CellDesigner Help

The BlockDiagramDialog

The BlockDiagramDialog gives a summary view of interactions with respect to a specific Species (especially Protein) and relation between its modification and activity as enzyme.

Using this block diagram editor, complex relations between Proteins can be understood at a glance and the relation between modification states enzymic activity can easily be constructed.

The BlockDiagramDialog consists of three parts:

The BlockDiagramDialog is still a prototype and user interface for editing is not fully functional.

To open the block diagram dialog

  1. Open the Ptotein dialog.
  2. Press edit block diagram button.
  3. The BlockDiagramDialog will appear.

Diagram Draw Area

Diagram Draw Area displays the following elements:

Block represented by a rounded square shape, indicating the target protein. The name of the protein is displayed on the upper right corner.
Block Area represented by a dotted-line square.
Residue represented by a circle with letters
BindingSite symbol of creating heterodimer with the specified protein(s)
EffectSite symbol of effect to the specified protein(s)
Degradation symbol of degradation
Operators represent the operation in the block.

Edit Tool Bar

Edit Tool Bar displays the following elements:

button
symbol
description
Protein Switch to the Edit Mode. move, resize the block diagram.
Residue Add selected residue by clicking on the upper side line.
Site Addition Add selected site (BindingSite, EffectSite, and Degradation) to the block diagram.
BindingSite Click on the left side of the diagram.
EffectSite Click on the bottom side, then on the right side of the diagram.
Degradation Click on the right side of the diagram.
Operator Addition Add Operator. Click inside the diagram.
Routing
Connect the items in the block diagram; routings, activate/inactivate residues.
To connect the items inside the diagram, click the items
To add activate/inactivate residues, click the line drawn from the residue, then click on the left side of the block area.
Delete Delete the selected item.
Caution: the items derived from the process diagram cannot be deleted.
Image Save Save the diagram as image file (.PNG / .JPEG format)
Print Print the block diagram.
Highlight Highlight the BindingSite, EffectSite and Degradation derived from the Process diagram.

Status Table

Status Table shows the information derived from the Process diagram, table of the status and the activity of the Species.

verify CellDesigner verifies the table and the diagram if there is any conflict between the diagram drawn with routing and the operators, and reflect its results onto the table.
update Update the block diagram with the data from the up-to-date process diagram.
apply Fix and apply the data edited by the block diagram dialog.
close Close the block diagram edit dialog.

 

About Us | Site Map | Privacy Policy | Contact Us | ©2010 The Systems Biology Institute All Rights Reserved.