PET User Manual


Table of Contents

1. Introduction
2. Concepts and Tasks
How PET Determines Parameter Values
While Simulating
While Estimating Parameters
How PET Determines Initial Condition Values
Undo/Redo History
SBML in PET
Overview
Importing SBML
Editting SBML
Parameter and Species Mapping
Basal Sets
Simulations
Simulating
Plotting
PDF Reports
Parameter Exploration
Parameter Estimation
Weights and Deltas
3. User Interface Reference
Menus
Toolbar
Undo Button
Redo Button
Import SBML Button
Edit SBML Button
Simulate Button
Estimate Button
Edit Basals
Edit Simulations
Edit Data
Plot Config
Simulator Settings
Estimator Settings
4. Algorithms and Their Settings
Transforms
Time Series
Time Series with Pre-simulation
Steady State or Fixed Time
Timelag
Threshold
User Defined
Optimization Algorithms
Local Optimization: ODRPACK95
Global Optimization: VTDirect
VTDirect Followed By ODRPACK95
What Settings Should I Use?
5. Examples
Time Series User Defined Transform
6. Tutorial on Simulating
Prerequisites
Basic Simulation
Glossary

List of Figures

2.1. Overview of How Parameter Values Are Determined
2.2. Parameter Determination Example 1
2.3. Parameter Determination Example 2
2.4. Parameter Determination During Parameter Estimation
2.5. Parameter and Species Mapper
2.6. Mapper Left Drop Down
2.7. Mapper Right Drop Down
2.8. Weights and Deltas Tab
2.9. User Defined Weights
3.1. Toolbar
4.1. Time Series Transform Configuration
4.2. Time Series Experimental Data
4.3. Time Series Transform Plot
4.4. Time Series Plot
4.5. Time Series With Pre-simulation Transform Configuration
4.6. Simulation Setup for "Reverse"
4.7. Pre-simulation and Simulation
4.8. Steady State or Fixed Time Transform Configuration
4.9. Experimental Data
4.10. Timeseries to 100 time units
4.11. Timeseries to 1 time unit
4.12. Steady State or Fixed Time transform plot
4.13. Timelags for MPF Activation
4.14. Timelag vs. MT
4.15. Timelag Transform Configuration
4.16. Threshold Transform Configuration
4.17. Threshold Transform Plot
4.18. User Defined Transform
4.19. Estimator Settings Tab
4.20. Orthogonal Distance
4.21. Ordinary Least Squares Error Illustration
4.22. VTDirect Example
4.23. Scatter Plot of Objective Function Values vs. Box Size
4.24. EPS Illustration

List of Tables

3.1. Undo Examples
4.1. Parameters and Initial Conditions
4.2. Parameters and Initial Conditions

List of Equations

2.1. Default X Weight
2.2. Default X Weight
4.1. Reaction Network
4.2. Reaction Network
4.3. Reaction Network
4.4. Right Hand Sides
4.5. Objective Function
4.6. Ordinary Least Squares Objective Function
See the PET website for the current copy of this manual at http://mpf.biol.vt.edu/pet.