E-Cell System 3.1.105

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