Background Proteins, individual cells, and cell populations denote different levels of an
organizational hierarchy, each of which with its own dynamics. Multi-level modeling is …

Tasks such as social network analysis, human behavior recognition, or modeling
biochemical reactions, can be solved elegantly by using the probabilistic inference …

The domain-specific modeling and simulation language ML-Rules is aimed at facilitating the
description of cell biological systems at different levels of organization. Model states are …

Multi-state modeling of biomolecules refers to a series of techniques used to represent and
compute the behavior of biological molecules or complexes that can adopt a large number …

Compartmentalization is vital for cell biological processes. The field of rule-based stochastic
simulation has acknowledged this, and many tools and methods have capabilities for …

The domain specific modeling and simulation language ML-Rules makes it possible to
describe cell biological systems at different levels of organization. A model is formed by …

The notion of (self-) adaptation, according to J. Holland (1975), describes the process of
iterative refinement of an entity's behavior or structure to improve its performance in its …

From the phosphorylation state of a molecule to the volume of a cell, parameters are
ubiquitous in systems biology. At the same time, most models involve static or dynamic …

Rule-based modeling is an established paradigm for specifying simulation models of
biochemical reaction networks. The expressiveness of rule-based modeling languages …

The Calculus of Wrapped Compartments (CWC) is a recently proposed modelling language
for the representation and simulation of biological systems behaviour. Although CWC has no …