PROTO-PLASM: parallel language for adaptive and scalable modelling of biosystems.

Full 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.

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Author information

Author/s: Bajaj, Chandrajit (C); DiCarlo, Antonio (A); Paoluzzi, Alberto (A);

Affiliation: Department of Computer Sciences, Center for Computational Visualization, Institute for Computational Engineering and Sciences, 201 East 24th Street, ACES 2.324, Austin, TX 78712-0027, USA. bajaj(-atsign-)cs.utexas.edu

Grants: P20-RR020647 (Agency:United States NCRR) ; R01-EB004873 (Agency:United States NIBIB) ; R01-GM07308 (Agency:United States NIGMS) ; R01-GM074258 (Agency:United States NIGMS)

Journal and publication information

Publication Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.

Journal: Philosophical transactions. Series A, Mathematical, physical, and engineering sciences (Philos Transact A Math Phys Eng Sci), published in England. (Language: eng)

Reference: 2008-Sep; vol 366 (issue 1878) : pp 3045-65

Dates: Created 2008/07/28; Completed 2008/09/30;

PMID: 18559320, status: MEDLINE (last retrieval date: 11/6/2008)

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Models, Cardiovascular
Models, Molecular
Models, Neurological
Neuromuscular Junction - physiology; ultrastructure
Physiology
Programming Languages
Systems Biology

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