Updated README files for tutorial folders

README.md

@@ -2,12 +2,12 @@
 
 Tutorials are here to get you started with using [The COBRA Toolbox](https://opencobra.github.io/cobratoolbox/latest/index.html). The tutorials are grouped according to the `src/` folder structure:
 
-- [analysis](analysis/)
-- [base](base/)
-- [dataIntegration](dataIntegration/)
-- [design](design/)
-- [reconstruction](reconstruction/)
-- [visualization](visualization/)
+- <img src="../docs/source/_static/images/icon_analysis.png" height="14px">&nbsp;&nbsp;[analysis](analysis/)
+- <img src="../docs/source/_static/images/icon_base.png" height="14px">&nbsp;&nbsp;[base](base/)
+- <img src="../docs/source/_static/images/icon_di.png" height="14px">&nbsp;&nbsp;[dataIntegration](dataIntegration/)
+- <img src="../docs/source/_static/images/icon_design.png" height="14px">&nbsp;&nbsp;[design](design/)
+- <img src="../docs/source/_static/images/icon_reconstruction.png" height="14px">&nbsp;&nbsp;[reconstruction](reconstruction/)
+- <img src="../docs/source/_static/images/icon_visualization.png" height="14px">&nbsp;&nbsp;[visualization](visualization/)
 
 All tutorials are provided in 4 formats: `.mlx`, `.m`, `.pdf`, and `.html`.
 
@@ -16,6 +16,8 @@ All tutorials are provided in 4 formats: `.mlx`, `.m`, `.pdf`, and `.html`.
 - For your reference, the `.pdf` version is also included for each tutorial.
 - The `.m` version of the tutorial can be opened and run directly in MATLAB. This is particularly useful to build new analysis scripts based on an existing tutorial.
 
+Additional tutorials can be found in [additionalTutorials](additionalTutorials/). These tutorials are currently being prepared.
+
 ## Do you want to contribute a new tutorial?
 
-A template for generating a new tutorial is provided [here](tutorial_template.mlx). You can use the [MATLAB.devTools](https://github.com/opencobra/MATLAB.devTools) to submit your tutorial. Please follow the [contributing guidelines](https://opencobra.github.io/cobratoolbox/docs/contributing.html).
+A template for generating a new tutorial is provided [here](additionalTutorials/tutorial_template.mlx). You can use the [MATLAB.devTools](https://github.com/opencobra/MATLAB.devTools) to submit your tutorial. Please follow the [contributing guidelines](https://opencobra.github.io/cobratoolbox/docs/contributing.html).

analysis/README.md

@@ -1,20 +1,11 @@
-# Tutorials - analysis
+# <img src="../../docs/source/_static/images/icon_analysis.png" height="22px">&nbsp;&nbsp;Tutorials - analysis
 
-- [FBA](FBA)
-- [FVA](FVA)
-- [SOP](SOP)
-- [browseNetwork](browseNetwork)
-- [fidelityTesting](fidelityTesting)
-- [minSpan](minSpan)
-- [minimalCutSets](minimalCutSets)
-- [modelProperties](modelProperties)
-- [numCharact](numCharact)
-- [pFBA](pFBA)
-- [pathVectors](pathVectors)
-- [relaxFBA](relaxFBA)
-- [relaxedFBA](relaxedFBA)
-- [robustness_PhPP](robustness_PhPP)
-- [sparseFBA](sparseFBA)
-- [thermo](thermo)
-- [uFBA](uFBA)
-- [uniformSampling](uniformSampling)
+- [Flux balance analysis and its variants (FBA)](FBA)
+- [Flux Variability Analysis (FVA)](FVA)
+- [Atomically resolve a metabolic reconstruction (atomicallyResolveReconstruction)](atomicallyResolveReconstruction)
+- [Minimal spanning pathway vectors (minSpan)](minSpan)
+- [Relaxed Flux Balance Analysis (relaxedFBA)](relaxedFBA)
+- [Sparse Flux Balance Analysis (sparseFBA)](sparseFBA)
+- [Uniform sampling of steady-state fluxes (uniformSampling)](uniformSampling)
+- [Variational kinetic modelling (variationalKinetics)](variationalKinetics)
+- [Thermodynamically constrain a metabolic model (vonBertalanffy)](vonBertalanffy)

base/README.md

@@ -1,3 +1,6 @@
-# Tutorials - base
+# <img src="../../docs/source/_static/images/icon_base.png" height="22px">&nbsp;&nbsp;Tutorials - base
 
-- [IO](IO)
+- [Input and output of reconstructions and models (IO)](IO)
+- [Engaging with the COBRA Toolbox Forum (engagingWithTheCommunity)](engagingWithTheCommunity)
+- [Initialise and verify The COBRA Toolbox (initializeAndVerify)](initializeAndVerify)
+- [Variational kinetic modelling (variationalKinetics)](variationalKinetics)

dataIntegration/README.md

@@ -1,4 +1,5 @@
-# Tutorials - dataIntegration
+# <img src="../../docs/source/_static/images/icon_di.png" height="22px">&nbsp;&nbsp;Tutorials - dataIntegration
 
-- [extraction_transcriptomic](extraction_transcriptomic)
-- [metabotools](metabotools)
+- [Integration of transcriptomic and proteomic data (extractionTranscriptomic)](extractionTranscriptomic)
+- [Integration of exometabolomic data (metabotools)](metabotools)
+- [Integration of endometabolomic data (uFBA)](uFBA)

design/README.md

@@ -1,6 +1,3 @@
-# Tutorials - dataIntegration
+# <img src="../../docs/source/_static/images/icon_design.png" height="22px">&nbsp;&nbsp;Tutorials - dataIntegration
 
-- [optForce](optForce)
-- [optForceGAMS](optForceGAMS)
-- [optGene](optGene)
-- [optKnock](optKnock)
+- [Strain design: optForce (optForce)](optForce)

reconstruction/README.md

@@ -1,10 +1,12 @@
-# Tutorials - reconstruction
+# <img src="../../docs/source/_static/images/icon_reconstruction.png" height="22px">&nbsp;&nbsp;Tutorials - reconstruction
 
-- [COBRAconcepts](COBRAconcepts)
-- [atomicallyResolveReconstruction](atomicallyResolveReconstruction)
-- [constrainingModels](constrainingModels)
-- [fastGapFill](fastGapFill)
-- [modelATPYield](modelATPYield)
-- [modelCreation](modelCreation)
-- [modelManipulation](modelManipulation)
-- [rBioNet](rBioNet)
+- [Reconstruction: create a generic subnetwork from Recon3D (createSubnetworkRecon)](createSubnetworkRecon)
+- [Gap Filling (fastGapFill)](fastGapFill)
+- [Testing biochemical fidelity (fidelityTesting)](fidelityTesting)
+- [Test for physiologically relevant ATP yields from different carbon sources (modelATPYield)](modelATPYield)
+- [Reconstruction manipulation (modelManipulation)](modelManipulation)
+- [Testing basic properties of a metabolic model (modelSanityChecks)](modelSanityChecks)
+- [Numerical properties of a reconstruction (numCharact)](numCharact)
+- [Reconstruction: rBioNet (rBioNet)](rBioNet)
+- [Convert a reconstruction into a flux balance analysis model (recon2FBAmodel)](recon2FBAmodel)
+- [Reconstruction: Standard Operating Procedure (reconstructionSO)](reconstructionSOP)

visualization/README.md

@@ -1,5 +1,4 @@
-# Tutorials - visualization
+# <img src="../../docs/source/_static/images/icon_visualization.png" height="22px">&nbsp;&nbsp;Tutorials - visualization
 
-- [cellDesigner](cellDesigner)
-- [paint4Net](paint4Net)
-- [remoteVisualisation](remoteVisualisation)
+- [Variable scope visualisation of a network with Paint4Net (paint4Net)](paint4Net)
+- [Human metabolic network visualisation: ReconMap (remoteVisualisation)](remoteVisualisation)