. Perhaps they work in biology and chemistry comprehension,
too?
For research information, please look at:
http://www.jyu.fi/ajankohtaista/arkisto/2008/04/tiedote-2008-04-15-10-04-09-740451/
I will become happy for any suggestions how to demonstrate my small
example in JMOL. Thanks!
Best regards
Erkki Laitila
SwMaster Ltd, Jyväskylä University, Finland
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