E-Cell System

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

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).

What is new in this release:

• This version adds various bugfixes.

What is new in version 3.1.107 RC2:

• Fixed a bug in ecell.Session.saveLoggerData(). (Moriyoshi)
• Fixed a bug in ecell.ECDDataFile. (Moriyoshi)

What is new in version 3.1.107 RC1:

• Fixed compilation problem on newer GCC (>= 4.3). (Moriyoshi)
• Integrated pyecs into pyecell. (Moriyoshi)
• Merged ecell.emc into ecell.ecs to avoid static initializer weirdness in some platform (including Mac OS X). (Moriyoshi)
• Two GUI frontends (session-monitor and model-editor) were renewed to be two packages of python modules, ecell.ui.osogo and ecell.ui.model_editor. (Moriyoshi)
• Moved GtkSessionMonitor to ecell.ui.osogo.GtkSessionMonitor that resides in ecell/frontend/session_manager. (Moriyoshi)
• Renamed ecell.SessionManager to ecell.session_manager. (Moriyoshi)
• Removed the following constants from ecell.ecs_constants. (Moriyoshi)