Hi developers,
I am in the brainstorming phase for a possible use of JSmol as an
interactive 3D network viewer.
In April 2008 there was a thread on the 'jmol-users' list ("Hub and
Non-Hub") where this kind of application was described to some extent by
Joe Ivanic. Although it is not a focus of JSmol I would agree with Joe
that JSmol would be very flexibel and powerful as a Javascript (and
Java) tool to visualize and manipulate complex networks. Now even much
more than in 2008. There are a few other tools available but none I
could find was nearly as powerful as JSmol. And besides I am already
quite familiar with the JSmo scripting language.
The major problem, as Joe also pointed out, will be to define the
coordinates for the nodes within the network.
Here is an example to illustrate one kind of network I am interested in:
Our group has developed 'AgefactDB' (http://agefactdb.jenage.de), an
ageing factor database. An ageing factor can be for example a gene like
'daf-16' in Caenorhabditis elegans that influences the lifespan of the
organism. Our database contains currently 398 individual experimental
observations where the effect on lifespan in combination with other
genes, chemical compounds or other factors like caloric restriction was
determined
(http://agefactdb.jenage.de/cgi-bin/jaDB.cgi?RKEY=r001&SEARCH=AF_005812&TYPE=d_fa&VIEW=detail#section_observation_d_fa).
In 291 observations the lifespan was decreased, in 56 it was increased
and in 51 there was no effect. This results in a network involving about
200 different ageing factors. I think it could be very helpful to
visualize this interactively with JSmol.
The idea would be to have two different types of nodes ("atoms"):
observations and ageing factors. And the edges ("bonds") would be the
connections between observations and ageing factors.
The result would be network ("molecule") where all nodes are connected
with at least one other node of the network.
Another level would be to combine several of these networks into a
single view, e.g. all ageing factors from a single species or all
homologous genes from several different species. This would lead to
several not connected networks ("molecules") which would most probably
require a different kind of positioning algorithm.
Q: I was wondering if it might be possible to achieve this by tuning the
'minimize' command with some extra parameters or maybe by enabling to
define a custom 'minimize' function?
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
Beutenbergstrasse 11
07745 Jena, Germany
Phone: +49 3641 65 6205
Fax: +49 3641 65 6210
E-Mail: rhue...@fli-leibniz.de
Website: http://www.fli-leibniz.de
Scientific Director: Prof. Dr. K. Lenhard Rudolph
Head of Administration: Dr. Daniele Barthel
Chairman of Board of Trustees: Dennys Klein
VAT No: DE 153 925 464
Register of Associations: No. 230296, Amtsgericht Jena
Tax Number: 162/141/08228
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