ScrumPy - Metabolic Modelling in Python

Contents

  1. ScrumPy - Metabolic Modelling in Python
    1. Introduction
      1. Metabolic Modelling
      2. Design Philosophy
      3. Python
        1. Knowing syntax vs programming
        2. Inbuilt types and classes
        3. Classes and sub-classes
        4. Repetiton and Decisions
        5. Functions
        6. Modules and Packages
        7. Standard libraries
    2. ScrumPy Model Description Language
      1. Overview
      2. Identifiers
      3. Reactions
      4. Directives
    3. Analysis of Models With ScrumPy
      1. The ScrumPy Modelling Environment
      2. The Matrix Class
      3. Anatomy of a ScrumPy Model
      4. Kinetic Modelling
      5. Structural Modelling
      6. Linear Programming
    4. Secondary Analysis of Model Results
      1. Data sets
      2. Fitting and Optimisation
    5. Automatic Model Building
    6. Bioinformatics Functions
    7. The Utility Package
      1. Dynamic Matrices

Introduction

Metabolic Modelling

Design Philosophy

Python

Knowing syntax vs programming

Inbuilt types and classes

int, float, str, list and dict

Classes and sub-classes

Repetiton and Decisions

Functions

Modules and Packages

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 ?

ScrumPy Model Description Language

Overview

Identifiers

Reactions

Directives

Analysis of Models With ScrumPy

The ScrumPy Modelling Environment

The Matrix Class

Fully described in utility section - enough here to understand SMs, datasets and monitors.

Anatomy of a ScrumPy Model

Kinetic Modelling

Structural Modelling

Linear Programming

Secondary Analysis of Model Results

Data sets

Fitting and Optimisation

Automatic Model Building

Bioinformatics Functions

The Utility Package

Dynamic Matrices