ANNOUNCE: CML (Chemical Markup Language) V1.0

peter murray rust pazpmr at unix.ccc.nottingham.ac.uk
Tue Jan 7 18:38:46 EST 1997

Chemical Markup Language supports the management of molecular information
across a wide spectrum (sequences and macromolecular structures being
particularly relevant to this newsgroup).  It is offered as a tool for
those wishing to develop an object-oriented approach to interoperability
of molecular information.  This posting describes the first stable public

CML V1.0 is finally ready and posted and available for anyone who wishes
to develop applications.  It's free, as are the supporting java classes,
and we are already starting to build a community of developers.  

CML V1.0 has many new features, and has vastly expanded its potential
applications.  I have tackled many different disciplines and files and
believe that CML is powerful enough to represent most of them, and
certainly the chemical/* MIME types that I'm grafting through.  

The greatest enhancement is that CML is completely supported by Java
classes.  It's also compatible with the latest SGML developments on the
Internet, so it represents a single universal mechanism for realising
chemical/* MIME philosophy in being able to send and receive molecules
regardless of the platform or software.  It is also far easier to extend
and develop and maintain software in Java than other languages.

I would be interested in hearing from anyone interested in adding CML to
their toolkit.  It's particularly suitable for processing legacy
information, database submission and retrieval, postprocessing and
visualisation of program output, glossary development, scientific
publication, searching of semi-structured information, etc.  

CML is being offered in close collaboration with the Open Molecule
Foundation, a non-profit consortium of those interested in developing
object-oriented approaches to molecules and their interoperability.




CML is an SGML-based approach to managing molecular information,
especially over the Inter- and Intra-networks.  Version 1.0 is a major
enhancement over previous releases and is available for anyone wishing to
develop robust, Object-Oriented molecular applications.  Among its
features (many of which are new): 

	Object-Oriented and implemented in JAVA with hundreds of classes

	Accepts many common file types, especially chemical/* MIME

	Can process arbitrarily large files with no information loss

	Human-readable and easy to learn

	Flexible and easily extensible to many disciplines

	Supported by a communal effort, including the Open Molecule Foundation

	Ideal for postprocessing output from calculations and instruments

	Supports complex documents, including scientific publications

	Applications in protein sequence, molecular and crystal structure, quantum
		chemistry, spectra, organic molecules, publication, education

	Closely linked to the new XML/SGML developments on the Internet

	Free, including Java classes and API.

The home page http://www.venus.co.uk/omf/ includes many screenshots of the
language at work, and Java applets are also served for those with
compatible clients (For those primarily interested in general SGML
applications, there is a complete package of java classes for SGML/XML
parsing and rendering (including Shakespeare)). 

Peter Murray-Rust 

Peter Murray-Rust (PeterMR, ) Director, Virtual School of Molecular Sciences
Pharmaceutical Sciences, Nottingham University, NG7 2RD, UK; Tel 44-115-9515100
Fax 5110 http://www.nottingham.ac.uk/vsms/; OMF: http://www.ch.ic.ac.uk/omf/

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