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

Margoninski, O; Saffrey, P; Hetherington, J; Finkelstein, A; Warner, A; (2006) A specification language and a framework for the execution of composite models in systems biology. TRANSACTIONS ON COMPUTATIONAL SYSTEMS BIOLOGY VII , 4230 163 - 184.

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Abstract

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.

Type:Article
Title:A specification language and a framework for the execution of composite models in systems biology
Location:San Francisco, CA
Keywords:COMPUTATIONAL CHALLENGES, CELL SIMULATION
UCL classification:UCL > Professional Services > Information Services Division > Research IT Services > Research Comp and Facilitating Services
UCL > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > School of BEAMS > Faculty of Engineering Science > Engineering Science Faculty Office

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