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. PeterMR -------------------------------------------------------------------------------- CHEMICAL MARKUP LANGUAGE (CML) V1.0 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/ ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver@ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa@ic.ac.uk)
Call me thick, but however much I poured over the CML tutorial, FAQ etc. and however much I tried to get my brain around it, I couldn't see how to actually set up my (Java enabled) Internet Explorer to see CML in full blood. This is probably because it is obvious to those more expert than me how you take all the Java class stuff from Peter MR's web site and get things going. But, like so many people, my only encounter with Java is those useless applets that welcome you to web sites and tell you the time of day in San Francisco. As I've never been anywhere that had a real Java application, I'd always assumed that Java happened by magic: if they want you to be able to run a program, it will (firewall's permitting) jump into your browser. So I expected something similar to happen with CML. I've gone on at length because I expect I'm not the only dummy in this list who will have some problems going from the CML web site to a contented useage of what looks like a wondeful system. Help! Steve Steven Abbott steven@abbott.demon.co.uk http://www.autotype.com ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver@ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa@ic.ac.uk)
On Wed, 8 Jan 1997, Steven Abbott wrote:
Call me thick, but however much I poured over the CML tutorial, FAQ
No! (you can call *me* incompetent!)
etc. and however much I tried to get my brain around it, I couldn't see how to actually set up my (Java enabled) Internet Explorer to see CML in full blood.
The first phase of the release was to show the language and not to confuse it with a particular method viewing it. I should have made it clearer. The language can do lots of things besides being viewed, e.g. interfacing with databases, acting as a transport medium, structured searches, input for programs, etc. However, since languages developed with no technology often don't work well, it was very important to develop a technology with which the language can be tested. I hope and expect that people will develop other systems. None of the pages within the CML tree is activated at present to display Java. I intend to add additional examples in a week or so when I am sure they are working. If you want a preview, there are two molecular hyperglossaries under: http://www.venus.co.uk/vhg/glossaries/ e.g. http://www.venus.co.uk/vhg/glossaries/pps/java.html and look at an amino acid (e.g. tryptophan). But - be warned, it takes about 30 sec+ to download and gives rather horrid dispplays on some system (e.g. W95). Also sometimes incorrect classes get cached and this gives rise to errors. Debugging java problem on someone else'e client is not possible - sorry. So - given that I have already goofed :-) - although it was a subtle problem - I want to be careful about releasing the applets before they have been tested.
This is probably because it is obvious to those more expert than me how you take all the Java class stuff from Peter MR's web site and get things going.
But, like so many people, my only encounter with Java is those useless applets that welcome you to web sites and tell you the time of day in San Francisco. As I've never been anywhere that had a real Java application, I'd always assumed that Java happened by magic: if they want you to be able to run a program, it will (firewall's permitting) jump into your browser. So I expected something similar to happen with CML.
It will (and it does!) I have run it on W95, SGI, Sun and they have all worked (the SGI has a grotty default font, W95 sometimes refreshes 10 times when the mouse moves in the scrollbar. BUT the new release of JDK (1.1) fixes many of these problems. BUT JDK 1.1 doesn't work with certain browsers (e.g. Netscape 3). These problems will rapidly go away. Java is only one way of using CML - there are many others.
I've gone on at length because I expect I'm not the only dummy in this list who will have some problems going from the CML web site to a contented useage of what looks like a wondeful system.
Thanks! I am very confident that that Java+SGML is going to have an important part in the WWW and that the technology will mature very rapidly. How many of you remember the *first* PC version of Mossaic? P.
Help!
Steve Steven Abbott steven@abbott.demon.co.uk http://www.autotype.com ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver@ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa@ic.ac.uk)
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/ ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver@ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa@ic.ac.uk)
participants (2)
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peter murray rust
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Steven Abbott