E-Cell Tutorial 2004

The E-Cell3 tutorial is an introductory text covering the basic elements required for modeling using the E-Cell3 software. The tutorial is structured such that each section is first introduced and described as a presentation, followed by some hands-on sessions on the subject.

Contents

The tutorial comprises of the following four sections:

1. E-Cell Basics:
   Basic concepts in E-Cell and first steps to modeling, including: Installing E-Cell3, using the E-Cell3 GUI, modeling a simple reaction using the Model Editor, modeling a toy pathway, scripting a simulation session and using the E-Cell Session manager
2. Glycolysis Modeling:
   Independent practice for deterministic modeling based on data from literature on erythrocyte glycolysis.
3. E-Cell Simulation Environment:
   Covers the architecture of E-Cell SE and simulation algorithms. For the hands-on session, users will create their own algorithm modules in C++ and Python
4. Composite modeling:
   A brief comparison on stochastic and deterministic modeling approaches is given using a heat-shock model implemented in three methods: deterministic, stochastic, and a hybrid of both approaches.

Requirements

• Intended Audience:
  This tutorial has been written for beginners who have never used the E-Cell3 software.
• Software Version:
  Contents of the tutorial have been written based on E-Cell version 3.1.101 (April 2004). Users may use newer versions of the software. However, some minor changes may have been implemented. Email e-cell-users@e-cell.org should you encounter any problems.
• Machine Environment:
  This tutorial has been tested on Redhat Linux v9 on an i386 platform. If you are using other operating systems, please refer to the following website for further download and installation information: http://ecell.sourceforge.net/download.html
• Supplementary Material:
  Template files used in the tutorial can be downloaded from the links below. In addition to template files, users are encouraged to refer to the E-Cell user manual, and other documents available in the E-Cell websites:
  - E-Cell3 Project: http://www.e-cell.org/software/documents
  - E-Cell3 Software: http://ecell.sourceforge.net/documentation.html

Section	Lecture Files (pdf)	Hands-on Text (pdf)	Supplementary Files
Basic Tutorial	1. About E-Cell 2. Introduction to E-Cell Modeling	E-Cell Basics (ver1.5)	Installation: ect04_rpms.tgz Toy Pathway: toy.em) Scripting: LTD.py / LTD2.py
Glycolysis Modeling	coming soon	coming soon	glycolysis.tgz glycolysis_answer.em
E-Cell Simulation Environment	E-Cell SE	1. Python Process 2. cpp Process	DMtemplate.cpp
Composite Modeling	Composite Modeling	HeatShock	HeatShock.tar.gz