catalog

1. Introduction

2. Getting Started

[2.1] System Requirements

[2.2] Installation Instructions

3. Quick Tour of Cellware

[3.1] Graphical User Interface

[3.2] Creating Model

[3.3] Defining Models

[3.3.1] Defining a Species

[3.3.2] Defining a Reaction

[3.4] Running Simulations

[3.5] Simulation Results

[3.6] Parameter Estimation Setup

[3.7] Parameter Estimation Results

[3.8] Loading pathways database

4. Cellware Modelling Environment

[4.1] Components

[4.1.1] Menu, Toolbar and Model Kit

[4.1.2] Species Editor

[4.1.3] Reaction Editor

[4.1.4] Compartment Editor

[4.2] Building a Model

[4.2.1] Adding Biological Components

[4.2.2] Adding Reactions

[4.2.3] Adding Compartments

[4.2.4] Editing Model

[4.3] Managing Models and SBML Support

[4.3.1] Saving Models

[4.3.2] Importing Models

[4.3.3] Exporting Models

[4.4] Simulating a Model

[4.4.2] Running Simulation on Local Computer and Accessing Results

[4.4.3] Submitting Simulation to Grid and Accessing Results

[4.4.4] Parameter Estimation

[4.5] Report Window

[4.6] Network analysis

5. Pathways Database Access

[5.1] Overview of Database Components

[5.1.1] Database node

[5.1.2] Organism node

[5.1.3] Pathways node

[5.1.4] Reaction node

[5.1.5] Compound node

[5.1.6] Enzyme node

6. Examples

[6.1] Michaelis Menten

[6.2] LacZ Operon Gene Expression Model

[6.3] Oregonator

[6.4] Signalling Enzyme Cascade

7. Technical Specifications

[7.1] Reaction Kinetics

[7.2] Simulation Algorithms

[7.2.1] Deterministic Algorithms

[7.2.2] Stochastic Algorithms

[7.2.3] Hybrid Algorithms

[7.3] Parameter Estimation Algorithms

[7.4] Graph Layout Algorithms

[7.5] Cellware Modelling & Simulation Environment

[7.5.1] Cellware Architecture

[7.5.2] Structure of Modeling and Simulation Environment

[7.5.3] Class Diagram of Pathway Model

[7.5.4] Object Structure of Algorithms Manager