Electro-Biological Simulation using a Web Front-End P. Schwaha, R. Heinzl, G. Mach, C. Pogoreutz, S. Fister, and S. Selberherr Institute for Microelectronics, TU Wien Gußhausstraße 27-29/E360, A-1040 Vienna, Austria E-mail: {schwaha | heinzl | mach | selberherr}@iue.tuwien.ac.at KEYWORDS Simulation, Biology, Web Application, Linux ABSTRACT We have developed a web application for the simula- tion in the field of electro-biology, particularly, for the analysis of a weakly electrically active fish. We investi- gated the charge relaxation due to the electric activity of the fish. The governing relaxation equation is dis- cretized with the finite volume method. The discretized equations are then implemented using a generic scientific simulation environment. To ensure high responsiveness and scalability we also included means to distribute the calculations to computers on a network. INTRODUCTION The pursuit and the acquisition of new insights is com- mon to all sciences. However, the methodologies and tools utilized to advance on the goal are quite different, due to the very different natures of the various scholarly disciplines. Simulation is a technique that has been ap- plied very successfully in several fields of science, such as physics, and has even spawned its own branch of re- search: scientific computing. While simulations have proven to be very important to understand the various phenomena in nature, some areas of research have all but neglected this technique. In order provide a means to quickly implement even complex algorithms directly in C++ we developed the scientific simulation environment (GSSE) [5, 6, 8, 13] which not only provides high performance but also takes into account the often neglected topic of software qual- ity. Although its roots can be traced to satisfy the needs of technology computer aided design (TCAD) [4, 11, 12, 14], its application is not limited to this field of research. Investigations concerning this during several student projects have been very positive [10]. One of these projects, that dealt with electric phenom- ena in biological organisms, also revealed that high per- formance is not the only important factor when coop- erating with scientists with very different backgrounds. In this context the benefit of appropriate visualization should also not be underestimated [2], as it often deter- mines how well the simulation results can be interpreted by the target audience. The goal therefore was to provide an user interface that is easily accessible by people from different fields of re- search with a minimum of effort. By following mod- ern application design rules, that components should be implemented orthogonally [7] it is made possible that the underlying simulation remains unmodified, which reduces sources of errors. Because access to the world wide web has become all but ubiquitous in the last years, it is a promising choice for a user interface. Most people are familiar with the interfaces and semantics established in web pages and HTML forms. It can be therefore viewed as common ground for people of scientifically different backgrounds. From this point of view web pages are well suited as an interface to applications that bridge the gap between different branches of science. THE SUBJECT UNDER INVESTIGATION Electric phenomena are common in biological organisms such as the discharges within the nervous system, but usually remain within a small scale. In some organisms, however, the electric phenomena take a more prominent role. Some species of fish, such as Gnathonemus petersii from the family of Mormyridae [3, 15, 16], use them for detection of their prey and for communication among their own kind. The nose region of G. petersii is modified to form a chin or snout like form. The shape representing the fish in the simulations is given in Fig. 1. The snouts possess very sensitive receptor cells which help to find small prey in the mud. Figure 1: A triangulated model of an electrically active fish. The position of the electrically active organ is marked in red. The goal of our simulations is to analyze the electric field generated by the fish, when different objects are introduced in the vicinity of the fish. This is difficult to obtain reliably with live specimen. The web application is described in the following section. 1 493