ScrumPy Manual
1. Introduction
1.1. Metabolic Modelling
1.2. Design Philosophy
1.3. Python
1.3.1. Knowing syntax vs programming
1.3.2. Inbuilt types and classes
1.3.3. Classes and sub-classes
1.3.4. Repetiton and Descissions
1.3.5. Modules and Packages
2. ScrumPy Model Description Language
2.1. Overview
2.2. Identifiers
2.3. Reactions
2.4. Directives
3. Analysis of Models With ScrumPy
3.1. The ScrumPy Modelling Environment
3.2. The Matrix Class
Fully described in utility section - enough here to understand SMs, datasets and monitors.
3.3. Anatomy of a ScrumPy Model
3.4. Kinetic Modelling
3.5. Structural Modelling
3.6. Linear Programming
4. Secondary Analysis of Model Results
4.1. Data sets
4.2. Fitting and Optimisation
5. Automatic Model Building
6. Bioinformatics Functions
7. The Utility Package