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University of Connecticut Health Center - Know Better Care VCell - The Virtual Cell

VCell: an introduction and its capabilities

Introduction

VCell primary documents are the BioModel, MathModel, Geometry, Application and Simulation.

BioModel consists of the

  • Physiology - conceptual representation of the model: structures, molecules, connectivity map, kinetics.
  • One or more Applications - virtual experiments that can be simulated: initial conditions, actual morphologies, electrical protocols, etc.
    • An Application can be compartmental or it can use a Geometry (see below).
    • Each Application has a mathematical representation that is automatically generated and can be viewed.
    • For each Application you can specify one or more
      • Simulations (time length, resolution, solvers to use, parameter overrides, etc.) that will run and produce Results. Results can be viewed in VCell or exported to a variety of formats.

MathModel is somewhat equivalent to the math description of a BioModel Application – it is a direct specification of the equations to be solved, using the VCell modeling language. It can be compartmental or it can use a spatial Geometry. One or more Simulations must be defined for each MathModel to run and produce Results.

  • The math from a BioModel Application is a valid MathModel, but MathModel can not be extended to a BioModels. MathModels are needed to override biology-driven limitations of BioModels.

Geometry is a representation of a spatial structure which a BioModel Application (or a MathModel) can use for spatially resolved simulation. It can be 1-D, 2-D, or 3-D, and either analytically defined or based on a digital image.

 

Capabilities

    Non-Spatial Deterministic (ODE) Solvers

  • Forward Euler (First Order, Fixed Time Step)
  • Runge-Kutta (Second Order, Fixed Time Step)
  • Runge-Kutta (Fourth Order, Fixed Time Step)
  • Adams-Moulton (Fifth Order, Fixed Time Step)
  • Runge-Kutta-Fehlberg (Fifth Order, Variable Time Step)
  • IDA (Variable Order, Variable Time Step, ODE/DAE)
  • CVODE (Variable Order, Variable Time Step)
  • Combined stiff solver CVODE/IDA
 

    Spatial Deterministic (PDE) Solvers

  • Semi-Implicit Finite Volume, Regular Grid (Fixed Time Step)
  • Semi-Implicit Finite Volume Compiled, Regular Grid (Fixed Time Step)
  • Fully-Implicit Finite Volume, Regular Grid (Fixed Time Step).
 

    Non-Spatial Stochastic Solvers

  • Gibson (Next Reaction Stochastic Method)
  • Hybrid (Gibson + Euler-Matuyama Method)
  • Hybrid (Gibson + Milstein Method)
  • Hybrid (Adaptive Gibson + Milstein Method)
 
 

Parameter Estimation using COPASI for Non-Spatial Deterministic Problems

(Only available in VCell 5.1 Beta version or later)
The Virtual Cell incorporates the COPASI parameter estimation capabilites to optimize parameters in non-spatial deterministic models to best fit experimental data. The available optmization solvers are listed below:
  • Evolutionary Programming
  • Evolution Strategy (SRES)
  • Genetic Algorithm
  • Genetic Algorithm SR
  • Hooke and Jeeves
  • Levenberg - Marquardt
  • Nelder - Mead
  • Particle Swarm
  • Random Search
  • Simulated Annealing
  • Steepest Descent
  • Praxis
  • Truncated Newton
 

    Model specification

  • Comaprtmental volumes and membrane sizes
  • Concentrations and/or molecule counts for species
  • 3D Diffusion
  • 2D Membrane Diffusion
  • Advection (Velocity)
  • Local and global parameters
  • Initial conditions can be specified in terms of other model parameters, reserved symbols and species.
 

    Geometry

  • Creating analytic shapes in geometry editor.
  • Protein Subcellular Location Image Database (PSLID) import and data handling in FieldData.
  • Allow membrane field data from simulation results.
  • Predefined ROIs for existing spatial compartments.
  • ROIs from user defined Boolean functions.
  • ROIs from user drawn polygons.
  • Improved spatial data analysis for ROIs.
 

    User Interface

  • Auto-complete text
  • Sort and search in Math Viewer and Math Model editor.
 

    Export-Import Features

  • Links to BioModels.net database
  • Basic CellML import into MathModels.
  • Formalize VCML as XML document
  • Annotations (MIRIAM compliant)
  • Create pdf report of models
 

    Simulations

  • Field data (using images data as input to simulations)
  • CVODE solver used for Optimization in parameter estimation.
  • Parameter scans
  • 3D Surface Visualization for spatial simulation results

The Virtual Cell, a project of NRCAM, is developed by the Center for Cell Analysis & Modeling (CCAM)