Cell Illustrator

Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools and Cross-Omics>Agent-Based Modeling/Simulation/Tools

Abstract Cell Illustrator (CI) is a software tool that enables biologists to draw, model, elucidate and simulate complex biological processes and systems.

In conjunction with its outstanding drawing capabilities, CI allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways and dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins.

Cell Illustrator models are used to visualize biological pathways, interpret experimental data and test hypotheses. In addition, it provides researchers with model diagrams of publication quality and simulation result charts.

Cell Illustrator Functionality --

With Cell Illustrator you can:

1) Draw a biological pathway model;

2) Define its simulation properties;

3) Run the simulation and display its results; and

All this can be done in one window.

Drawing Biological Diagrams - Cell Illustrator provides biochemists with comprehensive visual representations of biochemical processes which form large and complex networks.

The software enables the user to create pathways from scratch or to import single reactions or whole pathways from databases, such as TRANSPATH® - (see G6G Abstract Number 20121).

The created diagrams give the user a new insight to understanding these networks, and the relationships between chemical components in structurally complex dynamic interactions and processes.

Defining the Simulation Model - The easy-to-use Petri Net design methodology and the intuitive interface make Cell Illustrator an excellent tool for biologist, biochemists, and scientists conducting research in life sciences as well as for graduate level educators.

Cell Illustrator Simulation Engines --

Cell Illustrator (CI) allows researchers to simulate complex biological processes. The modeling and simulation engine of Cell Illustrator is based on an extension of the Petri-net methodology. Cell Illustrator offers two (2) modes of simulation.

1) Standard Simulation Engine - The standard simulation engine is dedicated to the creating and testing of simulation models. It is fully integrated within the CI workspace window and allows for interactive pathway simulation.

The CI user can:

2) SECG - (Simulation Engine Code Generator) - SECG is based on the same hybrid functional Petri net with extension (HFPNe) model as the standard simulation engine described above, however it is faster, more customizable and adds special viewing and running modes.

The SECG concept allows you to generate source code for the simulated pathway model. This source code can then be compiled and executed within the Cell Illustrator workspace or in an external program or framework.

SECG can be used to:

Scripting Languages - Compatibility - Scripts are used in Cell Illustrator to define the complex logic of the Petri Net.

The scripting languages are different in versions 4.0 and 5.0 of Cell Illustrator. Cell Illustrator 5.0 supports several scripting languages: simplemath, Java, JavaScript and Pnuts, while Cell Illustrator 4.0 only supports one scripting language - Pnuts.

Note: In rare cases, models created with Cell Illustrator 4.0 cannot be simulated in version 5.0 without going through a provided conversion process.

New in Cell Illustrator 5.0 (August 2010) --

New User Interface - The user interface of Cell Illustrator version 5.0 has been rewritten from scratch in order to facilitate and speed up common operations. The new CI window offers a modern and more intuitive layout including:

1) Docking Frames and Toolbars;

2) Customizable Perspectives and View Settings;

3) Tabbed Pane with Multiple Models; and

4) Multiple Views of a Model.

Simulation Engine Enhancements - Cell Illustrator 5.0 supports new, more common scripting languages (as stated above…): Java and JavaScript facilitate the definition of complex logic in the Petri Net model, while the dedicated simplemath script language enables very fast execution of pure mathematical formulas.

Also, additional improvements have been completed for its simulation mode:

1) Interactive simulation run (e.g. Step mode) for SECG and Reference Simulation;

2) Display of connector/process speed on charts and on the canvas;

3) Easy definition and insertion of Simulation Plug-ins; and

4) Simplified creation of simulation logs.

Unified Gene Net and Bio-pathway View - The new ‘Fact Edges’ feature connecting two (2) entities allows for the easier definition of gene networks. The Gene Net mode is now integrated with the Bio-pathway mode, in the same graph window.

Extensive Support for Biological Properties -

Handling of Biological Properties was improved by:

1) Support for predefined Cell System Ontology (CSO) classes and hierarchy trees;

2) Improvement in the creating/editing of predefined and user-defined biological properties;

3) The display of all properties in element tables. The new Biological Properties frame also allows for sorting/filtering and finding elements by their biological property values;

4) The display of the Chemical Structure on 2D graphs; and

5) The display of the selected Biological Property on the canvas, as an element label.

Updates in Element Lists, Graph Layout, CSMLDB Search, etc. - Many small enhancements have been completed to increase the usability of Cell Illustrator and simplify the creation of Cell System Markup Language (CSML) models:

1) The CSMLDB Search frame offers a new function of creating user-defined databases from a set of CSML input files, which is available in the new User Database Manager Dialog box;

2) The Element Lists offer filtering and sorting of elements by their properties, and dedicated editors to ease the editing of single properties; and

3) The Graph Layout frame has been simplified; all available layout algorithms can be customized using a special Layout Options dialog box.

CSMLPipeline - CSMLPipeline is a separate software application created by the University of Tokyo, which allows for the transformation and integration of pathway models, gene networks and other biological databases based on the CSML and CSO concepts.

The CSMLPipeline allows for the automation of often repeated operation flows and procedures.

The new Curated Executable Macrophage Database is based on the CSMLDB concept and allows for searching and browsing pathways, reactions and single molecules within a web browser. Each found pathway can be opened in Cell Illustrator for further analysis or modification.

Data Assimilation - The ‘Parameterized Simulation’ function was extended to facilitate estimation of unknown parameters in a pathway model from time-course information.

Data Assimilation (DA) - DA is a computational approach that estimates unknown parameters in a pathway model using time-course information (as stated above…). Particle filtering, the underlying method used, is a well-established statistical method which approximates the joint posterior distributions of parameters by using sequentially-generated Monte Carlo samples.

System Requirements

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Manufacturer Web Site Cell Illustrator

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G6G Abstract Number 20155R

G6G Manufacturer Number 104246