Abstract Systems Biology has taken advantage of computational tools and high-throughput
experimental data to model several biological processes. These include signaling, gene …

Quantitative models of biochemical networks (signal transduction cascades, metabolic
pathways, gene regulatory circuits) are a central component of modern systems biology …

Motivation: An increasing number of discrete mathematical models are being published in
Systems Biology, ranging from Boolean network models to logical models and Petri nets …

The biomolecules inside or near cells form a complex interacting system. Cellular
phenotypes and behaviors arise from the totality of interactions among the components of …

Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …

In recent years it has become clear that carcinogenesis is a complex process, both at the
molecular and cellular levels. Understanding the origins, growth and spread of cancer …

Computational systems biology is an emerging field in biological simulation that attempts to
model or simulate intra-and intercellular events using data gathered from genomic …

Highlights•The importance of biological models to systems biology is discussed.•The
principal role and desired characteristics of modeling languages in the development of …

How do living cells compute and control themselves, and communicate with their
environment? We describe the modeling and analysis of dynamic and reactive biological …

Understanding of the logic and dynamics of gene-regulatory and biochemical networks is a
major challenge of systems biology. To facilitate this research topic, we have developed a …