Biopathway databases have been developed, such as KEGG and EcoCyc, that compile interaction structures of biopathways together with biological annotations. However, these biopathways are not directly editable and simulatable. Thus, we have made an application, the Biopathway Executer (BPE), that reconstructs these two major biopathway databases to XML formats of modeling and simulation platform...

The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjec...

Interactions at the cellular level are essential for maintaining the fundamental life processes in biological systems. The relationships that are established due to the biochemical reactions occurring within the cells often give rise to extremely complex network structures that may be conveniently represented by bipartite graphs; such networks are often known as biological pathway graphs (BPGs)...

The Na+/K+ ATPase is an essential component of cardiac electrophysiology, maintaining physiological Na+ and K+ concentrations over successive heart beats. Terkildsen et al. (2007) developed a model of the ventricular myocyte Na+/K+ ATPase to study extracellular potassium accumulation during ischaemia, demonstrating the ability to recapitulate a wide range of experimental data, but unfortunately...

This paper discusses the design goals and the first developments of PROTO-PLASM, a novel computational environment to produce libraries of executable, combinable and customizable computer models of natural and synthetic biosystems, aiming to provide a supporting framework for predictive understanding of structure and behaviour through multiscale geometric modelling and multiphysics simulations....

Networks of molecular interaction in biological processes reveal different levels of granularities, as well as different levels of abstraction. It is difficult to provide formal and explicit representations of diverse biological entities and their relationships. As an ontological approach, we present CSO (Ontology based representation of Cell System markup language), a pathway representation la...