# HG changeset patch # User francesco_lapi # Date 1765451853 0 # Node ID d45a37837ffa8e76ff69f2f3441c211b0afad179 # Parent 4cf00f21f6091b278173960db93e5172c5bb1dc2 Uploaded diff -r 4cf00f21f609 -r d45a37837ffa ._COBRAxy Binary file ._COBRAxy has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/._.DS_Store Binary file COBRAxy/._.DS_Store has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/._.gitignore Binary file COBRAxy/._.gitignore has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/._GSOC project submission.html Binary file COBRAxy/._GSOC project submission.html has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/._README.md Binary file COBRAxy/._README.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/._dist Binary file COBRAxy/._dist has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/._docs Binary file COBRAxy/._docs has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/._src Binary file COBRAxy/._src has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/._test Binary file COBRAxy/._test has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/dist/._.DS_Store Binary file COBRAxy/dist/._.DS_Store has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/dist/._cobraxy Binary file COBRAxy/dist/._cobraxy has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/dist/cobraxy/._meta.yaml Binary file COBRAxy/dist/cobraxy/._meta.yaml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/._.nojekyll Binary file COBRAxy/docs/._.nojekyll has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/._README.md Binary file COBRAxy/docs/._README.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/.__media Binary file COBRAxy/docs/.__media has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/.__sidebar.md Binary file COBRAxy/docs/.__sidebar.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/._getting-started.md Binary file COBRAxy/docs/._getting-started.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/._index.html Binary file COBRAxy/docs/._index.html has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/._installation.md Binary file COBRAxy/docs/._installation.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/._quickstart.md Binary file COBRAxy/docs/._quickstart.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/._reference Binary file COBRAxy/docs/._reference has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/._tools Binary file COBRAxy/docs/._tools has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/._troubleshooting.md Binary file COBRAxy/docs/._troubleshooting.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/._tutorials Binary file COBRAxy/docs/._tutorials has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/_media/._logo-dark.png Binary file COBRAxy/docs/_media/._logo-dark.png has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/_media/._logo-light.png Binary file COBRAxy/docs/_media/._logo-light.png has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/_media/._logo.png Binary file COBRAxy/docs/_media/._logo.png has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/_media/._logoBLACK_GALAXY.png Binary file COBRAxy/docs/_media/._logoBLACK_GALAXY.png has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/_media/._logoBLACK_PURPLE.png Binary file COBRAxy/docs/_media/._logoBLACK_PURPLE.png has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/_media/._logoBORDERS.png Binary file COBRAxy/docs/_media/._logoBORDERS.png has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/_media/._logoWHITE_GALAXY.png Binary file COBRAxy/docs/_media/._logoWHITE_GALAXY.png has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/_media/._logoWHITE_PURPLE.png Binary file COBRAxy/docs/_media/._logoWHITE_PURPLE.png has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/reference/._built-in-models.md Binary file COBRAxy/docs/reference/._built-in-models.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tools/._README.md Binary file COBRAxy/docs/tools/._README.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tools/._export-metabolic-model.md Binary file COBRAxy/docs/tools/._export-metabolic-model.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tools/._flux-simulation.md Binary file COBRAxy/docs/tools/._flux-simulation.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tools/._flux-to-map.md Binary file COBRAxy/docs/tools/._flux-to-map.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tools/._import-metabolic-model.md Binary file COBRAxy/docs/tools/._import-metabolic-model.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tools/._marea-cluster.md Binary file COBRAxy/docs/tools/._marea-cluster.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tools/._marea.md Binary file COBRAxy/docs/tools/._marea.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tools/._ras-generator.md Binary file COBRAxy/docs/tools/._ras-generator.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tools/._ras-to-bounds.md Binary file COBRAxy/docs/tools/._ras-to-bounds.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tools/._rps-generator.md Binary file COBRAxy/docs/tools/._rps-generator.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tutorials/._README.md Binary file COBRAxy/docs/tutorials/._README.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tutorials/._galaxy-setup.md Binary file COBRAxy/docs/tutorials/._galaxy-setup.md has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/docs/tutorials/README.md --- 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: diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._exportMetabolicModel.py Binary file COBRAxy/src/._exportMetabolicModel.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._exportMetabolicModel.xml Binary file COBRAxy/src/._exportMetabolicModel.xml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._flux_simulation.py Binary file COBRAxy/src/._flux_simulation.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._flux_simulation.xml Binary file COBRAxy/src/._flux_simulation.xml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._flux_to_map.py Binary file COBRAxy/src/._flux_to_map.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._flux_to_map.xml Binary file COBRAxy/src/._flux_to_map.xml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._importMetabolicModel.py Binary file COBRAxy/src/._importMetabolicModel.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._importMetabolicModel.xml Binary file COBRAxy/src/._importMetabolicModel.xml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._local Binary file COBRAxy/src/._local has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._marea.py Binary file COBRAxy/src/._marea.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._marea.xml Binary file COBRAxy/src/._marea.xml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._marea_cluster.py Binary file COBRAxy/src/._marea_cluster.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._marea_cluster.xml Binary file COBRAxy/src/._marea_cluster.xml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._marea_macros.xml Binary file COBRAxy/src/._marea_macros.xml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._ras_generator.py Binary file COBRAxy/src/._ras_generator.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._ras_generator.xml Binary file COBRAxy/src/._ras_generator.xml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._ras_to_bounds.py Binary file COBRAxy/src/._ras_to_bounds.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._ras_to_bounds.xml Binary file COBRAxy/src/._ras_to_bounds.xml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._rps_generator.py Binary file COBRAxy/src/._rps_generator.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._rps_generator.xml Binary file COBRAxy/src/._rps_generator.xml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._setup.py Binary file COBRAxy/src/._setup.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._shed.yml Binary file COBRAxy/src/._shed.yml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/._utils Binary file COBRAxy/src/._utils has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/._ENGRO2_rules.csv Binary file COBRAxy/src/local/._ENGRO2_rules.csv has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/.___init__.py Binary file COBRAxy/src/local/.___init__.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/._mappings Binary file COBRAxy/src/local/._mappings has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/._medium Binary file COBRAxy/src/local/._medium has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/._models Binary file COBRAxy/src/local/._models has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/._pickle files Binary file COBRAxy/src/local/._pickle files has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/._readme.txt Binary file COBRAxy/src/local/._readme.txt has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/._svg metabolic maps Binary file COBRAxy/src/local/._svg metabolic maps has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/mappings/._genes_human.csv Binary file COBRAxy/src/local/mappings/._genes_human.csv has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/medium/._medium.csv Binary file COBRAxy/src/local/medium/._medium.csv has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/models/._ENGRO2.xml Binary file COBRAxy/src/local/models/._ENGRO2.xml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/models/._Recon.xml Binary file COBRAxy/src/local/models/._Recon.xml has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._ENGRO2_genes.p Binary file COBRAxy/src/local/pickle files/._ENGRO2_genes.p has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._ENGRO2_genes.pickle Binary file COBRAxy/src/local/pickle files/._ENGRO2_genes.pickle has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._ENGRO2_rules.p Binary file COBRAxy/src/local/pickle files/._ENGRO2_rules.p has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._HMRcore_genes.p Binary file COBRAxy/src/local/pickle files/._HMRcore_genes.p has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._HMRcore_genes.pickle Binary file COBRAxy/src/local/pickle files/._HMRcore_genes.pickle has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._HMRcore_rules.p Binary file COBRAxy/src/local/pickle files/._HMRcore_rules.p has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._RECON_genes.pickle Binary file COBRAxy/src/local/pickle files/._RECON_genes.pickle has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._Recon_genes.p Binary file COBRAxy/src/local/pickle files/._Recon_genes.p has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._Recon_rules.p Binary file COBRAxy/src/local/pickle files/._Recon_rules.p has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._black_list.pickle Binary file COBRAxy/src/local/pickle files/._black_list.pickle has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._reactions.pickle Binary file COBRAxy/src/local/pickle files/._reactions.pickle has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._substrate_frequencies.pickle Binary file COBRAxy/src/local/pickle files/._substrate_frequencies.pickle has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._synonyms.pickle Binary file COBRAxy/src/local/pickle files/._synonyms.pickle has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/pickle files/._synonyms_dict_recon_keys_filtered.pkl Binary file COBRAxy/src/local/pickle files/._synonyms_dict_recon_keys_filtered.pkl has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/svg metabolic maps/._ENGRO2_map.svg Binary file COBRAxy/src/local/svg metabolic maps/._ENGRO2_map.svg has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/svg metabolic maps/._ENGRO2_no_legend_map.svg Binary file COBRAxy/src/local/svg metabolic maps/._ENGRO2_no_legend_map.svg has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/svg metabolic maps/._HMRcore_map.svg Binary file COBRAxy/src/local/svg metabolic maps/._HMRcore_map.svg has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/svg metabolic maps/._HMRcore_no_legend_map.svg Binary file COBRAxy/src/local/svg metabolic maps/._HMRcore_no_legend_map.svg has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/local/svg metabolic maps/ENGRO2_map.svg --- a/COBRAxy/src/local/svg metabolic maps/ENGRO2_map.svg Mon Nov 03 14:49:49 2025 +0000 +++ b/COBRAxy/src/local/svg metabolic maps/ENGRO2_map.svg Thu Dec 11 11:17:33 2025 +0000 @@ -137,15 +137,15 @@ inkscape:pageopacity="0.0" inkscape:pagecheckerboard="0" inkscape:deskcolor="#d1d1d1" - inkscape:zoom="2.48" - inkscape:cx="431.85483" - inkscape:cy="2394.9596" + inkscape:zoom="3.5072497" + inkscape:cx="1878.2524" + inkscape:cy="1753.9384" inkscape:window-width="2560" inkscape:window-height="1494" inkscape:window-x="-11" inkscape:window-y="-11" inkscape:window-maximized="1" - inkscape:current-layer="Legend body" + inkscape:current-layer="Group 30" showgrid="true">sulfite3sPyr Legend:Up-regulated in dataset1Down-regulated in dataset1Flux-inversion: same direction of the arrow in dataset1, opposite direction in dataset2.Fold change under thresholdNot classifiedNot significantFlux-inversion: same direction of the arrow in dataset2, opposite direction in dataset1.Tickness is proportional to z-score5,10mTHFO⁺Hsulfite3sPyr 1 return (avg1 - avg2) / (abs(avg1) + abs(avg2)) -# TODO: I would really like for this one to get the Thanos treatment def fix_style(l :str, col :Optional[str], width :str, dash :str) -> str: """ Produces a "fixed" style string to assign to a reaction arrow in the SVG map, assigning style properties to the corresponding values passed as input params. diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/utils/._CBS_backend.py Binary file COBRAxy/src/utils/._CBS_backend.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/utils/.___init__.py Binary file COBRAxy/src/utils/.___init__.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/utils/._general_utils.py Binary file COBRAxy/src/utils/._general_utils.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/utils/._model_utils.py Binary file COBRAxy/src/utils/._model_utils.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/utils/._reaction_parsing.py Binary file COBRAxy/src/utils/._reaction_parsing.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/src/utils/._rule_parsing.py Binary file COBRAxy/src/utils/._rule_parsing.py has changed diff -r 4cf00f21f609 -r d45a37837ffa COBRAxy/test/._testing.py Binary file COBRAxy/test/._testing.py has changed