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Creative scientific documents in a modern computing environment.

Thanks to computers, creating scientific documents has in the last few years become a much simpler task. Hand-drawn chemical structures, pasted into spaces left in final drafts, have gone the way of the alembic. Several software suppliers offer scientific word processors with varying degrees of capability. The best of these let scientists create presentation-quality documents on their personal computers, complete with all graphic elements such as structures, charts and spectra. The time that researchers need to spend putting together a paper, report or presentation has decreased significantly, and the visual quality of the result has, in general, increased.

As beneficial as these programs are to scientists, room remains for improvement, both from the viewpoint of the individual scientist and from that of the entire organization. With recent advances in computer hardware and software technology and recent offerings by software vendors, needed improvements are not only possible but here today. Complete scientific wordprocessing packages are being replaced by individual specialized programs, often from different vendors, that work in concert to provide all of the capabilities of a packaged scientific word processor, plus substantial enhancements for broader scientific computing applications. Both individual scientists and research organizations as a whole can benefit from the new technology through greatly increased productivity.

Benefits to Each Scientist

Let us look first at how new systems can benefit the individual scientist? Information gathering is necessarily one of the most important steps in document creation. Yet information gathering has historically been divorced from the document-creation process, partly out of necessity due to technological restraints.

Using traditional technology, if a project leader wants to quickly put together a monthly report, all of the information needed from other software programs must be gathered for the report before entering a scientific wordprocessing program. The report can then be started and graphic elements created, such as chemical reaction schemes. If, midway through the report, the researcher realizes additional information is needed that resides in another computer program, say a corporate database, the document must be closed (after saving it, of course), the program exited, another program started to access the corporate database, write down or remember the needed information, exit that program, and, finally, add the missing information. Later the researcher may realize, with frustration, that additional information is needed from yet another software program. This all-too-common scenario is no longer necessary with programs available today that run in windowed computing environments.

Document creation in a windowed environment

For example, if our scientist were creating a document in a windowed word processing program, such as Microsoft Word running under Microsoft Windows on a PC, retrieving needed information would be much easier. Now if the scientist realizes information residing in a corporate database is needed, the program to access the information can be started, such as Molecular Design's ISIS/Base, while keeping Word running and the document active. Each program runs independently in its own window; each can be sized down to an icon or up to the size of the full screen. Once the information is retrieved, the chemist simply uses the windowing environment's cut-and-paste function to cut it out of ISIS/Base and paste it directly into the document in Word. ISIS/Base running while can be working on the document, in case additional information is needed later. This can be done with a few mouse clicks.

Because the researcher can simultaneously access multiple applications easily, the approach can be taken a step further and make information gathering an integral part of the document-creation process. While writing, the researcher can quickly access tables created in a windowed spreadsheet program such as Microsoft Excel or Lotus 1-2-3, and immediately paste pertinent information into the document. Figures created in a windowed graphics program such as CorelDraw or Micrografx Designer can be accessed. Spectra can be retrieved directly from windowed LIMS workstation software. Molecules, structures, activity data, physical data, bibliographic references, or a variety of other information from databases accessible through ISIS/Base, working in conjunction with ISIS/Host. If a structure or reaction can be retrieved does not already exist in an available database, the scientist can create it in a windowed chemical drawing package, such as ISIS/Draw, and paste it into the document. The researcher can access information and use it as needed as the document progresses, rather than having to gather it and record it beforehand, only to have to re-enter it in her document.

Information gathering in a distributed computing


Besides running in a windowed environment, ISIS/Base offers another important technological advantage that can make our researcher's job easier: it runs in a distributed computing environment. Translated, this means that individual computers in a corporate environment automatically do the tasks that they perform best, but the scientist only sees results on one computer. Thus, through ISIS/Base the chemist can access a world of scientific information -- whether from a project database on a nearby desktop or from a corporate database in a reaearch site on another continent using one desktop program.

Rick Belew, an assistant professor of computer sciences and engineering at the University of California, San Diego, describes this concept well as quoted in a recent special report on scientific computing in The Scientist: "The scientist sits at a PC to begin the search. If the computer has to go to the department file and then to the library file to find what the scientist seeks, it does so invisibly -- the scientist neither knows nor cares where the computer is searching. If the computation suddenly requires more memory than is available on the PC, the computer will go immediately to a larger computer to get what it needs. To the scientist in the lab it will all look as if it's happening on the desktop, not in another room or another state." [1]

If our researcher needs information on a specific compount for a report, one search for that compound can be done within ISIS/Base. The program may need to get structural data oan the compound from a corporate database residing down the hall, and activity test data from a relational database located in another building. In addition, the program may need to get the scientist's personal notes on the compound, which reside on the PC. Through one search, the program will gather all of the information from the various sources and present them simultaneously to the scientist in one coherent form. The needed information can be cut from the form and paste it in.

Document creation across multiple platforms

Now suppose that our project leader wants to add information from a junior researcher's weekly reports to her monthly report. However, he uses a Macintosh computer instead of a PC. With traditional scientific word processing programs, our senior researcher would have to rekey the information and redraw the structures from the hardcopy of the weekly report into her document on the PC.

Some modern windowed programs offer an important advantage: they can run on and share information across a variety of computing platforms. The benefits can be tremendous. For example the junior scientist finishes his weekly report in Microsoft Word on the Macintosh complete with a table and structures he drew in ISIS/Draw. (see Figure 1). He sends the report to his supervisor over a corporate network. The senior researcher retrieves the report in Word on her PC, running Microsoft Windows. She cuts a paragraph from his report and pastes it into her monthly report. She also decides to use one of his structures, but wants to make a slight modification to the chemical structure. So the project leader quickly pastes the structure into ISIS/Draw, and makes the modification. ISIS/Draw can make the changes because the structure retained its chemical significance even after being pasted into another application program and even after being moved to another computing platform. The scientist pastes the revised structure into the monthly report and sends it to the management staff and the research staff over the network, any of whom can use it as a foundation for their work.

Benefits to the Organization

Obviously, if individual scientists benefit by working faster and building on existing work, the organization benefits. A research organization can also derive additional benefits from standardizing their scientific computing with a windowed distributed computing system.

Efficient use of computer power

An important benefit of systems that rely on the concept of distributed computing is that organizations can add needed computing power incrementally as they need it, and they can use the power they have to its maximum efficiency. "A distributed environment solves the problem of adequately providing and using hardware resources," says Stephen Peacock, director of special projects as Molecular Design. [2] "Because of the modular architecture, distributed systems are ideal for growing companies. Computing power, in the form of individual servers, can be purchased as needed. Corporate planners are not forced to predict future computer power required. Computing power is also used most efficiently since servers are devoted to performing the jobs they do best."

Decreased training and support requirements

If half of a company's scientists use IBM PCs or PC compatibles and the other half use Macintosh computers, you might expect that they would require twice the amount of training and significantly more support services than if they all used the same kind of computer. This is in fact the case in many chemical research organizations. A significant advantage of the multiplatform software programs such as Microsoft Word, ISIS/Draw, and ISIS/Base is that research organizations can standardize with one word processor and one chemical drawing and data searching system, even if their chemists use a variety of computing platforms. If fact, the ISIS programs support six different computing platforms, with information transferable among all of them. Because the software looks essentially the same on all of the platforms, while still adhering to the 'look and feel' of each platform, one set of training materials and resources can be used to train all users, regardless of the computer they use.

An immeasurable advantage

An additional, less-tangible benefit of providing researchers with an integrated computing system as described above is perhaps the most valuable. By giving researchers unfettered access to needed information and a means to communicate it easily and effectively, an organization creates a fertile environment for scientific creativity. Unhampered by trivial barriers ineffective computing can present, new ideas can germinate and grow and bloom into even greater thoughts. If scientists are given time and freedom to tend their ideas, they will flourish, and results are sure to follow.


[1] Joel N. Shurkin and Rebecca Andrews, the Scientist, 23, (March 18, 1991)

[2] Stephen Peacock, Canadian Chemical News, pp. 26-7, (April 1990)
COPYRIGHT 1991 Chemical Institute of Canada
No portion of this article can be reproduced without the express written permission from the copyright holder.
Copyright 1991 Gale, Cengage Learning. All rights reserved.

Article Details
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Author:Dumont, Lise
Publication:Canadian Chemical News
Date:May 1, 1991
Previous Article:Can the computer alter our thinking?
Next Article:Chemistry at McMaster University.

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