--- a/COBRAxy/docs/tutorials/README.md	Mon Nov 03 14:49:49 2025 +0000
+++ b/COBRAxy/docs/tutorials/README.md	Thu Dec 11 11:17:33 2025 +0000
@@ -11,19 +11,216 @@
 
 To use a workflow, click the "Import" button, and it will be added to your personal workflow page.
 
-| Tutorial | Description |
-|----------|-------------|
-|[Flux Enrichment Analysis - separated datasets](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=a64417ff266b740e) | Creation of maps of the fluxes differently expressed between two conditions. One gene expression dataset different for each condition. |
-| [Flux Enrichment Analysis (sampling mean) - separated datasets](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=16e792953f5b45db) |  Creation of maps of the fluxes differently expressed between two conditions. One gene expression dataset different for each condition. |
-| [Flux clustering (sampling mean) + Flux Enrichment Analys](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=c851ab275e52f8af) | Creation of maps of the fluxes, using one dataset differently expressed for each condition and its sample group specification|
-| [Flux Enrichment Analysis (pFBA) - separated datasets](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=bf0806da5b28c6d9) | Creation of maps of the fluxes differently expressed between two conditions. One gene expression dataset different for each condition. |
-| [Flux clustering (pFBA) + Flux Enrichment Analysis](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=be0a27b9edd0db03) | Creation of maps of the fluxes, using one dataset differently expressed for each condition and its sample group specification |
-| [RAS clustering + Reaction Enrichment Analysis](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=81991b32733a4fc4) | Creation of RAS maps, one single expression gene dataset and its sample group specification |
-| [Reaction Enrichment Analysis - unified datasets](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=0d16186aaff7cbfd) |Creation of RAS maps starting from an expression dataset and its corresponding classes. One gene expression dataset as input and its classes to compare. |
-| [Reaction Enrichment Analysis - separated datasets](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=290670ee50ab85f0) | Creation of RAS maps using the tool MaREA. Confrontation of two datasets that must be different from one another. |
+| Tutorial | Description | 🌐 Galaxy Workflow | 📘 Documentation |
+|-----------|-------------|--------------------|------------------|
+| **Flux Enrichment Analysis (Sampling Mean) — Separated Datasets** | Generate flux maps highlighting differences between two conditions. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=16e792953f5b45db) | [📄 See section](#flux-enrichment-analysis-sampling-mean--separated-datasets) |
+| **Flux Clustering (Sampling Mean) + Flux Enrichment Analysis** | Cluster fluxes and identify condition-specific differences. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=c851ab275e52f8af) | [📄 See section](#flux-clustering-sampling-mean--flux-enrichment-analysis) |
+| **Flux Enrichment Analysis (pFBA) — Separated Datasets** | Compare fluxes between two conditions using pFBA simulations. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=bf0806da5b28c6d9) | [📄 See section](#flux-enrichment-analysis-pfba--separated-datasets) |
+| **Flux Clustering (pFBA) + Flux Enrichment Analysis** | Cluster pFBA-derived fluxes and analyze enriched pathways. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=be0a27b9edd0db03) | [📄 See section](#flux-clustering-pfba--flux-enrichment-analysis) |
+| **RAS Clustering + Reaction Enrichment Analysis** | Cluster RAS profiles and identify significantly enriched reactions. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=81991b32733a4fc4) | [📄 See section](#ras-clustering--reaction-enrichment-analysis) |
+| **Reaction Enrichment Analysis — Unified Datasets** | Compare RAS profiles between classes within one dataset. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=0d16186aaff7cbfd) | [📄 See section](#reaction-enrichment-analysis--unified-datasets) |
+| **Reaction Enrichment Analysis — Separated Datasets** | Analyze RAS differences between two distinct datasets. | [🔗 Open](http://marea4galaxy.cloud.ba.infn.it/galaxy/published/workflow?id=290670ee50ab85f0) | [📄 See section](#reaction-enrichment-analysis--separated-datasets) |
+
 
 A more detailed description of the tools is available on the corresponding GALAXY page.
 
+### Flux Enrichment Analysis (Sampling Mean) — Separated Datasets
+
+#### Goal
+Perform a **statistical analysis of fluxes** from two different datasets derived from flux simulations using the **sampling mean** method.
+
+#### Scenario
+You have **one gene expression dataset per condition** (e.g., *Cancer vs Normal*).
+
+#### 1. Import Metabolic Model
+- Load the metabolic model.  
+- Define the **medium** and the **gene nomenclature format**.
+
+#### 2. Expression to RAS
+- Transform a **gene expression file** into a **RAS dataset**.  
+- This step must be applied **individually for each dataset**.
+
+#### 3. RAS to Bounds
+- Use the **two RAS datasets** (one per condition) as input.  
+- Generate the corresponding **flux bounds**.
+
+#### 4. Flux Simulation
+- Use the **output from the RAS to Bounds** step as input.  
+- Select **sampling mean (mean)** as the simulation method.
+
+#### 5. Metabolic Flux Enrichment Analysis
+- Create a **map of significant differences** between fluxes from the two datasets.  
+- Use the **flux simulation output** together with the **RASToBounds results** to identify enriched pathways or reactions.
+
+
+### Flux Clustering (Sampling Mean) + Flux Enrichment Analysis
+
+#### Goal
+Creation of **flux maps** from two different datasets and **clustering** based on flux simulations using the **sampling mean** method.
+
+#### Scenario
+You have **one gene expression dataset**.
+
+#### 1. Import Metabolic Model
+- Load the metabolic model.  
+- Define the **medium** and the **gene nomenclature format**.
+
+#### 2. Expression to RAS
+- Transform a **gene expression file** into a **RAS dataset**.  
+- This step must be applied **for each dataset**.
+
+#### 3. RAS to Bounds
+- Use **two different RAS datasets** as input.  
+- Generate the corresponding **flux bounds**.
+
+#### 4. Flux Simulation
+- Use the **output from the RAS to Bounds** step as input.  
+- Select **sampling mean (mean)** as the simulation method.
+
+#### 5. Cluster Analysis
+- Perform **clustering** on the **flux dataset** obtained from the simulation.  
+- Identify patterns or groups within the flux profiles.
+
+#### 6. Metabolic Flux Enrichment Analysis
+- Create **flux maps** showing **significant differences** between clusters.  
+- Use:
+  - The **clusters** as the *sample group specification*.  
+  - The **mean of each sample** from flux sampling as the *input flux data*.  
+
+
+### Flux Enrichment Analysis (pFBA) — Separated Datasets
+
+#### Goal
+Perform a **statistical analysis of fluxes** from two different datasets obtained from flux simulations using **pFBA** (parsimonious Flux Balance Analysis).
+
+#### Scenario
+You have **one gene expression dataset per condition** (e.g., *Cancer vs Normal*).
+
+#### 1. Import Metabolic Model
+- Load the metabolic model.  
+- Define the **medium** and the **gene nomenclature format**.
+
+#### 2. Expression to RAS
+- Transform a **gene expression file** into a **RAS dataset**.  
+- This step must be applied **individually for each dataset**.
+
+#### 3. RAS to Bounds
+- Use the **two RAS datasets** (one per condition) as input.  
+- Generate the corresponding **flux bounds**.
+
+#### 4. Flux Simulation
+- Use the **output from the RAS to Bounds** step as input.  
+- Select **pFBA** as the simulation method.
+
+#### 5. Metabolic Flux Enrichment Analysis
+- Perform **analysis and visualization** of **significant differences** between fluxes of the two groups (e.g., *Normal* vs *Cancer*).  
+- Use the **flux simulation output** together with the **RASToBounds results** to identify enriched or altered metabolic pathways.  
+
+
+### Flux Clustering (pFBA) + Flux Enrichment Analysis
+
+#### Goal
+Perform a **statistical analysis of fluxes** from two datasets using **clusters derived from flux simulations** with **pFBA** (parsimonious Flux Balance Analysis).
+
+#### Scenario
+You have **two gene expression datasets**.
+
+#### 1. Import Metabolic Model
+- Load the metabolic model.  
+- Define the **medium** and the **gene nomenclature format**.
+
+#### 2. Expression to RAS
+- Transform each **gene expression file** into a **RAS dataset**.  
+- This step must be applied **for each dataset**.
+
+#### 3. RAS to Bounds
+- Use the **two RAS datasets** as input.  
+- Generate the corresponding **flux bounds**.
+
+#### 4. Flux Simulation
+- Use the **output from the RAS to Bounds** step as input.  
+- Select **pFBA** as the simulation method.
+
+#### 5. Cluster Analysis
+- Perform **clustering** on the **flux dataset** obtained from the pFBA simulation.  
+- Identify clusters or groups within the flux profiles.
+
+#### 6. Metabolic Flux Enrichment Analysis
+- Perform **analysis and visualization** of **significant differences** between fluxes of different clusters.  
+- Use:
+  - The **clusters** as the *sample group specification*.  
+  - The **output from the pFBA flux simulation** as the *input flux data*.  
+- Optionally, specify **p-value** and **fold change** thresholds to refine the analysis.  
+
+
+### RAS Clustering + Reaction Enrichment Analysis
+
+#### Goal
+Perform **RAS statistical analysis** using the **MaREA** tool.  
+Compare **RAS clusters** obtained from a **single gene expression dataset**.
+
+#### Scenario
+You have **one gene expression dataset**.
+
+#### 1. Import Metabolic Model
+- Load the metabolic model.  
+- Define the **medium** and the **gene nomenclature format**.
+
+#### 2. Expression to RAS
+- Transform the **gene expression file** into a **RAS dataset**.
+
+#### 3. Cluster Analysis
+- Perform **clustering** on the **RAS dataset**.  
+- Identify distinct clusters or groups within the data.
+
+#### 4. Metabolic Reaction Enrichment Analysis (MaREA)
+- Perform **analysis and visualization** of **significant differences** between RAS values of different clusters.  
+- Use **MaREA** to detect enriched reactions and metabolic changes.  
+- Optionally, specify **p-value** and **fold change** thresholds to refine the analysis.  
+
+### Reaction Enrichment Analysis — Unified Datasets
+
+#### Goal
+Perform **RAS statistical analysis** using the **MaREA** tool.  
+Compare **groups within the same gene expression dataset**.
+
+#### Scenario
+You have **one gene expression dataset** along with the **corresponding class labels** (e.g., *Normal* vs *Cancer*).
+
+#### 1. Import Metabolic Model
+- Load the metabolic model.  
+- Define the **medium** and the **gene nomenclature format**.
+
+#### 2. Expression to RAS
+- Transform the **gene expression file** into a **RAS dataset**.
+
+#### 3. Metabolic Reaction Enrichment Analysis (MaREA)
+- Perform **analysis and visualization** of **significant differences** between RAS values of different groups (e.g., *Normal* vs *Cancer*).  
+- The **classes** are provided as input and used for **sample group specification** in the tool.  
+- Optionally, specify **p-value** and **fold change** thresholds to refine the analysis.  
+
+### Reaction Enrichment Analysis — Separated Datasets
+
+#### Goal
+Perform **RAS statistical analysis** using the **MaREA** tool with **different gene expression datasets**.
+
+#### Scenario
+You have **one gene expression dataset per condition** (e.g., *Cancer* vs *Normal*).
+
+#### 1. Import Metabolic Model
+- Load the metabolic model.  
+- Define the **medium** and the **gene nomenclature format**.
+
+#### 2. Expression to RAS
+- Transform each **gene expression file** into a **RAS dataset**.  
+- This step must be applied **individually for each dataset**.
+
+#### 3. Metabolic Reaction Enrichment Analysis (MaREA)
+- Perform **analysis and visualization** of **significant differences** between RAS values from two different datasets.  
+- In this scenario, the **two RAS datasets** are provided as **separate inputs**.  
+- Optionally, specify **p-value** and **fold change** thresholds to refine the analysis.  
+
+
 ## Tutorial Data
 
 Download example datasets used in tutorials: