E-Cell 3 Features

This page describes specific features of E-Cell System Version 3 (as of v3.1.103)

(as of version 3.1.103)

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.

(Simulation methods below can be mixed in any combination in a model.)

Algorithm	Corresponding modules	Maintainer	Status
Gillespie-family Stochastic Simulation Algorithms
Gillespie-Gibson	GillespieProcess/NRStepper	shafi/kaizu	S
Explicit/implicit Tau-leap	TauLeapProcess/Stepper	kaizu/tomo	B
Langevin method		(kaizu)	D

Ordinary Differential Equations
Radau5/Dormand-Prince adaptive	ODEStepper	kaizu	S
Dormand-Prince 4(5)7M explicit	ODE45Stepper	kaizu	O
Fehlberg 2(3) explicit	ODE23Stepper	kaizu	O
Euler explicit	FixedODE1Stepper	kaizu	O

Differential-Algebraic Equations
Radau5 implicit	DAEStepper	kaizu	S

Power-law formalisms
S-System	SSystemProcess/Stepper	(kmaru)	DU
Generalized Mass-Action	GMAProcess/Stepper	(kmaru)	DU

Other simulation methods
Flux distribution hybrid		tomo	S
Discrete-time simulator	DiscreteTimeStepper	shafi	S
Generic discrete event	DiscreteEventStepper	shafi	B

The scripting interface is provided in Python language.

Feature	Corresponding modules	Maintainer	Status
Simulation session scripting	ecell3-session command	shafi	S
Analysis session scripting	ecell3-session-manager command	sugi	S
Model file generation	ecell.emllib Python module	zak	S

Feature	Corresponding modules	Maintainer	Status
SBML level 1/2 importing	ecell3-sbml2eml command	(ishida)	SU
SBML level 1/2 exporting	ecell3-eml2sbml command	(ishida)	SU

Feature	Corresponding modules	Maintainer	Status
Parallel Stepper scheduling	libecs/Scheduler	satya	D
Distributed computing	ecell3-session-manager command	msugi	S

Definitions:

Simulation session is..: A single run of a model under certain parameter set / condition. Also available as ecell.Session Python module.
Analysis session is..: A simulation experiment that involves many runs of simulation sessions (such as parameter tuning, metabolic control analysis etc..). Also available as ecell.SessionManager Python module.
Model file generation is..: Automated model generation, e.g. from databases.
Parallel Stepper scheduling is..: A shared-memory, multi-thread parallelization of a single simulation session by stepping multiple Steppers simultaneously, when possible. (to be merged into the main branch.)
Distributed computing is..: Running multiple simulation sessions on different computation nodes on cluster or grid environments. Currently Sun Grid Engine and Globus toolkit are supported.

Status::: S -- Stable. B -- Beta. D -- Under development. O -- Old (Deprecated; possibly removed from package in future releases). U -- Currently unmaintained, but intended to be part of the feature set.