Chemistry and the World-Wide-Web

Omer Casher[1], David C. Doherty[2], Peter C. FitzGerald[3], Jonathan Goodman[4], Martin Hargreaves[5], Jan K. Labanowski[6], Peter Murray-Rust[5], Henry S. Rzepa[1,7], Mark J. Winter[8] and Benjamin J. Whitaker[9].

[1] Department of Chemistry, Imperial College, London, SW7 2AY, UK. [2] Minnesota Supercomputer Center, Inc., 1200 Washington Avenue, South Minneapolis, MN 55415 USA [3] CMBS/DCRT, National Institutes of Health, Bethesda, Maryland, USA [4] Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK. [5] Glaxo Research and Development Ltd, Greenford Road, Greenford, Middlesex, UK. [6] Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163, USA. [7] Workshop chairman. [8] Department of Chemistry, University of Sheffield, Sheffield, UK. [9] School of Chemistry, University of Leeds, Leeds, UK.
Workshop Summary: A review of some of the existing chemical applications of World-Wide-Web was presented by the workshop chairman. It was generally recognised that the existing implementations of html as supported by browsers such as Mosaic V2.4 were chemically deficient, and that the proposed standards html 3.0 and beyond would serve the subject better. Following the earlier submission of an Internet Draft introducing chemical MIME types, several presentations illustrated how these could used for novel chemical information delivery. The World-Wide-Web was considered to have an important role in chemical industry, in teaching and in research.

The Workshop Topics.

The 16 participants attending the workshop in person represented a diversity of interests, which contributed to an interesting and highly productive discussion initiated by the contributions received prior to the workshop. One general theme to emerge was the apparently recursive nature of many existing chemical servers in citing each other, but not offering much novel or original material. It was suggested that servers providing largely local or parochial information should indicate this function clearly, and since such a server was unlikely to be of much interest to users outside the home institution, there would be little need for many external links to it. Servers with a significant component of original material or offering a "value-added" service should help to identify this function, perhaps via a keyword summary in the home page, and it was clearly appropriate that other servers should be linked to it. There is currently little discrimination between these two types of servers in the existing chemical lists.

Several of the workshop contributions involved the use of chemical MIME types in conjunction with programs such as RasMol and XMol as 3D molecular visualisers. This caused much interest, since such 3D applications are not yet common outside molecular chemistry and biology. It was noted that several companies will shortly be bringing to market a set of low cost "active" 3D glasses designed to fit to the graphics board of Windows or Macintosh systems, and what was now needed was the development of suitable software. This was placed in the context of the proposed VRML (Virtual Reality Markup Language) discussed in another workshop, and it was agreed that chemical applications of such concepts to molecular sciences hold immense potential. To fulfill this potential, the chemistry and molecular biology communities should be aware of and perhaps even involved in the development of standards, and should press for the incorporation of chemical syntax and semantics into future html definitions and the common-graphical-interface (cgi) standards. The way forward was seen as having molecular structures represented within the protocols as "live molecules" rather than as "dead" bitmaps as at present.

Future directions such as molecular mapping and 3D mapping, molecular indexing and searching, integrated videoconferencing and whiteboarding techniques were identified as active development areas.

Summary of Workshop contributions.

These were submitted in the form of URL references prior to the workshop, and are indicated here by title only. In the electronic version of this workshop summary, these hyperlinks are active.
  1. A List of WWW Chemistry servers
  2. Molecular Whiteboarding. Omer Casher and Henry S Rzepa.
  3. XMol as an Internet Tool for Computational Chemistry David C. Doherty, Joel Neisen and David Pratt
  4. A WWW Forms interface to facilitate access (browsing, searching and viewing) of the molecular structure data contained within the Brookhaven Protein Data Bank (PDB). Peter FitzGerald
  5. Boron Mediated Aldol condensations. Jonathan Goodman.
  6. The Use of RasMol and WWW in Chemical Industry. Martin Hargreaves and Roger Sayle
  7. The Computational Chemistry List and WWW Server. Jan K. Labanowski and R. Berry
  8. An Internet Draft: draft-rzepa-chemical-mime-type-00.txt Henry S. Rzepa and Peter Murray-Rust
  9. The Use of Chemical MIME Types and Forms in Chemistry. Henry S Rzepa and Benjamin J. Whitaker
  10. Chemical Electronic Publishing, Chemical On-line Presentations and Talks and Chemical Structure Mapping. Henry S. Rzepa
  11. The Use of HyperCard and Applescript with WWW. Mark J. Winter