Architectural mismatch or why it's hard to build systems out of existing parts
Proceedings of the 17th international conference on Software engineering
Model composability: formulating a research thrust: composable simulations
Proceedings of the 32nd conference on Winter simulation
Proceedings of the 35th conference on Winter simulation: driving innovation
The potential coupling interface: metadata for model coupling
WSC '04 Proceedings of the 36th conference on Winter simulation
Foundations of validating reusable behavioral models in engineering design problems
WSC '04 Proceedings of the 36th conference on Winter simulation
A case study of model context for simulation composability and reusability
WSC '05 Proceedings of the 37th conference on Winter simulation
Challenges for modeling and simulation methods in systems biology
Proceedings of the 38th conference on Winter simulation
Fusing and composing macromolecular regulatory network models
SpringSim '07 Proceedings of the 2007 spring simulation multiconference - Volume 2
Model Composition for Macromolecular Regulatory Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Today's macromolecular regulatory network models are small compared to the amount of information known about a particular cellular pathway, in part because current modeling languages and tools are unable to handle significantly larger models. Thus, most pathway modeling work today focuses on building small models of individual pathways since they are easy to construct and manage. The hope is someday to put these pieces together to create a more complete picture of the underlying molecular machinery. While efforts to make large models benefit from reusing existing components, unfortunately, there currently exists little tool or representational support for combining or composing models. We have identified four distinct modeling processes related to model composition: fusion, composition, aggregation, and flattening. We present concrete proposals for implementing all four processes in the context of the Systems Biology Markup Language (SBML).