The Bio-PEPA Eclipse Plug-in
User Manual
The Bio-PEPA Eclipse Plug-in
User Manual
http://www.biopepa.org/
1 Acknowledgements
2 Thanks
3 Introduction
4 Getting started
4.1 Installation Instructions
4.2 Managing The Bio-PEPA Perspective
4.3 The Navigator view
4.4 Creating a new project
5 Using the editor
5.1 A simple model of one species decay
5.2 Syntax errors
5.3 Semantic errors
5.4 Warnings and semantic errors
5.5 Inspecting your model in the Outline view
6 Invoking commands
6.1 Managing the Graph View
7 Time-series Analysis
7.1 Solving continuous ODE models using Bio-PEPA
7.2 Performing stochastic simulation using Bio-PEPA
8 Experimentation using Bio-PEPA
8.1 A model of oscillations
8.2 Creating experiments
8.3 Saving and re-running an experiment
8.4 Comparing with external data
9 PRISM Export
10 Inference of Invariants
11 Simulation Distributions
12 Export Wizard
13 Simulation Trace
A The Bio-PEPA plugin syntax
A.1 Locations
A.2 Species Attributes
A.3 Parameter Definitions
A.4 Functional Rates
A.5 Species Components
A.6 Model Component
A.7 Syntax Example: The Enzyme-Substrate model - Reactant and Product
A.8 Syntax Example: Activator and Inhibitor
A.9 Syntax Example: Unidirectional Transportation, Modifier
A.10 Syntax Example: Bidirectional Transportation, Modifier
B Managing Eclipse
B.1 Checking the Eclipse platform version
B.2 Checking for Updates
C Bibliography
The Bio-PEPA Eclipse Plug-in
User Manual
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