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 chemical solutions that consist of dynamically nested, attributed entities. The model dynamics are described by rules that are constrained by arbitrary functions, which can operate on the entities’ attributes, (nested) solutions, and the reaction kinetics. Thus, ML-Rules supports an expressive hierarchical, variable structure modeling of cell biological systems. The formal syntax and semantics of ML-Rules show that it is firmly rooted in continuous-time Markov chains. In addition to a generic stochastic simulation algorithm for ML-Rules, we introduce several specialized algorithms that are able to handle subclasses of ML-Rules more efficiently. The algorithms are compared in a performance study, leading to conclusions on the relation between expressive power and computational complexity of rule-based modeling languages.

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In agent-based modeling and simulation, discrete-time methods prevail. While there is a need to cover the agents’ dynamics in continuous time, commonly used agent-based modeling frameworks offer little support for discrete-event simulation. Here, we present a formal syntax and semantics of the language ML3 (Modeling Language for Linked Lives) for modeling and simulating multi-agent systems as discrete-event systems. The language focuses on applications in demography, such as migration processes, and considers this discipline’s specific requirements. These include the importance of life courses being linked and the age-dependency of activities and events. The developed abstract syntax of the language combines the metaphor of agents with guarded commands. Its semantics is defined in terms of Generalized Semi-Markov Processes. The concrete language has been realized as an external domain-specific language. We discuss implications for efficient simulation algorithms and elucidate benefits of formally defining domain-specific languages for modeling and simulation.

Individuals' decision processes play a central role in understanding modern migration phenomena and other demographic processes. Their integration into agent-based computational demography depends largely on suitable support by a modelling language. We are developing the Modelling Language for Linked Lives (ML3) to describe the diverse decision processes of linked lives succinctly in continuous time. The context of individuals is modelled by networks the individual is part of, such as family ties and other social networks. Central concepts, such as behaviour conditional on agent attributes, age-dependent behaviour, and stochastic waiting times, are tightly integrated in the language. Thereby, alternative decisions are modelled by concurrent processes that compete by stochastic race. Using a migration model, we demonstrate how this allows for compact description of complex decisions, here based on the Theory of Planned Behaviour. We describe the challenges for the simulation algorithm posed by stochastic race between multiple concurrent complex decisions.

With the increasing size and complexity of models, developing models by composing existing ones becomes more important. We exploit the idea of reusing simulation experiments of individual models for composition to automatically generate experiments for the composed model. First, we illustrate the process of modeling based on composition and discuss the role simulation experiments can play in this process. Our focus is on semantic validation of the composed model. We explicitly specify simulation experiments in simulation experiment specification via a Scala layer, including the desired model behavioral properties and their required experiment setups. Models are annotated with experiment specifications, and upon composition, these specifications are adapted and automatically executed for the composed model. The approach is applied in a case study of developing a Wnt/b-catenin signaling pathway model by successively composing three individual models, where we exploit metric interval temporal logic to describe model behavioral properties and check averages of stochastic simulation results against these properties.