A specification language and a framework for the execution of composite models in systems biology

When modelling complex biological systems it is often desirable to combine a number of distinct sub-models to form a larger composite model. We describe an XML based language that can be used to specify composite models and a lightweight computational framework that executes these models. The language supports specification of structure and implementation details for composite models, along with the interfaces provided by each sub-model. The framework executes each sub-model in its native environment, allowing extensive reuse of existing models. It uses mathematical and computational connectors and translators to unify the models computationally. Unlike other suggested approaches for model integration, our approach does not impose one modeling scheme, composition algorithm or underlying middleware framework. We demonstrate our approach by constructing a composite model describing part of the glucose homeostasis system. © Springer-Verlag Berlin Heidelberg 2006.