Additional file 1:

SBMLsqueezer: Kinetic Laws. This supplement provides a complete list of all currently supported kinetic laws together with conventions according to the graphical notation of CellDesigner and points out all special cases that are considered for an automatic equation generation including all available SBO terms for mathematical expressions. The derivation of the formula for the rapid equilibrium random order ternary-complex mechanism with one product as well as the ordered ternary-complex bi-uni mechanism can also be found in this document.

Format: PDF Size: 375KB Download file

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Additional file 2:

SBMLsqueezer: Tutorial. This tutorial provides installation instructions and guides the user through a real-world example of a T-cell signaling network. It highlights the modeling capabilities and the application of SBMLsqueezer to create a quantitative biochemical model. Finally it is shown how to apply CellDesigner's simulation module to the network to produce a dynamic simulation of the temporal changes of the species' concentrations.

Format: PDF Size: 960KB Download file

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Additional file 3:

SBMLsqueezer.jar. This is the current version (1.0) of the SBMLsqueezer plug-in for CellDesigner.

Format: JAR Size: 362KB Download file