The Modeler's Workspace: Making model-based studies of the nervous system more accessible

Abstract

A realistic neuronal model represents a modeler's understanding of the structure and function of a part of the nervous system. The increasing number of such models represents a significant accumulation of knowledge about the structural and functional organization of nervous systems. However, locating appropriate models and interpreting them becomes increasingly more difficult as the number of online model and experimental databases grows. The central motivation for the Modeler's Workspace project is to address these problems. The Modeler's Workspace is a collection of software tools being created to enable users to interact with databases of models and data. It will provide facilities for: searching multiple remote databases for model components based on various criteria; visualizing the characteristics of the components retrieved; creating new components, either from scratch or derived from existing models; combining components into new models; linking models to experimental data as well as online publications; and interacting with simulation packages such as GENESIS to simulate the new constructs. It is being written in Java for portability and extensibility. It is modular in design and uses pluggable components. To increase the probability that the Modeler's Workspace will be compatible with future databases and tools, we arc using the XML, the eXtensible Markup Language, as the interchange format for communicating with databases.