JCE Software, 5C2: Editorial

Dynamic Publications

John W. Moore
University of Wisconsin-Madison, Madison, WI 53706-1396

Note:
This issue is out of print.

This issue represents a giant step forward in electronic publishing of Journal of Chemical Education material. The article by Henderson, titled How a Photon Is Created or Absorbed: A Dynamic Publication is an electronic reprint of a paper that appeared in the October 1979 issue of the Journal (1) --but what a reprint! The still images in the original article have been converted to interactive spreadsheets or reader- controllable animations. These make it possible to explore the mathematical models presented and visualize the mechanism by which a hydrogen atom absorbs or creates a photon. The electronic document is far more effective in getting its points across than the original print article was.
We publish this electronic document here not only as a much enhanced version of the original, but also as a model for what publishing of chemical education materials can become in an era of electronic communication. Transfer of information can be greatly facilitated by including features that only computers and multimedia can provide: interactive, what if? simulations; animations; video; audio; etc. This dynamic publication shows that enhanced communication can be applied to academic discourse as well as to interactions with students. Use of computers, video, and other nonstandard materials is beginning to be seen in presentations at ACS national meetings and in academic journals. As journals become available electronically as well as in print, such improvements in academic communication will become more widely used. We expect that in ten years multimedia will be commonplace-even essential-in a well written communication of scientific results. What you see in this issue is only the beginning of an ongoing process.
Creating the first of a new breed of publications is not a trivial thing to do. A great deal of time and effort went into conceiving, preparing, and publishing what we fondly refer to as DynaPub I. At the fall 1992 ACS National Meeting we saw an example of a Microsoft Word document with embedded computer animations that had been created by programmers from Autodesk (2). It was clear that such a document was what electronic publishing is all about, and we initiated plans to create one. At about the same time we became aware that Bob Rittenhouse had created a raytracing algorithm that could produce well rendered figures and animations. Among other things Bob used his algorithm to prepare animations of atomic and molecular orbitals (3), and we concluded that Giles Henderson's 1979 paper would be an excellent choice to transform into a dynamic publication. During the summer of 1993 Bob Rittenhouse collaborated with John Wright to prepare prototype isosurface animations using MS-DOS computers, and Bob also wrote the spreadsheets that accompany Figures 4 and 5.
In August 1993 we approached Giles Henderson about making an electronic version of his paper, and he was enthusiastic and most helpful. He wrote BASIC code that produced individual frames in dot-density format, and he annotated the C code that Rittenhouse and Wright had created to show where changes were needed to make it correspond with the dot-density diagrams that he was generating. Giles also tried several cutaway views of the 2s to 1s transition in hopes of showing why the isosurface jumps in and out rather than varying smoothly in Figure 6 in the paper. Eventually we decided that showing both dot-density and isosurface formats separately but at the same time was the best way to deal with this. Giles went through the entire paper, rewriting sections and figure captions that needed to be modified to correlate with the new kinds of figures that were created. John Wright also carefully annotated the entire manuscript, adding his expertise in the teaching of laser spectroscopy to the revision process.
Jon Holmes translated into C the BASIC code that Giles Henderson sent us, incorporated Giles' annotations into Bob Rittenhouse's isosurface code, and modified the code so that the isosurfaces corresponded to the dot-density diagrams. The two programs were then combined and ported from MS-DOS to the Macintosh. A Quadra 800 was used to generate the frames in the final animations. There are 201 frames in each of these, and it requires about four minutes to calculate and render each frame. Once everything was ready, the Quadra spent a total of 24 hours making the two animations. Finally, Jon embedded the Excel spreadsheets and QuickTime animations into the written document, creating the final product you see here. Like anything new, this process took longer than we expected--it was conceived in 1992, begun during the summer of 1993, and was not completed until March 1994.
In addition to requiring considerable effort on the part of a dedicated group of people, this dynamic publication requires considerable electronic storage space. This issue consists of six disks, and the dynamic publication occupies five of them in compressed form. Roughly 12 MB of hard disk space is consumed when it has been uncompressed and installed. This is characteristic of animations where each frame is a full-screen color image and there are hundreds of frames. However, we are just getting into the era of multimedia software stored on CD-ROM drives, which provides an excellent solution to the problem of storing and delivering large quantities of information. Within the year JCE: Software will publish its first CD, and we expect this to become a major part of our operation in the next couple of years.
Though this first dynamic publication consumed a great deal of time and effort, we believe that the results are well worth it. What appears in this issue is far more instructive and valuable than the printed version. In addition we have learned a great deal that will facilitate preparation of subsequent dynamic papers. We would be happy to share that information with anyone else who is interested in creating and submitting similar papers to JCE: Software. If you might be such a person, let us know. We will welcome you aboard this new vehicle for communicating the ideas of chemistry as effectively as possible!
Literature Cited

Henderson, Giles F. J. Chem. Educ., 1979 56 (10), 631-635.
Voelz, J.; Mascitti, R.; Glauser, B.; Xue, W. "Hypermedia in chemistry: A new paradigm for dynamic information retrieval and exchange." Paper 16, Division of Chemical Information, ACS National Meeting, Washington, DC, August 25, 1992.
Rittenhouse, R. C. "Using 3D Graphics and Animation to Visualize Reality at the Atomic Level." Paper 345, Division of Chemical Education, ACS National Meeting, Denver, CO, March 31, 1993.

First Published: March 1994
Citation: Moore, J. W. Dynamic Publications J. Chem. Educ. Software 5C2
Keywords:

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Last Updated: April 26, 2001
Created: December 3, 1996 Created by: J. L. Holmes
Comments to: jceonline@chem.wisc.edu

© 1997 Division of Chemical Education, Inc., American Chemical Society. All rights reserved.



Dynamic Publications
John W. Moore University of Wisconsin-Madison, Madison, WI 53706-1396

Note:	This issue is out of print.

This issue represents a giant step forward in electronic publishing of Journal of Chemical Education material. The article by Henderson, titled How a Photon Is Created or Absorbed: A Dynamic Publication is an electronic reprint of a paper that appeared in the October 1979 issue of the Journal (1) --but what a reprint! The still images in the original article have been converted to interactive spreadsheets or reader- controllable animations. These make it possible to explore the mathematical models presented and visualize the mechanism by which a hydrogen atom absorbs or creates a photon. The electronic document is far more effective in getting its points across than the original print article was. We publish this electronic document here not only as a much enhanced version of the original, but also as a model for what publishing of chemical education materials can become in an era of electronic communication. Transfer of information can be greatly facilitated by including features that only computers and multimedia can provide: interactive, what if? simulations; animations; video; audio; etc. This dynamic publication shows that enhanced communication can be applied to academic discourse as well as to interactions with students. Use of computers, video, and other nonstandard materials is beginning to be seen in presentations at ACS national meetings and in academic journals. As journals become available electronically as well as in print, such improvements in academic communication will become more widely used. We expect that in ten years multimedia will be commonplace-even essential-in a well written communication of scientific results. What you see in this issue is only the beginning of an ongoing process. Creating the first of a new breed of publications is not a trivial thing to do. A great deal of time and effort went into conceiving, preparing, and publishing what we fondly refer to as DynaPub I. At the fall 1992 ACS National Meeting we saw an example of a Microsoft Word document with embedded computer animations that had been created by programmers from Autodesk (2). It was clear that such a document was what electronic publishing is all about, and we initiated plans to create one. At about the same time we became aware that Bob Rittenhouse had created a raytracing algorithm that could produce well rendered figures and animations. Among other things Bob used his algorithm to prepare animations of atomic and molecular orbitals (3), and we concluded that Giles Henderson's 1979 paper would be an excellent choice to transform into a dynamic publication. During the summer of 1993 Bob Rittenhouse collaborated with John Wright to prepare prototype isosurface animations using MS-DOS computers, and Bob also wrote the spreadsheets that accompany Figures 4 and 5. In August 1993 we approached Giles Henderson about making an electronic version of his paper, and he was enthusiastic and most helpful. He wrote BASIC code that produced individual frames in dot-density format, and he annotated the C code that Rittenhouse and Wright had created to show where changes were needed to make it correspond with the dot-density diagrams that he was generating. Giles also tried several cutaway views of the 2s to 1s transition in hopes of showing why the isosurface jumps in and out rather than varying smoothly in Figure 6 in the paper. Eventually we decided that showing both dot-density and isosurface formats separately but at the same time was the best way to deal with this. Giles went through the entire paper, rewriting sections and figure captions that needed to be modified to correlate with the new kinds of figures that were created. John Wright also carefully annotated the entire manuscript, adding his expertise in the teaching of laser spectroscopy to the revision process. Jon Holmes translated into C the BASIC code that Giles Henderson sent us, incorporated Giles' annotations into Bob Rittenhouse's isosurface code, and modified the code so that the isosurfaces corresponded to the dot-density diagrams. The two programs were then combined and ported from MS-DOS to the Macintosh. A Quadra 800 was used to generate the frames in the final animations. There are 201 frames in each of these, and it requires about four minutes to calculate and render each frame. Once everything was ready, the Quadra spent a total of 24 hours making the two animations. Finally, Jon embedded the Excel spreadsheets and QuickTime animations into the written document, creating the final product you see here. Like anything new, this process took longer than we expected--it was conceived in 1992, begun during the summer of 1993, and was not completed until March 1994. In addition to requiring considerable effort on the part of a dedicated group of people, this dynamic publication requires considerable electronic storage space. This issue consists of six disks, and the dynamic publication occupies five of them in compressed form. Roughly 12 MB of hard disk space is consumed when it has been uncompressed and installed. This is characteristic of animations where each frame is a full-screen color image and there are hundreds of frames. However, we are just getting into the era of multimedia software stored on CD-ROM drives, which provides an excellent solution to the problem of storing and delivering large quantities of information. Within the year JCE: Software will publish its first CD, and we expect this to become a major part of our operation in the next couple of years. Though this first dynamic publication consumed a great deal of time and effort, we believe that the results are well worth it. What appears in this issue is far more instructive and valuable than the printed version. In addition we have learned a great deal that will facilitate preparation of subsequent dynamic papers. We would be happy to share that information with anyone else who is interested in creating and submitting similar papers to JCE: Software. If you might be such a person, let us know. We will welcome you aboard this new vehicle for communicating the ideas of chemistry as effectively as possible! Literature Cited Henderson, Giles F. J. Chem. Educ., 1979 56 (10), 631-635. Voelz, J.; Mascitti, R.; Glauser, B.; Xue, W. "Hypermedia in chemistry: A new paradigm for dynamic information retrieval and exchange." Paper 16, Division of Chemical Information, ACS National Meeting, Washington, DC, August 25, 1992. Rittenhouse, R. C. "Using 3D Graphics and Animation to Visualize Reality at the Atomic Level." Paper 345, Division of Chemical Education, ACS National Meeting, Denver, CO, March 31, 1993.


News \| Issues \| CD-ROM / Video \| Find It! \| Technical Support \| For Authors
JCE Online \| Journal \| Software \| Internet \| Happenings \| About JCE \| Contact JCE

Last Updated: April 26, 2001 Created: December 3, 1996	Created by: J. L. Holmes Comments to: jceonline@chem.wisc.edu

© 1997 Division of Chemical Education, Inc., American Chemical Society. All rights reserved.