InfoD-Cafe: the future of scientific publishing?

[Deborah Taylor-Pearce]

Cafe,

As documented in an article from the _San Diego Union-Tribune_ for 28
Nov. 2009:

	"The company MolSoft, recently launched a platform it calls
	ActiveICM that enables authors to include three-dimensional,
	interactive graphics with the text of their articles. That
	means readers can click at the appropriate point in an
	article, call up an exhibit and view it from any angle.

	"This fall, scientists from the international Structural
	Genomics Consortium used the technology to publish a series of
	articles with 3-D representations of protein molecules
	believed to be related to disease. The first articles appeared
	in the journal _PLoS ONE_, but the consortium is also talking
	with the journal _Nature_.

	"'Essentially we're looking at proteins, which are very
	complex,' MolSoft founder Ruben Abagyan said. 'You can compare
	that with a planet or with a city, where you need to navigate.
	It's sort of like Google Earth in some degree.'

	"Abagyan, a professor in the School of Pharmacy at the
	University of California San Diego, had developed previous
	visualization programs as part of his work developing methods
	to design new drug candidates. He started MolSoft in 1994 to
	offer software tools to biotechnology and pharmaceutical
	companies.

	"While the initial uses relate to drug research, Abagyan
	thinks the potential applications of the technology are
	virtually limitless. For example, it might be useful in any
	publishing that involves displaying a product, from shoes to
	real estate.

	"The interface is straightforward, with an article's text on
	one side of the screen and whatever exhibit the reader has
	chosen to look at on the other. Authors can include
	Internet-like links in the text as frequently as they want to
	direct readers to the exhibits.

	"'It's not just animation,' Abagyan said. 'It's a fully
	interactive environment, which is extremely powerful, where
	you can look for things and in theory you can build it into
	any view (of the exhibit).'

	"Abagyan said a big advantage of the platform is that it works
	both online and off. So a reader can look at an article on the
	Web, where academic journals get much of their readership
	these days, or download it to read on a laptop whenever it's
	convenient.

  	"The company started moving in the direction of publishing
	about four years ago, when the Structural Genomics Consortium
	approached it about finding a way to better visualize the
	protein structures it was studying. The consortium, which
	operates from the United Kingdom, Sweden and Canada, aims to
	place three-dimensional structures of medical relevance into
	the public domain.

	"Brian Marsden, a principal investigator in research
	informatics with the consortium, said consortium scientists
	used the platform internally to communicate about their work
	as it gradually became powerful enough for broader use. In
	2006, the consortium and MolSoft felt confident enough to
	publish an article headlined, 'From a data dump to an
	automated story.'

	"'This time last year we felt comfortable enough to go to a
	number of publishing entities around the world and say: "This
	is cool. This is the new way of publishing this information in
	an interactive format,"' said Marsden, who is based at the
	University of Oxford in England. 'It's not like you have these
	2-D bits of paper with some jargon on it and a couple of
	images that even people like me can't really understand.'

	"While Abagyan thinks the potential for the software is vast,
	he's in no rush to expand his company. With about 10 employees
	at an office near The Scripps Research Institute, MolSoft
	brings in more than $2 million a year in revenue and has been
	consistently profitable.

	"Abagyan said he has never taken on outside investors and
	doesn't plan to do so. For now, he sees the publishing
	application as mainly a conduit for the advancement of
	science. The software to read articles is free, and licenses
	for the publishing software cost $100 for students and $200
	for academics.

	"'We're happy to be part of that noble mission and participate
	in this public dissemination,' Abagyan said. 'So we don't
	really care that it doesn't bring a large revenue stream at
	this point. But we know that the potential is there. I can
	apply it to shoes, casinos, whatever.'"

Their website is at

http://www.molsoft.com/index.html

and the download page for their ActiveICM product is at

http://www.molsoft.com/activeicm.html

Lots of possibilities....

Deborah
_____

Deborah Taylor-Pearce
dtp at she-philosopher.com