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Mendel® SBML Editor User Guide Table of Contents

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Mendel® SBML Editor User Guide Table of Contents Introduction. 1 Mendel® SBML Editor overview . 1 Mendel® SBML Editor features . 1 Getting started . 2 Installation notes . 2 Basic tutorial: Describing Reaction Network of Dimerization . 3 Tasks . 13 Navigating the workbench . 13 Basics. 14 Open existing SBML Model . 14 New SBML Model. 15 Save SBML Model . 15 Save SBML Model graph as image. 15 Adding and configuring Nodes . 15 Adding a Species, Reaction or Compartment . 16 Configuring a Species, Reaction or Compartment. 16 Adding and configuring Relations . 17 Adding a Reactant, Modifier or Product . 17 Configuring a Reactant, Modifier or Product . 18 Adding and configuring Kinetic Laws . 18 Adding and configuring Function Definitions . 19 Adding and configuring Unit Definitions. 19 Adding and configuring Parameters . 20 Adding and configuring Rules, Initial Assignments and Constraints . 20 Adding and configuring Events . 21 Adding Notes . 22 Deleting elements. 22 Reference . 24 Graphical User Interface overview . 24 Menu Bar . 24 File Menu Actions . 24 Edit Menu Actions . 25 Diagram Menu Actions. 26 Window Menu Actions. 27 Help Menu Actions . 27 Toolbar . 28 Model outline tab . 29 Graphical overview tab . 30 Graphical Editor tab . 31 Properties tab . 32 Nodes . 32 Species . 32 Reactions . 33 Compartment . 33 Relations . 34 Kinetic Laws . 34 Function Definitions . 34 Unit Definitions . 35 Parameters . 35 Initial Assignments . 35 Rules . 36 Algebraic Rules . ..
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