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 own simulation program from CI Workspace can do so by replacing the default engine component at the Cell Illustrator Server with his 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.