Figure 1
From: SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks
The SBMLsqueezer work flow. This graphic depicts the progression through SBMLsqueezer. The first step is to construct or open a diagrammatic model in CellDesigner. Then SBMLsqueezer can be started through the plug-in menu (step 1). The first window shows the standard kinetics and enables the user to specify the type of kinetics to be applied whenever there are multiple choices. By clicking on “Generate” (step 2), the kinetics are compiled and presented. If necessary, warnings are indicated along with the respective formula. The kinetic equations summarized in the table can be altered by double-clicking on the name of the equation, which is taken from the SBO. SBMLsqueezer then offers a list of all applicable kinetic equations for the given reaction. Subsequently, all kinetics can be assigned to the SBML model and exported to plain text or LaTeX.