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<h1>
Tutorials
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¶
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<div class="section" id="analysis">
<h2>
Analysis
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¶
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<h3>
Analysis
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¶
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<div class="sectionContent">
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<li>
<a class="reference internal" href="tutorialPFBA.html">
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A step-by-step guide to parsimoneous enzyme usage Flux Balance Analysis - pFBA
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Analyze Steady-State Community COBRA Models
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<a class="reference internal" href="tutorialAtomicallyResolveReconstruction.html">
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Atomically resolve a metabolic reconstruction
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Browse Networks in the Matlab Command Window Using surfNet
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Computation and analysis of microbe-microbe metabolic interactions
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Computation and analysis of rescued lethal gene deletions in a host-microbe model
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Creation and simulation of personalized microbiota models through metagenomic data integration
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Determining MinSpan vectors of COBRA model
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Flux Balance Analysis (FBA)
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Flux Balance Analysis: Alternate optimal solutions
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Flux Balance Analysis (FBA) and its variants
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Flux Variability analysis (FVA)
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genetic Minimal Cut Sets - gMCS
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Proton shuttle testing with sparse flux balance analysis
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Quadruple precision Flux Balance Analysis
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Reaction essentiality across multiple models
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Relaxed Flux Balance Analysis: Recon 3
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Relaxed Flux Balance Analysis: Toy model
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Robust Metabolic Transformation Analysis - rMTA
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Sensitivity of a flux balance analysis solution with respect to input data
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Sparse Flux Balance Analysis
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Sparse flux balance analysis test for a minimial stoichiometrically balanced cycle involving ATP hydrolysis
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Sparse Linear Optimisation
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Thermodynamically constrain a metabolic model
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Uniform sampling of E. coli core
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Uniform sampling a genome-scale model
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Variational Kinetics
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Varying Parameters analysis
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ICON-GEMs
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<h2>
Base
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¶
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<h3>
Base
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¶
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<div class="sectionContent">
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<a class="reference internal" href="tutorialContribute.html">
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Contribute to the COBRA Toolbox with MATLAB.devTools
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Engaging with The COBRA Toolbox community
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Initialise and verify The COBRA Toolbox
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Introduction to MATLAB
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Input and output of reconstructions and models
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Primer on Flux Balance Analysis and its applications
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Primer on Non-FBA based COBRA methods
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Verify the COBRA Toolbox
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Data integration
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Data integration
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Extraction of context-specific models
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Metabotools tutorial I
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Metabotools tutorial II - Integration of quantitative metabolomic data
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unsteady-state Flux Balance Analysis (uFBA)
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<h2>
Design
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Design
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OptForce
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OptForce GAMS
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OptGene Tutorial
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OptKnock Tutorial
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<h2>
Reconstruction
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Adding biological constraints to a flux balance model
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Adding more complex constraints on a model
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Constraint-based modelling concepts
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Convert a reconstruction into a flux balance analysis model
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Create a generic subnetwork from Recon 3D
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Create an overview table with model properties
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Creating a Model
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E.coli Core Model for Beginners (PART 1)
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E.coli Core Model for Beginners (PART 2)
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E.coli Core Model for Beginners (PART 3)
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Example use of functions listed in the Standard operating procedure for metabolic reconstruction.
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FastGapFill tutorial
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Find leakage and siphon modes in a reconstruction
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Generation and manipulation of reconstructions with rBioNet
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How to use modelBorgifier
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Model manipulation
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Numerical properties of a reconstruction
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Refinement of genome-scale reconstructions through the DEMETER pipeline
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Test physiologically relevant ATP yields from different carbon sources for a metabolic model
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Testing basic properties of a metabolic model (aka sanity checks)
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<a class="reference internal" href="tutorialFidelityTesting.html">
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Testing chemical and biochemical fidelity
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<div class="section" id="visualization">
<h2>
Visualization
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¶
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<h3>
Visualization
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¶
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</h3>
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<div class="sectionContent">
<ul class="simple">
<li>
<a class="reference internal" href="createMeIntrcNetworkTutorial.html">
<span class="doc">
createMetIntrcNetwork: Metabolite-Metabolite network function for COBRA
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</li>
<li>
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Introduction to Cell Designer
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<li>
<a class="reference internal" href="tutorialRemoteVisualisation.html">
<span class="doc">
Metabolic visualisation in ReconMap (Minerva)
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<li>
<a class="reference internal" href="tutorialPaint4net.html">
<span class="doc">
Paint4Net: visualisation toolbox for COBRA
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</li>
<li>
<a class="reference internal" href="tutorialSammi.html">
<span class="doc">
SAMMI Interactive Network Visualization Tool
</span>
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<li>
<a class="reference internal" href="tutorialMetabolicCartography_part1.html">
<span class="doc">
Visualisation and map manipulation in Cell Designer (PART 1)
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<li>
<a class="reference internal" href="tutorialMetabolicCartography_part2.html">
<span class="doc">
Visualisation and map manipulation in Cell Designer (PART 2)
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<li>
<a class="reference internal" href="tutorialEfmviz_ecoli.html">
<span class="doc">
Visualize Elementary Flux Modes from E. coli model
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<li>
<a class="reference internal" href="tutorialEfmviz_recon.html">
<span class="doc">
Visualize Elementary Flux Modes from Human model
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