E-Cell System is a concept of constructing virtual cells on computers.
E-Cell System is an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells, architected by Kouichi Takahashi and written by a wonderful team of developers. Core part of the system, E-Cell Simulation Environment version 3, allows many components driven by multiple algorithms with different timescales to coexist.
E-Cell Project is an international research project aiming at developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation.
E-Cell System consists of the following three major parts:
- E-Cell Simulation Environment (or E-Cell SE)
- E-Cell Modeling Environment (or E-Cell ME)
- E-Cell Analysis Toolkit
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Here are some key features of "E-Cell System":
Basic capabilities:
· Object-oriented modeling and simulation of complex systems.
· Plug-in architecture. New user-object classes can be developed, dynamically loaded, and used in simulation.
· Real-time user interaction and visualization during the simulation.
Scripting:
· Python scripting of a simulation session (run/stop/parameter manipulation/data processing etc...).
· Python scripting of a simulation experiment that involves many runs of the simulation sessions (such as parameter tuning, metabolic control analysis etc..)
· Python scripting of model file generation (e.g. for automated model construction from databases).
Compatibilities:
· SBML level 1/2 importing.
· SBML level 1/2 exporting.
Parallel computation:
· Shared-memory, multi-thread parallelization of a single simulation session. (to be merged into the main branch.)
· Cluster and grid distributed computation of multiple simulation sessions. Sun Grid Engine, (Globus toolkit).
What's New in This Release: [ read full changelog ]
· This version adds various bugfixes.
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