1                   Introduction

Cell Illustrator™ (CI) is a software tool that enables biologists to model, elucidate and simulate complex biological processes and systems.  It allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways as well as dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins.   Cell Illustrator models are used to visualize biopathways, interpret experimental data and test hypotheses. In addition, it provides researchers with model diagrams of publication quality and simulation result charts.

Using a graphical user interface environment, researchers can create and simulate their own molecular pathway models.  Some of  the key features of Cell Illustrator are: (a) Pathway construction and visualization—construct models graphically by drag and drop Entities that represent bio-components in the biological pathways; (b) Pathways simulation—specify mathematical formulas for biochemical reactions in the pathway for simulation; The simulation can be run inside the workspace window in an interactive mode, or it can be sent to a remote server (Cell Illustrator Server) (c) Simulation replay – the simulation results can be logged and then visualized and analyzed in Cell Illustrator Player; (d) Simulation animation—Cell Illustrator?fs simulation results can be edited into an animation script file and then be used as the input to Cell Animator—a module that produces high quality presentation of the studied mechanism?fs dynamic behavior; (e)  Model import - previously created models or sub-models can be imported from SBML, CellML files or from public or proprietary libraries and databases like KEGG.

Since the version 3.0, Cell Illustrator enables the users to view and analyze gene relationships networks. This functionality is available in the special Gene Network mode. Therefore the graphical user interface of CI offers the user two modes of working:

(i)                  The Biopathway Modeling mode dedicated for simulation and modeling of complex biological processes and systems using Petri Net models – described in this manual

(ii)                The new Gene Network dedicated for analysis and exploration of gene relationship networks. This mode is described separately in the CI Gene Net Reference Manual.

 

The documentation for the Cell Illustrator software includes the manuals listed below:

Cell Illustrator User Guide:  Introduction to Cell Illustrator system

Cell Illustrator Reference Manual: Detailed description of Cell Illustrator functions

Cell Illustrator Player Reference Manual: Detailed description of Cell Illustrator Player functions

Cell Illustrator Server Installation Manual: Installation instructions for Cell Illustrator Server product (for IT System Administrators)

Cell Illustrator Gene Net Reference Manual: Detailed description of Cell Illustrator functions (Gene Network mode)

Cell Illustrator Gene Net User Guide: Introduction to the Gene Network mode of Cell Illustrator system

 

This manual is a reference for the functional features of Cell Illustrator version 3.0 (CI3.0) for the Biopathway modeling mode. It can be used to answer questions about specific system commands. For installation instructions and an introduction to modeling biological pathways with Cell Illustrator, please refer to the User Guide.