New features in Cell Illustrator 3.0 (latest version)

• Import of SBML/CellML files
  

New input filters allow importing models stored in the widely used CellML and SBML formats. The imported SBML/CellML models are converted to Cell Illustrator models and can be edited, analyzed, simulated or saved as any other Cell Illustrator model. This function converts SBML/CellML models, which use differential equations for representing relationships between entities, to CI models, which use the Petri Net formalism used in CI.

• Library of SVG graphical elements
  

The library of Biological Elements has been extended with SVG images representing biological entities, processes and cellular components. The library consists of: about 40 images for biological entities, more than 250 images for biological processes and about 70 images for cell components. Each image corresponds to one Cell System Ontology term. Each image can be edited in the SVG editor included in Cell Illustrator.

• Enhancements in the Petri net simulation engine
  

New options for a better control of the simulation flow have been added. The weak firing and firing accuracy options available in the Simulation Settings facilitate the simulation of continuous models.

• Improved charts
  

Charts dialog boxes have been enhanced for improved viewing, analysis and control of simulation results.

• External references
  

Since the version 3.0, Cell Illustrator offers an extensive support for external references to public databases, Gene or Cell Ontology terms, etc. These references can be defined in the new Biological tab of the Element Setting dialog box, as well as in the redesigned External References dialog box. Also, URL Templates can be defined to access public databases. The URLs of the external references can be opened in the web browser.

• Gene network view
  

The added Gene Network Mode enables the user to view and explore gene relationship networks. This mode offers a special visualization style and tools for the analysis of gene relationship networks, such as Pathway Search, Sub-network Extraction and Network Merge.

This release note for Cell Illustrator 3.0 is available for download (PDF, 60KB).

• New kinetic styles for easier simulation of biological processes
  

With the new kinetic styles of a process: mass, stochastic mass and connector rate you can build models more easily and define the kinetics of chemical reactions and biological processes. You just need to define reaction parameters such as stoichiometry, rate, mass coefficients and the process speed will be automatically calculated. Additionally, you can introduce random perturbations using the stochastic mass function, which allows for modeling reactions and processes of stochastic nature.

• The Element Settings and Element Lists dialogs have been improved
  

The Element Settings and Element Lists dialogs have been redesigned to simplify model building and analysis. For all process types, you can now view and set all process kinetic properties in one place; the Process Sheet.

• New graph layout algorithms
  

Using the Graph Layout dialog, you can “beautify” the layout of the model elements on the active canvas. This option can be especially useful when importing models from the BioPACS database or converting models from other formats.

• Support for SVG files
  

Scalable Vector Graphics (SVG) files can be added to the models as any other image files (PNG, JPEG). An editor of SVG files has been included into Cell Illustrator. All image files, in the PNG, JPEG and now also SVG format can be saved internally or externally in the Cell Illustrator models (CSML files).

• The simulation can be executed at a remote Cell Illustrator Server
  

Large, time-consuming simulations can now be executed at a remote server, outside of the Cell Illustrator workspace. For this, Cell Illustrator Server, a new companion product of Cell Illustrator needs to be installed at the simulation server. One server can be accessed by multiple users of the Cell Illustrator desktop package, and the other way around: you can connect to more than one CI Server from your desktop. After the simulation is submitted to a remote server you can continue to work with Cell Illustrator or other software without any loss of performance since the simulation does not take the CPU time of your workstation. The simulation results are returned by the server in the form of a CI log file, and can be viewed and analyzed in the CI Player application.
This solution is recommended for laboratories with a larger number of CI users.

• Use Cell Illustrator as a front-end to your own simulation program
  

The advanced user of Cell Illustrator who would like it to run his/her own simulation program from CI Workspace can do so by replacing the default engine component at the Cell Illustrator Server with his/her program. The user-created engine must read an input model and write a log file in the Cell System Markup Language (CSML) which is the native format of Cell Illustrator files.

• Integrate the command line Cell Illustrator simulation engine into your modeling environment
  

Cell Illustrator can be used to run simulations in the command line mode. This simulation engine works with Cell System Markup Language (CSML) input/output and can be called from user scripts or integrated with a custom GUI. Alternatively, you can utilize Cell Illustrator Server web service in your modeling environment.

• The maximum memory for Cell Illustrator can be customized
  

The new auxiliary program (CIMemoryConfiguration) allows you to customize the maximum memory for both Cell Illustrator applications: CI and CI Player.

• The results of each simulation can be logged and saved into CI log files (CILs). The CIL files can be viewed and analyzed in the Cell Illustrator Player program.
  With Cell Illustrator Player, you can:
  • deterministically replay a simulation run, even if the original simulation was of stochastic nature
  • display logged entity values and process states in the model view in the canvas
  • visualize entity value changes over time in a chart
  • quickly move forward and backward to a specific part of a simulation log
  • replay a simulation run in a step mode for debugging purposes
  • compare results of several simulation runs
• The new Simulation History dialog allows you to view and manage all the simulation log files (CILs) for your model
• The set of predefined elements in the Biological Elements dialog box has been expanded
  

• Enhanced implementation of hybrid Petri nets for bio-pathway modelling. The Cell Illustrator modeling features have been refined in the version CI 1.5; The parameters of discrete and continuous elements are unified now. Also, default parameter settings have been improved to make model creation easier for novice modelers.
• Faster and more accurate simulation engine. In Cell Illustrator 1.0, the minimum sampling interval was 0.001[pt]. In Cell Illustrator 1.5, the minimum sampling interval is 0.000001[pt]. Cell Illustrator 1.5 can realize 1000 times more accurate simulations and 10 times faster simulation than CI1.0.
• Improved GUI for model editing
• Added set of predefined Biological Elements

• Commertialized version of Genomic Object Net is released.