Virtual Cell modelling and simulation software environment

I.I. Moraru, F. Morgan, Y. Li, L.M. Loew, J.C. Schaff, A. Lakshminarayana, B.M. Slepchenko, F. Gao, M.L. Blinov
2008 IET Systems Biology  
The Virtual Cell (VCell; http://vcell.org/) is a problem solving environment, built on a central database, for analysis, modeling 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,
more » ... ient-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 modeling decisions, assumptions, and approximations. The result is a physically consistent, mathematically rigorous, spatial modeling 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 reactiondiffusion-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 standardized 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 customized, experiment-centric modeling tools using a new plug-in based platform. NIH Public Access
doi:10.1049/iet-syb:20080102 pmid:19045830 pmcid:PMC2711391 fatcat:wql4fuivczgo7jakavcffuszgi