ScrumPy - Metabolic Modelling in Python

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

int, float, str, list and dict

1.3.3. Classes and sub-classes

1.3.4. Repetiton and Decisions

1.3.5. Functions

1.3.6. Modules and Packages

1.3.7. Standard libraries

Not all of them ! In practice math and random are the most commonly with ScrumPy. sys and os are also useful - any other suggestions ?

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

7.1. Dynamic Matrices