We address important design considerations in effecting a network server-based experiment modeling system intended for integrative biology and biomedical research. We proceed to that end by following the progressive development of application features for our experimental qualitative process (QP) modeling system. Early work on a PC-based system for experimental biology focused on multiple-level visualizations of cellular immune responses, as well as receptor-mediated processes regulating protooncogene expression. Other practical applications focused on lymphocyte circulation and organopedesis, hyperbaric oxygenation effects on angiogenesis, macrophage migration, and fibroblast elaboration of ground substance. With the introduction of stabile Java technology in the mid-90s, work began on migrating the original PC-based modeling system environment (TSC) to a framework that would eventually support parallel execution of inference processes in a server-based environment. As the project has evolved, we have had to consider incorporating output functions of cooperative applications, issues for database and ontology importing, and technical challenges in representing level-unifying knowledge and experimental process rules.