E-Cell Simulation Environment Version 3.2.3pre2 User’s Manual

Koichi Takahashi

ktakahashi@riken.jp

RIKEN Quantitative Biology Center, Furuedai, Suita, Osaka 565-0874, Japan

• Legal
  • Feedback
• Introduction
  • What is ECELL
  • Organization of This Manual
• Getting Started
  • Preparing Simulation
    • Converting EM to EML
    • Compiling C++ Dynamic Modules
  • Starting APP
    • GUI mode
    • Scripting mode
    • DM search path and ECELL3_DM_PATH environment variable
• Modeling with ECELL
  • Objects In The Model
    • Types Of The Objects
    • Object Identifiers
    • Object Properties
  • E-Cell Model (EM) File Basics
    • What Is EM?
    • EM At A Glance
    • General Syntax Of EM
    • Macros And Preprocessing
    • Comments
  • Structure Of The Model
    • Top Level Elements
    • Systems
    • Variables And Processes
    • Connecting Steppers With Entity Objects
    • Connecting Variable Objects With Processes
  • Modeling Schemes
    • Discrete Or Continuous ?
    • Some Available Discrete Classes
    • Some Available Continuous Classes
  • Modeling Convensions
    • Units
• Modeling Tutorial
  • Running the model
  • Using Gillespie algorithm
    • A Trivial Reaction System
    • Specifying the Next Reaction method
    • Defining the compartment
    • Defining the variables
    • Defining reaction processes
    • Putting them together
  • Using Deterministic Differential Equations
    • Choosing Stepper and Process classes
    • Converting the model
  • Making the Model Switchable Between Algorithms
  • A Simple Deterministic / Stochastic Composite Simulation
    • A tiny multi-timescale reactions model
    • Writing model file
  • Custom equations
    • Complex flux rate equations
    • Algebraic equations
  • Other Modeling Schemes
    • Discrete events
• Scripting A Simulation Session
  • Session Scripting
  • Running ECELL Session Script
    • Running ESS in command line mode
    • Loading ESS from OSOGO
    • Using SessionManager
  • Writing ECELL Session Script
    • Using Session methods
    • Getting Session Parameters.
    • Observing and Manipulating the Model with OBJECTSTUBs
  • Handling Data Files
    • About ECD file
    • Importing ECDDataFile class
    • Saving and loading data
    • ECD header information
    • Using ECD outside ECELL SE
    • Binary format
  • Manipulating Model Files
    • Importing EML module
  • Other Methods
    • Getting version numbers
    • DM loading-related methods
  • Advanced Topics
    • How ECELL3-SESSION runs
    • Getting information about execution environment
    • Debugging
    • Profiling
  • ECELL Python Library API
    • SESSION Class API
• Creating New Object Classes
  • About Dynamic Modules
  • Defining a new class
    • DMTYPE, CLASSNAME and BASECLASS
    • Filename
    • Include Files
    • DM Macros
    • Constructor And Destructor
    • Types And Declarations
    • Polymorph class
    • Other C++ statements
  • PropertySlot
    • What is PropertySlot
    • How to define a PropertySlot
    • Using PropertySlots In Simulation
  • Defining a new Process class
  • Defining a new Stepper class
  • Defining a new Variable class
  • Defining a new System class
• Standard Dynamic Module Library
  • Steppers
    • DifferentialSteppers
    • DiscreteEventSteppers
    • DiscreteTimeStepper
    • PassiveStepper
  • Process classes
    • Continuous Process classes
    • Discrete Process classes
    • Other Process classes
  • Variable classes
• Simulation Mechanism of E-Cell
• Empy Module Manual

index

• Index
• Module Index
• Search Page