Proto-Plasm : parallel language for adaptive and scalable modelling of biosystems

Abstract

This paper discusses the design goals and the first developments of Proto-Plasm, a novel computational environment to produce libraries of executable, combinable and customizable computer models of natural and synthetic biosystems, aiming to provide a supporting framework for predictive understanding of structure and behaviour through multiscale geometric modelling and multiphysics simulations. Admittedly, the Proto-Plasm platform is still in its infancy. Its computational framework—language, model library, integrated development environment and parallel engine—intends to provide patient-specific computational modelling and simulation of organs and biosystem, exploiting novel functionalities resulting from the symbolic combination of parametrized models of parts at various scales. Proto-Plasm may define the model equations, but it is currently focused on the symbolic description of model geometry and on the parallel support of simulations. Conversely, CellML and SBML could be viewed as defining the behavioural functions (the model equations) to be used within a Proto-Plasm program. Here we exemplify the basic functionalities of Proto-Plasm, by constructing a schematic heart model. We also discuss multiscale issues with reference to the geometric and physical modelling of neuromuscular junctions.

CAD models from medical images using LAR

“…Every d-cell is identified by a d-tuple of integer coordinates, mapped to a single integer, in order to compute the basis vector corresponding to the cell in the linear space C 3 …”

“…Their resolution is (0.004682 mm) 3 . The size of the image subset selected for visualization is 370 × 228 × 237.…”

“…In turn, the easiness of producing and collecting data in digital form has triggered a progressive paradigm shift from experiments on model organisms to simulation based on virtual prototypes and mathematical modeling [21,22,26,45,47,3].…”

“…In the near future, the collected knowledge of multifarious physiological subsystems on a hierarchy of dimensional scales and of a variety of biological functions will be formalized, catalogued, organized, shared and combined in many ways, providing integration across subsystems, temporal and spatial scales, biomedical and bioengineering disciplines, to give rise to personalized healthcare [3,22,47,21].…”

Cardiac electrophysiology numerical models using symmetric multiprocessing (SMP)

“…The current trend in electrophysiological modeling is to express and exchange biological models using extended mark up languages like CellML [2] and SBML [3]. We have studied a variety of tools performing cell tissue simulations: OxSoft Heart [4], E-Cell [5] [6] SimTool, Gepasi, STOCKS, StochSim, MCell [7], PROTO-PLASM [8]. All these tools cover different needs and no direct comparison can be performed.…”