Major New Features:

• Enhanced Graphical Notation
  CellDesigner's Graphical Notation conforms to SBGN (Systems Biology Graphical Notation) proposal of April 2008 draft (* not complete SBGN Process Diagram Level1 which became available in August 2008).
• Enhanced KineticLaw Edit Dialog: MathML rendering in KineticLaw.
• Simulation / Control Panel enhancement
  
• Export Species/Reactions information including Notes into CSV file
• Validation of files when opening (libSBML3)
• Native file chooser support for Mac OS X
• Enhanced Edit Functions
• [Layout] menu: Automatic Layout function (using yFiles layout library.)
• Layer Function (alpha version) to add comments / arrows on top of the models.
• Database link to Genome Network Platform
  
• Plugin development framework.
  Develop your plugin on Eclipse, and you can call the plugin from [Plugin] menu.
  > Plug-In Tutorial [pdf] > http://celldesigner.org/plugins.html
  
  
• Export of Pure Level 1 Version 1 is no longer supported.
• Windows 2000 is no longer supported.

Graphical Notation:

CellDesigner 4.0 now enables you to preview for the new graphical notation conform to SBGN Level 1 draft. (*click to enlarge the upper right image.) (* not complete SBGN Process Diagram Level1 which became available in August 2008).

• New Species: Drug, Tag
• New Reactions: physical stimulation, modulation, trigger, Boolean logic gates
• Process nodes of the reactions are introduced to connect modifiers such as catalysis, inhibition.
• Protein states (open, close), binding region
  
• Protein residue modification types enhanced (Glycosylated, Myristoylated, Palmtoylated, Prenylated, Protonated, Sulfated)
• Gene modification regions enhanced: (phospholyrated, acetylated, methylated), coding regions, regulatory regions, transcriptionstartingSiteL/R
• Allow to draw Complexes within a Complex

Macro Function:

• 13 quick-to-draw sets of components available.
  

KineticLaw Editor:

• Preview for the selected reaction in the editor
• Utilize Predefined Function for "math"
  
  

MathML rendering in "math"

Switch ID/Name display in the "math"

Control Panel:

• Copasi integration >> How to setup Copasi
• Solver selection in the ControlPanel : SOSlib and Copasi
  
• Simulation results displayed in Table format
• Show Scatter Plot
  

File:

• Export Species / Reactions information including Notes into CSV file.
• Validation of files when opening (libSBML3)
• Native file chooser support for Mac OS X

Edit:

• Changes color/shape change for multiple Species/Reactions.
• Highlight List of Proteins selected in the Draw area.
• Sort (ascend/descent) by click in the list
• [Find All] menu added.
• [Species ID Replace] dialog
• Edit the position of the name of the Compartment display
• Reaction ID Display on screen
• Toolbar display ON/OFF by "View-Change Toolbar Visible" menu

User Interface Enhancements:

• Change display position of the list: [View]-[List] menu, then [Right] or [Down]
• Display Reaction ID on screen: [View]-[Show Reaction ID]
• Change display position of Compartment name: drag the name to the new position.
• Change Icon display size: [Preference] - [Set Icon Size]
• [Preference]-[Set Macro UI]
• Popup setting dialog: [Preference]-[Popup]

Layer Function (previsionary)

• to add comments / arrows on top of the models.

 

Installation:

New Installer is being adopted. For details on installation procedure, check here.