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Multiscale modeling within the computational biology initiative simulator framework

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Hugo S. Cornelis and Allan D. Coop (2023). Multiscale modeling within the computational biology initiative simulator framework. Journal of Multiscale Neuroscience 3(1) 




Extension of simulator functionality may result in the unintentional creation of a monolithic software platform. This greatly increases the difficulty of extending simulator software code to support new functionality, such as efficient multi-scale modeling. Analysis suggests that the difficulties of simulator extensibility faced by many software developers originate primarily in the biological and mathematical implementation of a model at the expense of considering the underlying software architecture. This limits software development efforts, thus simulator functionality and extensibility. Here, axioms defining the domain of computational neuroscience are developed. They provide a logical framework that organizes this approach to multiscale simulation. A framework underpins the modular design of the Computational Biology Initiative federated software architecture (for convenience, referred to here as the CBI federated software architecture) employed to reconfigure the GENESIS simulator. This has resolved many problems associated with multiscale modeling with this simulator. The approach to simulator structure and function development is outlined by describing the essential components of a simulator for multiscale modeling. Careful consideration of the issues identified greatly facilitates the development of a simulator capable of transparently supporting multiscale biological modeling across levels ranging from ionic and molecular to complete systems


Conflict of Interest

The authors declare no conflict of interest

Copyright: © 2023 The Author(s). Published by Neural Press.

This is an open access article distributed under the terms and conditions of the CC BY 4.0 license.

Disclaimer: The statements, opinions, and data in the Journal of Multiscale Neuroscience are solely those of the individual authors and contributors, not those of the Neural Press™ or the editors(s).

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