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From the ACS meeting
Chemistry
on the World Wide Web is picking up speed like a runaway train. A remarkable
number of groups are devoting considerable time, effort, and money to a wide
variety of chemical web applications.
The burgeoning activity was clear from presentations at two symposia in Orlando. Both had "intranets" in their names, referring to organization-specific information systems compatible with web standards. But the titles - "Intranets: Chemical Applications and Uses of Web Technologies" in the Division of Computers in Chemistry and "Chemical Information Intranets" in the Division of Chemical Information - turned out to be misnomers to a large extent.
Instead of homing in on internal networks in particular, the symposia focused primarily on web-based chemical applications in general. That approach carried over to an electronic poster session associated with the first symposium, which is accessible to anyone, not just registered ACS meeting participants (http://hackberry.chem.niu.edu/intranets/).
Chemistry professor Henry S. Rzepa of Imperial College, London, made the first presentation at the Computers in Chemistry symposium - most appropriate, given that Rzepa has staked out a reputation as a guru of all things chemical on the web. His talk, available on the Internet (http://www.ch.ic.ac.uk/talks/intranets/), provides a concise source of addresses for chemical developments on the web and, in fact, contains many of the links listed in this article.
Rzepa points out that the first chemistry articles specifically citing the web appeared only about three years ago and that the first book on chemistry and the web appeared around the end of 1995. However, the word "chemistry" recently yielded some 400,000 hits on the Alta Vista search engine and more than half a million on HotBot.
The language of the web, Hypertext Markup Language (HTML), is now beginning to become more friendly toward chemistry. For example, the newest web browsers - Netscape Navigator 3.0 and Microsoft Internet Explorer 3.0 - now make it possible to view Greek letters, an integral part of chemical nomenclature, in English HTML pages.
Peter Murray-Rust, director of the Virtual School of Molecular Sciences at the University of Nottingham, England, and others are working on a customized version of HTML called Chemical Markup Language as a basis for creating much richer chemical symbolism on web pages ( http://www.venus.co.uk/OMF/cml/index.html). Software for the language is available for download at that site.
A Chemical Markup Language browser is to be released this month. "It will, in fact, be a Java 'applet,' so it will run within Netscape Navigator or Microsoft Internet Explorer," says Rzepa. Java applets are small platform-independent programs that can be downloaded to a user's computer from a web page. The Java language was written by Sun Microsystems.
Also continuing to improve is Virtual Reality Modeling Language (VRML), which promises enhanced capabilities for creating, viewing, and manipulating three-dimensional molecular "objects" on the web. VRML ( http://www.ch.ic.ac.uk/vrml/) is being developed by a loose group of collaborators with some degree of coordination provided by Silicon Graphics, which has a related application called Molecular Inventor.
Groups at several universities have picked up the VRML standard for use in exchanging chemical visualization files. The first group to use VRML, and still one of the most active in the field, is that of chemistry professor Jürgen Brickmann of the Technical University of Darmstadt, Germany (http://ws05.pc.chemie.th-darm stadt.de/vrml/). (See Letter to the Editor). Researchers at the University of Erlangen-Nuremberg, Germany, have begun a service for generating VRML files from molecular data (http://schiele.organik.uni-erlangen.de/services/vrml.html).
In addition, a set of standards known as chemical MIME is being developed to enhance the transfer of chemical content over the web (http://www.ch.ic.ac.uk/chemime/iupac.html). MIME (multipurpose Internet mail extensions) is a set of standards for e-mail messages and hypertext documents. The adoption of chemical MIME standards is currently being considered by the International Union of Pure & Applied Chemistry. A related concept is chemical metadata (http://www.ch.ic.ac.uk/chemime/chemeta.html), a set of standards for identifying HTML documents as having chemical content, making them easier to index and search.
Web-based chemical education initiatives include Principles of Protein Structure, a course sponsored by Birkbeck College of the University of London (http:// www.cryst.bbk.ac.uk/PPS2/); WebElements, a periodic table on the World Wide Web with links to chemical data, developed by chemistry professor Mark J. Winter of the University of Sheffield, England (http://www.shef.ac.uk/ (http://www.shef.ac.uk/~chem/web-elements/); and the Virtual School of Molecular Sciences at the University of Nottingham (http://www.nottingham.ac.uk/vsms/), a set of courses on molecular design.
The first web robot for chemistry has been used to assemble thousands of chemical structures into the Chemical Structures Database (http://schiele.organik.uni-erlangen.de/services/webmol.html). The database was created by researcher Wolf-Dietrich Ihlenfeldt in chemistry professor Johann Gasteiger's group in the Computer Chemistry Center of the University of Erlangen-Nuremberg. The database contains chemical structures automatically collected from the Internet, with references to the web sites from which they were obtained. The file is searchable by structure and substructure, formula, name, and other properties. Ihlenfeldt has also developed a unique automated system that consults a network of databases to retrieve information about chemical compounds (http://schiele.organik.uni-erlangen.de/cactvs/).
Chemscape Chime, launched by MDL Information Systems as a free Netscape Navigator plug-in, allows scientists to view and manipulate molecules on an HTML page (http://www.mdli.com/chemscape/index.html). MDL later intends to release and market Chemscape Chime Pro, a program that will have the added capability of using molecules as a basis for queries to locate related structures in large molecular and reaction databases.
A group called the CLIC (Cambridge, Leeds, Imperial College) consortium is using software of the same type as a basis for an advanced electronic version of the journal Chemical Communications (http://chemcomm.clic.ac.uk/). Molecular Simulations' WebLab Viewer (http://www.msi.com/weblab/index.html) is another free program, similar to Chemscape Chime, that makes it possible to display and manipulate chemical structures interactively.
CambridgeSoft's ChemFinder WebServer (http://chemfinder.camsoft.com/) is a free web program that can be used to search and view molecular structures on other web sites. For example, a search on paclitaxel turns up nine sites with information on the anticancer agent. The ChemFinder database adds value to these links by providing physical property data on the molecules.
Chemically oriented Java applets are also proliferating. For example, WebSketch (formerly Sketch & Fetch) from Tripos (http://www.tripos.com/SandF.html) is a Java program that is used to draw molecules. The resulting structures can be used to perform chemical structure searches on molecular databases. Structures matching queries can then be displayed in a 3-D viewer (also a Java applet) on the WebSketch browser page.
Tripos senior product manager Dean Goddette points out that there are a number of advantages to using a web application like WebSketch instead of a traditional software program for structure searching. Goddette explains that Java applets don't have to be disseminated and installed like conventional programs, one form of code works on a wide variety of hardware platforms, and the applets enable people to work on their own desktop computers instead of having to borrow time on more powerful workstations.
Other Java applets include a chemical drawing module called Molecule Editor (http://www.chem.leeds.ac.uk/ICAMS/people/denis/moledit.html); ChemSymphony (http://www.cherwell.com/cherwell/ChemSymphony14/), a set of Java applets that facilitate the insertion of chemical structures into web documents; and HyperSpec (http://www.ch.ic.ac.uk/java/HyperSpec), a Java-based nuclear magnetic resonance spectral viewer.
Rzepa, Murray-Rust, and others are currently launching the Open Molecule Foundation (http://www.ch.ic.ac.uk/omf/) to promote the development of chemical and biological Java applets. "We hope this will serve as a nonproprietary independent mechanism - a bit like the Quantum Chemistry Program Exchange, I suppose - to promote the interchange of chemical and bioinformatics tools," says Rzepa. The Open Molecule Foundation will be the primary sponsor of Chemical Markup Language.
However, not everybody agrees on the benefits of Java. In fact, some information systems specialists recommend that users disable Java in their web browsers owing to security and system stability issues. Lockheed-Martin scientist Manton R. Frierson of the National Environmental Supercomputing Center, Bay City, Mich., says computer personnel at the center recommend against use of Java applets in part because executing foreign programs on one's computer is a "hacker's dream come true."
For example, Frierson says he's been warned that Java could permit Trojan- horse-type viruses to be loaded onto a user's computer and activated later. Another disadvantage of Java is that it causes slower downloading of web pages because of the extra code required.
To such objections, Rzepa replies that viewing Java applets is no more dangerous than running any other software program. In any case, he says, Java security is slated to be improved in future versions of Netscape Navigator. Murray-Rust adds that he believes Java to be "the most secure way of downloading resources from the World Wide Web and running them locally."
Whether or not reservations about Java will delay the development of chemical web applications is unclear. But if recent experience is any guide, the odds are against it. In its venerable three years of existence, development of the chemical web is proving to be anything but stoppable.
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