1. Download and Install
- Go to the Download section and click "Download Setup (.exe)" for Windows.
- Once downloaded, double-click
metabodesk_setup.exe to start the installer.
- Follow the installation wizard: accept the license agreement (CC BY-NC-ND 4.0), choose your preferred installation folder (default:
C:\Program Files\MetaboDesk), and click Install.
- Wait for the installation to complete. This may take 1-2 minutes depending on your system.
- After installation completes, launch MetaboDesk from the Start Menu or desktop shortcut.
System Requirements: Windows 10/11 (64-bit), 4 GB RAM minimum, 500 MB disk space.
2. Open a Model
- Click "Open SBML..." in the top toolbar.
- Navigate to your SBML file (e.g.,
e_coli_core.xml) and click Open.
- The model will load and you'll see a summary: number of reactions, metabolites, and genes.
- The status bar at the bottom will show "Model loaded successfully" with statistics.
Where to get models: Download curated genome-scale models from
BiGG Models or
BioModels. Popular choices include
e_coli_core (small, good for learning) and
iML1515 (full E. coli model).
3. Understanding Analysis Types
MetaboDesk offers multiple analysis methods. Here's what each one does:
📊 Flux Balance Analysis (FBA)
FBA is the core method for predicting metabolic fluxes. It uses linear programming to maximize an objective function (usually biomass/growth) subject to stoichiometric constraints and reaction bounds.
Example: Load e_coli_core, run FBA, and see the predicted growth rate (~0.87 h⁻¹) along with flux values for all 95 reactions.
⚡ Parsimonious FBA (pFBA)
pFBA first optimizes for maximum growth (like FBA), then minimizes total flux while maintaining that growth. This yields more realistic, sparse flux distributions.
Use case: When you want to identify the most efficient pathways without unnecessary flux loops.
📈 Flux Variability Analysis (FVA)
FVA determines the minimum and maximum possible flux through each reaction while maintaining optimal (or near-optimal) growth. Reactions with wide ranges are flexible; narrow ranges indicate constrained reactions.
Example: Run FVA to identify which reactions are "blocked" (min=max=0) and which have flexibility for metabolic engineering.
🧬 Single Gene Deletion (SGD)
SGD systematically knocks out each gene one at a time and measures the impact on growth. Essential genes cause lethality (growth = 0) when deleted.
Example: In e_coli_core, deleting b2779 (ENO enzyme) eliminates growth because it's essential for glycolysis.
🔗 Double Gene Deletion (DGD)
DGD tests all pairwise gene knockouts to find synthetic lethal pairs—genes that are individually non-essential but lethal when both are deleted.
Use case: Identifying backup pathways and redundancy in metabolism.
⚗️ Single Reaction Deletion (SRD)
Similar to SGD but deletes reactions instead of genes. Useful when gene-protein-reaction associations are incomplete.
📉 Robustness Analysis
Varies the bounds of a specific reaction (e.g., glucose uptake) over a range and tracks how the objective changes. Shows sensitivity and identifies critical thresholds.
Example: Vary EX_glc__D_e from 0 to -20 mmol/gDW/h and observe how growth rate responds. You'll see a linear increase up to saturation.
🎯 Production Envelope
Shows the trade-off between biomass and a target product. As you force more production of a metabolite, growth typically decreases. The envelope shows all feasible combinations.
Example: Plot growth vs. ethanol production to see the maximum theoretical yield while maintaining cell viability.
🎲 Flux Sampling
Uses Monte Carlo sampling (ACHR algorithm) to explore the entire feasible flux space. Returns distributions (mean, std, min, max) for each reaction.
Use case: When you want probabilistic insights rather than a single optimal solution.
4. Run Your First Analysis
- With a model loaded, select "FBA" from the Analysis dropdown.
- Click "Run Analysis".
- Wait for computation (usually < 1 second for FBA).
- View results in the Results tab: objective value, flux chart, and detailed table.
5. Review and Filter Results
- Use the search boxes to filter by reaction ID.
- Set delta threshold to show only significant flux changes.
- Click table headers to sort by column.
- Double-click cells to see full details in a popup.
6. Export Results
Each analysis tab has an "Export CSV" button. Click it, choose a save location, and your results are exported for further analysis in Excel, Python, or R.
7. Modify the Medium (Exchange Reactions)
- Go to the Medium tab.
- Search for exchange reactions (e.g.,
EX_glc__D_e for glucose).
- Double-click the Lower/Upper bound cells to edit uptake limits.
- Negative lower bound = uptake allowed; zero = no uptake.
- Use built-in presets: "Minimal M9" or "Rich LB" for common media.
Example: To simulate anaerobic growth, set EX_o2_e lower bound to 0 (no oxygen uptake).
8. Gene Knockouts (Manual)
- Go to the Gene knockout tab.
- Search for the gene (e.g.,
b0720).
- Select it and click "Add knockout".
- The knockout list shows all active knockouts.
- Run FBA to see how growth is affected.
- Use "Clear knockouts" to reset.
9. Overexpression
- Go to the Overexpression tab.
- Search for a reaction (e.g.,
PFK for phosphofructokinase).
- Set the overexpression factor (e.g., 2x doubles the upper bound).
- Click "Add overexpression".
- Run analysis to observe effects on metabolism.
10. Network Map Visualization
- Go to the Map tab.
- Search: Enter a reaction/metabolite ID to focus on.
- Depth: How many neighbors to show (1-5).
- Flux threshold: Hide reactions with |flux| below threshold.
- View mode: Color by flux magnitude, gene KO impact, or FVA bounds.
- Click "Render Map" to generate.
- Click nodes to see details. Use toolbar to zoom/pan.
- Export as image or CSV using the buttons.
11. Model Editor (Patch-Based)
The Model Editor lets you modify models without altering the original SBML file. Changes are tracked as a "patch" that can be applied, saved, or exported.
Add Metabolites
- Go to Model Editor → Metabolites sub-tab.
- Enter metabolite ID (e.g.,
new_met_c), name, formula, and compartment.
- Click "Add Metabolite".
Add Genes
- Go to Model Editor → Genes sub-tab.
- Enter gene ID and name.
- Click "Add Gene".
Add or Modify Reactions
- Go to Model Editor → Reactions sub-tab.
- Enter reaction ID, name, equation (e.g.,
atp_c + h2o_c -> adp_c + pi_c), and bounds.
- Optionally add GPR (gene-protein-reaction rule).
- Click "Add/Update Reaction".
Disable or Delete Reactions
- Go to Model Editor → Disable/Delete sub-tab.
- Search for the reaction to remove.
- Use "Disable" (sets bounds to 0) or "Delete" (removes entirely).
View and Export Patch
- Go to Model Editor → Patch sub-tab to see all changes as JSON.
- Copy or save the patch for later.
Export Modified SBML
- Go to Model Editor → Export SBML sub-tab.
- Click "Export as SBML" to save the modified model as a new file.
12. Tools: memote (Model Quality)
memote is an automated tool that evaluates genome-scale metabolic models for quality, completeness, and MIRIAM annotation compliance.
- Go to the Tools tab.
- Make sure tools are installed: click "Check tools". If missing, click "Repair tools".
- Load your SBML model.
- Click "Run memote report (current model)".
- Wait for the analysis (can take 1-5 minutes depending on model size).
- A detailed HTML report opens in your browser with scores for:
- Stoichiometry consistency
- Mass/charge balance
- Annotation completeness (KEGG, ChEBI, UniProt, etc.)
- Biomass composition
- And many more checks...
Tip: Use memote reports to identify issues before publishing your model.
13. Tools: CarveMe (Model Reconstruction)
CarveMe reconstructs genome-scale metabolic models from annotated genome files (protein FASTA or GenBank).
- Go to the Tools tab.
- Ensure tools are installed ("Check tools").
- Click "Run CarveMe (genome → SBML)".
- Select your input file (protein FASTA or GenBank).
- Choose output location for the generated SBML.
- Wait for reconstruction (can take 5-30 minutes depending on genome size).
- The reconstructed model is saved and can be opened in MetaboDesk.
Use case: Quickly generate a draft model for a new organism from its genome annotation.
14. Saving and Loading Scenarios
- Use File → Save Scenario to save current settings (knockouts, overexpressions, medium changes).
- Use File → Load Scenario to restore a saved configuration.
- Recent scenarios appear in the File menu for quick access.
15. Keyboard Shortcuts
Ctrl+O — Open SBML fileCtrl+R — Run analysisCtrl+S — Save scenarioCtrl+Z — UndoCtrl+Y — Redo
Troubleshooting
- Model won't load: Ensure it's a valid SBML Level 3 file. Try opening in COBRApy first.
- Analysis stuck: Large models (>5000 reactions) may take longer. Check the status bar.
- memote/CarveMe not working: Go to Tools tab and click "Repair tools" to reinstall dependencies.
- Solver errors: Try switching to a different solver (Auto, glpk, or highs) in the toolbar.
Need more help? Check the Tools tab log output for detailed error messages, or contact support.
Windows Available
Linux Coming Soon
macOS Coming Soon