Using Java in scientific research Part one: An introduction
Using Java in scientific research Part one: An introduction
By Bernd Binder
The basic language of scientific rules is coded to be platform independent. By knowing a few basic definitions, classes, and procedures, even aliens landing on earth should be able to quickly understand them. Consequently, a tool to communicate and simulate these rules should also obey this philosophy. Since it is unlikely the aliens could immediately run a Java-capable browser on their systems (though it would be one of their first efforts), I'll focus on human researchers around the world.
People can read new results in their favorite browser shortly after the author has finished his or her last sentence.
Pure research was one of the first areas to recognize the power of Java, as the Internet in its early stages was mainly a platform for scientists. The success of Java in science is only partly connected to the role of electronic publishing. Web pages became a new medium to present research results around 1992. The capabilities of the new medium are in a state of flux; but since 1996 with Java and contemporary browsers, these have reached a new stage. With enhanced versions, more and more scientific data is now being communicated through browsers (with or without plug-ins and add-ons) reading scientific files from public or private sites in standard HTML, Java, TeX, LaTeX, Postscript, DVI, PDF, and so forth.
Both writer and reader benefit from the new media. Preprints are sent to search-engines and servers (e.g., see arXiv.org), and people can read new results in their favorite browser shortly after the author has finished his or her last sentence. Soon, online archives combined with databases could become the primary form of reference (statistics from these servers show a strong increase in access rates).
Using the active links on a paper or the access to a searchable server is, obviously, much easier and faster than going to a library or to a copy machine. These active links are primarily used to connect readers to materials outside the publication and also allow them to jump inside the publication. Another advantage of electronic publications is the speed with which they can be widely disseminated. Part of the reduction in distribution time comes from shortening the refereeing process. To secure, verify, and document originality and accessibility, all files are mirrored and archived on servers distributed around the world. What is missing is the integration of a standard simulation platform into the TeX format. Implementing Java into scientific publications requires new standards. Tex or LaTeX could be another second-level Java platform. I suggest the inclusion of applet tags into the TeX language and to use a browser plug-in or a Java applet capable of displaying standard TeX/LaTeX scripts that include applets in a Java-enabled browser.
Change is constant
Because science is basically very conservative, and a good publication printed in a well-known journal traditionally has a better chance to appear in the standard literature, the primary medium to report and to preserve research results is the research paper — but the situation is changing. No one can stop the evolution from static material and prerecorded image sequences to interactive applications. Technically, Gordon H. Bradley in 1996 described the role of Java in research and publishing in, "Dynamic and Interactive Electronic Research Publications Using Java". He and others soon realized that applets offer the user a more-powerful way to interact with and publish material via Web pages. They can employ animation, graphics, games, sound, video, real-time updates, real-time interaction, and other functionality. However, in general, they have not had a major impact on the way that research is conducted. Java could change this.
Top scientists know very well that good results have to be promoted and communicated and not just published.
Most importantly, Java offers enhanced capabilities for conducting research over the Internet. Research authors can construct electronic publications that allow readers to execute applets to reproduce computational results. Authors can also include dynamic and interactive applets to present results and insights in ways not possible with static media. This brings an immediacy to research that was not possible before and thus could change not only how research is published but how research is conducted and what research is done. What was and is not clear is how this resource will be used in the future. To a highly satisfying degree Java has reached three primary goals:
- portability of applets without modification to all computers
- efficient execution of all tasks on all computers
- complete security for the user's computer environment and data.
The 1998 SCS International Conference on Web-Based Modeling and Simulation was the first conference dedicated to simulation and the Web. This paradigm represents a convergence of computer simulation methodologies and applications within the World Wide Web. Many thousands of wonderful applets and applications have been written over the last four years for the public. Excellent tools for displaying scientific results and generating simulations are extant, and there are already some candidates for standards.
The medium is the message
Scientific results must have broad public access, because it is the publication of a message that guarantees the impact of the result and the authorship of its contributor. Top scientists know very well that good results have to be promoted and communicated and not just published. Publication is an act of giving and demonstrating know-how while receiving feedback from the community. To promote results via visualization and simulation increases the chance of acceptance by the scientific community. Therefore, I suspect that in many cases a good Java simulation would have a stronger and broader impact than the boring and hard-to-read formalism of traditional presentations. Realistically, though, we can expect some scientists are going to be afraid to lose a headstart and/or some know-how by exposing their work to public simulation and reverse engineering.
This is not the case in the educational field, where applets nowadays can often be found. Combined with applets for remote control in the tech area, a lot of things in this arena become visual and even virtual. Virtual schools, colleges, and universities arise, and their power is based on the new technologies. Since more and more students and young scientists can handle C++ and Java or learn it in courses, these people are candidates for using sophisticated applets — with source.
Such users could well benefit from new venues of peer review, in the form of rating services that weigh the merits of scientific and educational Java resources. Well-organized repositories such as JARS and Gamelan fulfill some of the needs in this regard, but more could be done to satisfy scientific interests. (Often, highly honored researchers and clever students face the problem that, for example, a simulation of the dynamics of a black hole or a virus is judged by the same criteria as, say, a race-car game). Reviewing and rating scientific applets can guide users and at the same time be a stimulus for Web developers to improve the presentation and understanding of their own work. Let's look to this as a future opportunity for enhancing scientific communication.
[Ed. note: The author will explore the uses of Java as a scientific tool in future articles over the coming months.]
About the author
Dr. Bernd Binder is president and founder, 1994, of FITIN.com (FITIN: Fractal Iteration of Information) and currently participates in national and international IT projects. In 1996, he developed a cellular algorithm for creating fractals useful for encryption.