RT Journal Article
A1 I.I. Moraru
A1 J.C. Schaff
A1 B.M. Slepchenko
A1 M.L. Blinov
A1 F. Morgan
A1 A. Lakshminarayana
A1 F. Gao
A1 Y. Li
A1 L.M. Loew

PB iet
T1 Virtual Cell modelling and simulation software environment
JN IET Systems Biology
VO 2
IS 5
SP 352
OP 362
AB The Virtual Cell (VCell; http://vcell.org/) is a problem solving environment, built on a central database, for analysis, modelling and simulation of cell biological processes. VCell integrates a growing range of molecular mechanisms, including reaction kinetics, diffusion, flow, membrane transport, lateral membrane diffusion and electrophysiology, and can associate these with geometries derived from experimental microscope images. It has been developed and deployed as a web-based, distributed, client–server system, with more than a thousand world-wide users. VCell provides a separation of layers (core technologies and abstractions) representing biological models, physical mechanisms, geometry, mathematical models and numerical methods. This separation clarifies the impact of modelling decisions, assumptions and approximations. The result is a physically consistent, mathematically rigorous, spatial modelling and simulation framework. Users create biological models and VCell will automatically (i) generate the appropriate mathematical encoding for running a simulation and (ii) generate and compile the appropriate computer code. Both deterministic and stochastic algorithms are supported for describing and running non-spatial simulations; a full partial differential equation solver using the finite volume numerical algorithm is available for reaction–diffusion–advection simulations in complex cell geometries including 3D geometries derived from microscope images. Using the VCell database, models and model components can be reused and updated, as well as privately shared among collaborating groups, or published. Exchange of models with other tools is possible via import/export of SBML, CellML and MatLab formats. Furthermore, curation of models is facilitated by external database binding mechanisms for unique identification of components and by standardised annotations compliant with the MIRIAM standard. VCell is now open source, with its native model encoding language (VCML) being a public specification, which stands as the basis for a new generation of more customised, experiment-centric modelling tools using a new plug-in based platform.
K1 partial differential equation solver
K1 stochastic algorithms
K1 reaction kinetics
K1 electrophysiology
K1 cell biological processes
K1 simulation software environment
K1 Virtual Cell modelling
K1 finite volume numerical algorithm
K1 lateral membrane diffusion
K1 molecular mechanisms
K1 native model encoding language
K1 membrane transport
DO https://doi.org/10.1049/iet-syb:20080102
UL https://digital-library.theiet.org/;jsessionid=259fc4ktp4m0k.x-iet-live-01content/journals/10.1049/iet-syb_20080102
LA English
SN 1751-8849
YR 2008
OL EN