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ANNOUNCE: Collaborative Clickable Biology

P. Murray-Rust mbglx at s-crim1.dl.ac.uk
Mon Jun 13 18:39:02 EST 1994


CCB is an experiment in collaborative computing which is made possible
through the technology developed by the World Wide Web.  One of the 
fundamental ideas of the WWW is to develop collaborative tools and methods
of working which can overcome geographical separation.  WWW has been 
extremely successful in biology, where many of the major databases are
accessible through URL's and use HTML to link to other sites; this is often
done *without needing central coordination*.  Personally I feel that the 
biological pages on the Web capture this informal collaboration more
than other disciplines and there is wide acceptance that this a valuable
approach.  At the WWW94 conference in Geneva (May), we (Reinhard Doelz, 
Brad Sherman and me) ran a workshop, where amongst many topics we discussed
the creation of communal biological resources.  You may have seen that
Reinhard (http://beta.embnet.unibas.ch/conference/welcome.html) is taking
forward our suggestion for a bionet newsgroup on www, whilst Brad 
(http://s27w007.pswfs.gov) and I are taking forward the idea of communal,
collaborative dictionaries and other resources.  

        My initial contribution is CCB (still very experimental!) which 
explores the use of *remote entry of data* using WWW.  CCB allows any user 
to add mark-up information to a *cooperating* remote site.  This information
can be added asynchrously, using the WWW forms technology, without human
involvement at the remote site.  (The remote site can decide exactly what 
can/not be done, so that proper security can be ensured).  

        Because so much biology is *graphical* (molecules, cells, genomes,
organisms are all frequently represented like this) I have used the WWW
*clickable map* as the basis.  the map has 'hotspots' which, when clicked,
route the user to another URL.  I have mounted a demonstration of this
using the HIV-1 genome, pointing to a URL (file) for each protein.  These 
files have futher markups to URL-entries in SWISS-PROT, but there is
opportunity for *you* to add more URL's (e.g. to PDB, OMIM, GDB, EC, etc).

        At present the diagrams themselves cannot be edited, but I hope very
shortly to add this feature (i.e. you can outline a hotspot on a diagram
and add that geometrical information to the remote *.gif).  That will then
allow the world community to create any number of clickable diagrams,
without having to seek 'central permission' from system managers.  The type
of diagram is only limited by your imagination but I intend to post a few
key examples such as:
        2-D protein structure (3-d markups are being thought about!)
        proteins in cells
        biochemical pathways
        geographical maps

At present the system relies on a responsible, collaborative, response from
yourselves.  The information should be *very* brief (1-line) and signed
(name+e-mail - not yet PGP!).  Obviously we shall need to consider the way 
in which we regulate the central information when there is fuzziness or 

The system is very kindly hosted by Alan Bleasby and his colleagues at 
Daresbury, so please be considerate.  I have no idea of the likely impact
on bandwidth, cpu or filestore! 


	Gudge Chandramohan (akc22282 at ggr.co.uk) has collaborated with me
		in developing the markup technology.  More is coming!
	Several brave people who have found the bugs in the server over
		this weekend


Peter Murray-Rust (pmr1716 at ggr.co.uk) Glaxo Research and Development, Greenford
mbglx at seqnet.dl.ac.uk (Mailbox at Daresbury by kind permission of Alan Bleasby)

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