This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The continued evolution of the virtual cell requires the ability to gracefully extend the supported modeling domains as well as provide additional tools for analysis and interoperability. Drawing on our experience with the development of the existing Virtual Cell, we are now poised to define a generalized architecture for modeling and simulation for spatial and non-spatial modeling and simulation of cell physiology. The existing layered modeling approach of the Virtual Cell will be considerably generalized into a specification of abstract layers with clear semantics, clear interfaces and flexible representation and implementations. We will define a number of abstract services on these abstract data types and provide reference implementations of both data (models, data, mathematics) and services (solvers, analyzers, translators, mappings between layers). Through the use of an extensible set of translators and adapters, existing data formats (e.g. SBML, CellML, VCML) and tools (exiting and third party solvers, model analysis, data analysis and fitting) can be integrated within the modeling process. A high level modeling ontology will be created to formalize the semantic definitions, referencing or importing appropriate domain specific ontologies such as SBO.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR013186-12
Application #
7956407
Study Section
Special Emphasis Panel (ZRG1-CB-L (40))
Project Start
2009-05-01
Project End
2010-04-30
Budget Start
2009-05-01
Budget End
2010-04-30
Support Year
12
Fiscal Year
2009
Total Cost
$81,372
Indirect Cost
Name
University of Connecticut
Department
Anatomy/Cell Biology
Type
Schools of Medicine
DUNS #
022254226
City
Farmington
State
CT
Country
United States
Zip Code
06030
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Schaff, James C; Gao, Fei; Li, Ye et al. (2016) Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology. PLoS Comput Biol 12:e1005236
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Ditlev, Jonathon A; Mayer, Bruce J; Loew, Leslie M (2013) There is more than one way to model an elephant. Experiment-driven modeling of the actin cytoskeleton. Biophys J 104:520-32

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