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Chemistry & Life Science

Newsletter

Cell Illustrator

Cell Illustrator is a software tool that enables biologists to draw, model, elucidate and simulate complex biological processes and systems. It has outstanding drawing capabilities, moreover 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 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 has been successfully utilized to model biological processes like Circadian Rhythms of Drosophila melanogaster, Glycolytic pathway and Fas ligand induced Apoptosis.
Functionality
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 his pathway from the scratch or to import single reactions or whole pathways from databases, such as Transpath. The created diagrams give the user a new insight to understanding these networks and relationships between chemical components in structurally complex dynamic interactions and processes.



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

All-in-One Window
Cell Illustrator lets you combine and integrate graphical, biological and mathematical properties and save it into one CSML model. The models can be simulated and the simulation results can be displayed and analyzed on charts. All this can be done within one and the same window.

 
Key Features
Creating Models:
  • Easy installation on all universal platforms, e.g. Windows, Linux, Mac.
  • Intuitive User Interface.
  • SVG Library of biological elements.
  • Properties of all model elements are tabulated and are easy to modify.
  • Asocciate with external Databases.
  • Integrated visualization mode for the analysis of Gene Relationship Networks.



Simulation:
  • Five simulation modes: three different continuous simulation modes, step simulation and step simulation with animation.
  • Variables' actual values can be displayed during simulation.
  • Discrete processes have unique animated simulation option to observe quantities flow through the system.
  • Simulation results can be presented on real-time graphs or exported to common format files.
  • A simulation run can be saved in a log file and replayed in Cell Illustrator Player.
  • The Simulation History dialog provides access to previous versions of a model and simulation results.
  • Parameterized Simulation allows to run a batch of similar simulation by varying one or more parameter. The simulation result can be compared on 3D charts.
  • Export the simulation model to source code. This source code can be customized, compiled and executed in an external application.

 
Simulation Engines
Cell Illustrator 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 modes of simulation described below.



Standard Simulation Engine:
The standard simulation engine is dedicated for 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:
  • Specify mathematical formulas for biochemical reactions.
  • Define complex logic of the Petri-net by writing scripts.
  • Test/run the simulation inside the CI workspace in an interactive way.
  • View/compare the simulation results on charts.
  • Save the simulation log and then visualize it in Cell Illustrator Player.

SECG - Simulation Engine Code Generator:
SECG is based on the same HFPNe model as the standard simulation engine described above, however it is faster, more customizable and adds special viewing and running modes. The SECG idea is to generate source code for the simulated pathway model. This source code can be compiled and executed within the Cell Illustrator workspace or in an external program or framework.

SECG can be used to:
  • Simulate large models.
  • Run parameterized simulations - perform a serious of simulations of the same model with varying values of selected parameter(s).
  • Compare the results of parameterized simulations in order to obtain the optimum values for the parameters.
  • Export the simulation model to a programming language, e.g. Java, C, C++, Fortran, Perl, Python.

Scripting Languages. Compatibility
Scripts are used in Cell Illustrator to define complex logic of the Petri Net. The scripting languages are different in the versions 4.0 and 5.0 of Cell Illustrator. Cell Illustrator 5.0 supports several scripting languages: simplemath, Java, JavaScript (js) and Pnuts, while Cell Illustrator 4.0 supports one language only - Pnuts. In rare cases it can happen that models created with Cell Illustrator 4.0 cannot be simulated in the version 5.0. The document Writing and Porting Scripts in Cell Illustrator 5.0 describes how to port such CSML models created with CI 4.0 and run simulations in CI 5.0.


 
Case Studies
Lineup
Cell Illustrator Professional
Contains a complete range of features for pathway modeling, allowing users to optimize productivity and efficiency. 

Cell Illustrator Draw
For general users, includes all functions of Cell Illustrator Professional for viewing, analyzing and drawing pathways.

Cell Illustrator Player (Free License)
Offers those aspiring to be medical professionals a package containing basic features, available without charge, to view pathways.


Software Comparison for Cell Illustrator Desktop 5.0 Editions:
Function Professional Draw Player
View pathways (Load CSML files) Yes Yes Yes
Create/edit pathways Yes Yes No
Simulate pathways Yes No No
Pathway samples Yes Yes Yes

 

Cell Illustrator

Cell Illustrator is a software tool that enables biologists to draw, model, elucidate and simulate complex biological processes and systems. It has outstanding drawing capabilities, moreover 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 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 has been successfully utilized to model biological processes like Circadian Rhythms of Drosophila melanogaster, Glycolytic pathway and Fas ligand induced Apoptosis.
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 his pathway from the scratch or to import single reactions or whole pathways from databases, such as Transpath. The created diagrams give the user a new insight to understanding these networks and relationships between chemical components in structurally complex dynamic interactions and processes.



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

All-in-One Window
Cell Illustrator lets you combine and integrate graphical, biological and mathematical properties and save it into one CSML model. The models can be simulated and the simulation results can be displayed and analyzed on charts. All this can be done within one and the same window.

 
Creating Models:
  • Easy installation on all universal platforms, e.g. Windows, Linux, Mac.
  • Intuitive User Interface.
  • SVG Library of biological elements.
  • Properties of all model elements are tabulated and are easy to modify.
  • Asocciate with external Databases.
  • Integrated visualization mode for the analysis of Gene Relationship Networks.



Simulation:
  • Five simulation modes: three different continuous simulation modes, step simulation and step simulation with animation.
  • Variables' actual values can be displayed during simulation.
  • Discrete processes have unique animated simulation option to observe quantities flow through the system.
  • Simulation results can be presented on real-time graphs or exported to common format files.
  • A simulation run can be saved in a log file and replayed in Cell Illustrator Player.
  • The Simulation History dialog provides access to previous versions of a model and simulation results.
  • Parameterized Simulation allows to run a batch of similar simulation by varying one or more parameter. The simulation result can be compared on 3D charts.
  • Export the simulation model to source code. This source code can be customized, compiled and executed in an external application.

 
Cell Illustrator 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 modes of simulation described below.



Standard Simulation Engine:
The standard simulation engine is dedicated for 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:
  • Specify mathematical formulas for biochemical reactions.
  • Define complex logic of the Petri-net by writing scripts.
  • Test/run the simulation inside the CI workspace in an interactive way.
  • View/compare the simulation results on charts.
  • Save the simulation log and then visualize it in Cell Illustrator Player.

SECG - Simulation Engine Code Generator:
SECG is based on the same HFPNe model as the standard simulation engine described above, however it is faster, more customizable and adds special viewing and running modes. The SECG idea is to generate source code for the simulated pathway model. This source code can be compiled and executed within the Cell Illustrator workspace or in an external program or framework.

SECG can be used to:
  • Simulate large models.
  • Run parameterized simulations - perform a serious of simulations of the same model with varying values of selected parameter(s).
  • Compare the results of parameterized simulations in order to obtain the optimum values for the parameters.
  • Export the simulation model to a programming language, e.g. Java, C, C++, Fortran, Perl, Python.

Scripting Languages. Compatibility
Scripts are used in Cell Illustrator to define complex logic of the Petri Net. The scripting languages are different in the versions 4.0 and 5.0 of Cell Illustrator. Cell Illustrator 5.0 supports several scripting languages: simplemath, Java, JavaScript (js) and Pnuts, while Cell Illustrator 4.0 supports one language only - Pnuts. In rare cases it can happen that models created with Cell Illustrator 4.0 cannot be simulated in the version 5.0. The document Writing and Porting Scripts in Cell Illustrator 5.0 describes how to port such CSML models created with CI 4.0 and run simulations in CI 5.0.


 
Cell Illustrator Professional
Contains a complete range of features for pathway modeling, allowing users to optimize productivity and efficiency. 

Cell Illustrator Draw
For general users, includes all functions of Cell Illustrator Professional for viewing, analyzing and drawing pathways.

Cell Illustrator Player (Free License)
Offers those aspiring to be medical professionals a package containing basic features, available without charge, to view pathways.


Software Comparison for Cell Illustrator Desktop 5.0 Editions:
Function Professional Draw Player
View pathways (Load CSML files) Yes Yes Yes
Create/edit pathways Yes Yes No
Simulate pathways Yes No No
Pathway samples Yes Yes Yes