Smoldyn User`s Manual

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1. Smoldyn User`s Manual

Smoldyn User s Manual for Smoldyn version 2 38 October 2015 Steve Andrews Part I User s manual 1 1 Overview of Smoldyn 2 2 Installing Smoldyn 4 3 Using Smoldyn 9 3 1 Running Smoldyn 9 3 2 The configuration file 11 3 3 Space and time 15 3 4 Molecules 19 3 5 Graphics 25 3 6 Runtime commands 29 3 7 Surfaces 34 3 8 Reactions 43 3 9 Compartments 64 3 10 Simulation settings 67 3 11 Ports 69 3 12 Rule based network generation 70 3 13 Filaments 71 3 14 Hybri
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1. Smoldyn User`s Manual

Smoldyn User s Manual for Smoldyn version 2 38 October 2015 Steve Andrews Part I User s manual 1 1 Overview of Smoldyn 2 2 Installing Smoldyn 4 3 Using Smoldyn 9 3 1 Running Smoldyn 9 3 2 The configuration file 11 3 3 Space and time 15 3 4 Molecules 19 3 5 Graphics 25 3 6 Runtime commands 29 3 7 Surfaces 34 3 8 Reactions 43 3 9 Compartments 64 3 10 Simulation settings 67 3 11 Ports 69 3 12 Rule based network generation 70 3 13 Filaments 71 3 14 Hybri
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