E-Cell System 3.1.105 review

E-Cell System is a concept of constructing virtual cells on computers. E-Cell System is an object-oriented software suite for mode

License: GPL (GNU General Public License) File size: 0K Developer: Kouichi Takahashi

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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

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:
This release includes improved ODE/DAE solvers, support for numpy, an updated empy preprocessor, and some more minor improvements.