BPS2026 - VCell 8.0: Analysis of complex spatial simulations with ImageJ and Langevin dynamics modeling of multivalent assembly with SpringSaLaD

Virtual cell (VCell) is a comprehensive computational framework for modeling cell biology. It has an interface that is easily accessible to cell biologists and that permits construction of models, application of numerical solvers to perform simulations, and analysis of simulation results. VCell supports a number of key biophysical mechanisms, including reaction kinetics, diffusion, flow, membrane transport, lateral membrane diffusion, electrophysiology, and rule-based models of multi-state/multimolecular interactions. Simulations can be based on 0D, 1D, 2D, or 3D analytical or experimental image-based geometries. Users may choose among multiple available simulation approaches: ordinary differential equations, partial differential equations, stochastic reaction kinetics, network-free simulations, spatial particle-based simulations, and spatial hybrid stochastic/deterministic simulations. VCell is also built on a database for storage, reuse and sharing of models. Here, we introduce a significant release, VCell 8.0, with new functionality through extensive integration with ImageJ for analysis of spatial simulation results and integration of the SpringSaLaD simulator for highly coarse-grained simulations of molecular interactions. The former includes a newly developed ImageJ plugin that enables complex analysis protocols on multi-variable spatial simulation time series; these may be retrieved directly from the VCell database. SpringSaLaD models are constructed through an interface that leverages the pre-existing graphical rule-based modeling infrastructure in VCell for combinatorially complex multivalent binding reactions, adding the ability to specify coarse beads-on-a-string approximations for molecular shapes; the Langevin dynamics solver allows for the simulation and analysis of multiple stochastic trajectories. These new computational modeling tools will be illustrated, respectively, with analysis of simulations of FRAP experiments and the activation of SOS downstream of EGFR. (Supported by NIH grant R24 GM137787.)