E-Cell3 User Guide Table of Contents

Note: This document is currently under heavy construction. Please check back soon

Getting Started

  1. Introduction to the User Guide
    • Model ontology
    • Model flow
    • File types

1. The E-Cell User Interface - Osogo

  1. Session Monitor?
  2. Entity List Window?
  3. Message Window?
  4. Logger Window?
  5. Stepper Window?
  6. Interface Window?
  7. Board Window?
  8. About Window?
  9. Plugin Windows:
    1. Tracer Window?
    2. DigitalWindow?
    3. Variable Window?
    4. Bargraph Window?
    5. Property Window?

2. Running Models in E-Cell

  1. Basic Operation using Osogo
    1. Starting the E-Cell System
    2. Load a sample file
    3. Preparing result display from the Entity List Window
    4. Running a simulation
    5. Changing the Step Size
    6. Saving simulation results
    7. Shutting down the E-Cell System
  1. Basic Operation in script mode
    1. Starting the E-CELL System in Script Mode
    2. Running a simulation
    3. Saving simulation results
    4. Shutting down the E-Cell System

3. Constructing Models using E-Cell

  1. About E-Cell Model Files
    1. EML
    2. EM
  1. How to create a model file
    1. Writing an EM file
    2. Creating an EML file using the Model Editor
  1. Converting E-Cell Model files
    1. Using the Tool Launcher
    2. Command Line
  1. About Process Files
    1. Using Expression Flux Process
    2. Using Gillespie Process
    3. Composite Modeling
  1. Converting Process files
    • Creating Process files --> see E-Cell3 users manual

4. Plug-in / Tools

  1. Model Editor
  2. Tool Launcher
  3. Genome-based E-Cell Modeling (GEM)
  4. SBML support

Appendix

  1. Default Process Files
    1. Michaelis Uni Uni Process
    2. Mass Action Flux Process
    3. Catalyzed Mass Action Flux
    4. Michaelis Uni Uni Reversible
    5. Ping Pong Bi Bi Flux
    6. Iso Uni Uni Flux
    7. Ordered Bi Bi Flux Process
    8. Ordered Bi Uni Flux Process
    9. Ordered Uni Bi Flux Process
    10. Random Bi Bi Flux Process
    11. Random Bi Uni Flux Process
    12. Random Uni Bi Flux Process
    13. Rapid Equilibrium Process
    14. Gillespie Process

How to …

  • How to rename a window
  • How to change step size
  • How to add windows in a board window
  • How to add additional entities in a Tracer Window