Mathematical and computational modelling are emerging as important techniques for studying the behaviour of complex biological systems. We argue that two advances are necessary to properly leverage these techniques: firstly, the ability to integrate models developed and executed on separate tools, without the need for substantial translation and secondly, a comprehensive system for storing and man-ageing not only the models themselves but also the parameters and tools used to execute those models and the results they produce. A framework for modelling with these features is described here. We have developed of a suite of XML-based services used for the storing and analysis of models, model parameters and results, and tools for model integration. We present these here, and evaluate their effectiveness using a worked example based on part of the hepatocyte glycogenolysis system. (c) 2006 Elsevier Ltd. All rights reserved.