Pycotools’s Documentation

QuickStart

• Quick Start

Tutorials

Tutorial 0: Installation and Configuration

• Installation, dependencies, versions, environment variables

Tutorial 1: The Model

• Get Zi Model for this Example
• Parse a Model into Pycotools
• Open and Save
• Get Model Information
• Get, Set, Add and Remove

Tutorial 2: Time Course

• TimeCourse
• Get Model Object
• Deterministic Time Course
• Visualization
• Alternative Solvers

Tutorial 3: Scan

• Parameter Scan
• Get Model String
• Parse Model
• Parameter Scan
• 2 Way Parameter Scan
• Repeat Scan Items

Tutorial 4: Single Parameter Estimations

• Parameter Estimation
• Imports and Getting Test Model
• Setup and run single parameter estimation
• Visualization
• Multiple Data Files
• Visualization
• Steady State data

Tutorial 5: Multiple Parameter Estimation, analysis and Identifiability Analysis

• Multiple Parameter Estimations
• The MultipleParameterEstimation Class
• Visualization

Tutorial 2

• Table of Contents
• Vizualization
• Simulate parameter estimation data to work with
• RSS Versus Iteration
• Visualize distributions with boxplots and histograms
• Time Course Ensemble
• PCA
• Identify parameters with similar variance with PCA

Tutorial 2

• InsertParameters
• From File
• From Folder of Parameter Estimation Files

Examples

• Examples

API

• API Documentation

Caveats

• Caveats
• Units
• Assignments
• Duplicate Names

Indices and tables

• Index
• Module Index
• Search Page