E-CELL: software environment for whole-cell simulation

E-CELL: software environment for whole-cell simulation

We present E-CELL, a generic computer software environment for modeling a cell and conducting experiments in silico. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, in terms of a set of reaction rules. The system then executes those reactions iterativ...

E-CELL Project: Towards Whole Cell Simulation

Virtual Cell modelling and simulation software environment.

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...

The Virtual Cell Modeling and Simulation Software Environment

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 ...

Parallel Simulation Engines for Whole-Cell Models

The enormous complexity of whole-cell models needs new algorithmic approaches and high performant simulators. Our goal is the integration of deterministic and stochastic simulation algorithms in a highly scalable parallel simulator. Our hardware platform is a cluster of workstations as they are available in most research institutions. Therefore our parallel simulation engines are based on the M...