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Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases.

ABSTRACT: Semantics-based model composition is an approach for generating complex biosimulation models from existing components that relies on capturing the biological meaning of model elements in a machine-readable fashion. This approach allows the user to work at the biological rather than computational level of abstraction and helps minimize the amount of manual effort required for model composition. To support this compositional approach, we have developed the SemGen software, and here report on SemGen's semantics-based merging capabilities using real-world modeling use cases. We successfully reproduced a large, manually-encoded, multi-model merge: the "Pandit-Hinch-Niederer" (PHN) cardiomyocyte excitation-contraction model, previously developed using CellML. We describe our approach for annotating the three component models used in the PHN composition and for merging them at the biological level of abstraction within SemGen. We demonstrate that we were able to reproduce the original PHN model results in a semi-automated, semantics-based fashion and also rapidly generate a second, novel cardiomyocyte model composed using an alternative, independently-developed tension generation component. We discuss the time-saving features of our compositional approach in the context of these merging exercises, the limitations we encountered, and potential solutions for enhancing the approach.

SUBMITTER: Neal ML

PROVIDER: S-EPMC4696653 | biostudies-other | 2015

REPOSITORIES: biostudies-other

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Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases.

Neal Maxwell L ML Carlson Brian E BE Thompson Christopher T CT James Ryan C RC Kim Karam G KG Tran Kenneth K Crampin Edmund J EJ Cook Daniel L DL Gennari John H JH

PloS one 20151230 12

Semantics-based model composition is an approach for generating complex biosimulation models from existing components that relies on capturing the biological meaning of model elements in a machine-readable fashion. This approach allows the user to work at the biological rather than computational level of abstraction and helps minimize the amount of manual effort required for model composition. To support this compositional approach, we have developed the SemGen software, and here report on SemGe ...[more]

PMID: 26716837

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Dataset Information

Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases.

Publications

Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases.

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