Rule-based approaches (as in our own Kappa, or the BNG language, or many other
propositions allowing the consideration of" reaction classes'') offer new and more powerful …

We present two quantitative behavioral equivalences over species of a chemical reaction
network (CRN) with semantics based on ordinary differential equations. Forward CRN …

Rule-based modelling is particularly effective for handling the highly combinatorial aspects
of cellular signalling. The dynamics is described in terms of interactions between partial …

We introduce a graph-theoretic formalism suitable for modeling biochemical networks
marked by combinatorial complexity, such as signal-transduction systems, in which protein …

In systems biology modeling, important steps include model parameterization, uncertainty
quantification, and evaluation of agreement with experimental observations. To help …

We introduce Catalyst. jl, a flexible and feature-filled Julia library for modeling and high
performance simulation of chemical reaction networks (CRNs). Catalyst acts as both a …

The detailed structure of molecular networks, including their dependence on conditions and
time, are now routinely assayed by various experimental techniques. Visualization is a vital …

We apply the methods of optimal experimental design to a differential equation model for
epidermal growth factor receptor signalling, trafficking and down-regulation. The model …

Recent advances in genomics have led to the rapid and relatively inexpensive collection of
patient molecular data including multiple types of omics data. The integration of these data …

Objectives: To familiarize clinicians with advances in computational disease modeling
applied to trauma and sepsis. Data Sources: PubMed search and review of relevant medical …