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| = ScrumPy Documentation = | ## page was renamed from Software/ScrumPy/Doc #pragma section-numbers 2 = ScrumPy - Metabolic Modelling in Python = <<TableOfContents>> |
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| === Metabolic Modelling === === Design Philosophy === Scrumpy is unusual, but not unique, in that the primary user interface is a language (it is an oversimplification to refer to it as a command line interface) rather than a more conventional GUI. The underlying reason for this choice is a simple one: A GUI restricts the user to only those actions which the programmer mpredicted the user might wish to perform. In some contexts this is not a problem, simple text editing and web-browsing being examples. |
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| === Why Python ? === | However, in metabolic modelling (and scietific/research contexts in general) it is much harder for the programmer to predict what a user may wish to do. MORE HERE - |
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| 'cause it's great. | Furthermore, in the twenty or so years in which I have been involved in the field, I have lost count of the number of presentations I've listened to for software (not only modelling or scientific) making the claim that the software is intuitive and user friendly, to the extent that this has become a mantra to be uttered at the begining of every presentation. Most of it has been unconvincing at best. |
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| === Tutorials === | |
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| === What ScrumPy Is === | ==== Introduction to Python ==== |
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| === What ScrumPy Isn't === | [[ScrumPy/Doc/Tutorial/PyIntro | Introduction to Python]] ==== Introduction to ScrumPy ==== [[ScrumPy/Doc/Tutorial/ScrumPyIntro | Introduction to ScrumPy]] |
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| === Quick examples === | === Python Notes === [[ScrumPy/Doc/PyNotes|Python notes]] |
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| == ScrumPy Model Description Language == === Overview === [[SpyMDL#Overview|Overview]] === Identifiers === [[SpyMDL#Identifiers|Identifiers]] === Reactions === [[SpyMDL#Reactions|Reactions]] === Directives === [[SpyMDL#Directives|Directives]] |
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| == ScrumPy model format == | == Analysis of Models With ScrumPy == === The ScrumPy Modelling Environment === ==== Running ScrumPy ==== [[ScrumPy/Doc/ModEnv#RunSpy | Running ScrumPy]] |
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| == Structural Analysis of Models == | ==== Loading Models ==== [[ScrumPy/Doc/ModEnv#LoadSpy | Loading Models]] ==== Structural Modelling ==== [[ScrumPy/Doc/StruMod | Structural Modelling ]] ==== Linear Programming ==== [[ScrumPy/Doc/LinProg | Linear Programming ]] ==== Kinetic Modelling ==== [[ScrumPy/Doc/KinMod | Kinetic Modelling ]] |
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| == Kinetic Analysis of Models == |
== Secondary Analysis of Model Results == === Data sets === === Fitting and Optimisation === == Automatic Model Building == |
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| == The Utility Package == === Dynamic Matrices === |
ScrumPy - Metabolic Modelling in Python
Contents
1. Introduction
1.1. Metabolic Modelling
1.2. Design Philosophy
Scrumpy is unusual, but not unique, in that the primary user interface is a language (it is an oversimplification to refer to it as a command line interface) rather than a more conventional GUI. The underlying reason for this choice is a simple one: A GUI restricts the user to only those actions which the programmer mpredicted the user might wish to perform. In some contexts this is not a problem, simple text editing and web-browsing being examples.
However, in metabolic modelling (and scietific/research contexts in general) it is much harder for the programmer to predict what a user may wish to do. MORE HERE -
Furthermore, in the twenty or so years in which I have been involved in the field, I have lost count of the number of presentations I've listened to for software (not only modelling or scientific) making the claim that the software is intuitive and user friendly, to the extent that this has become a mantra to be uttered at the begining of every presentation. Most of it has been unconvincing at best.
1.3. Tutorials
1.3.1. Introduction to Python
1.3.2. Introduction to ScrumPy
1.4. Python Notes
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
3.1.1. Running ScrumPy
3.1.2. Loading Models
3.1.3. Structural Modelling
3.1.4. Linear Programming
3.1.5. Kinetic Modelling
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