Step 1: Build SBtab Pathway Model
Click here for an overview of the process. Skip this step if you already have an SBtab model file.
Pathway definition CSV (example)
Minimum concentration mM
Maximum concentration mM
pH
Ionic strength [M]
Analysis method
MDF   ECM
The default concentration range of 1 μM - 10 mM reflects the fact that metabolite concentrations are constrained from above by osmotic pressure and toxicity considerations and from below by enzyme affinities.
Default concentrations for ubiquitous cofactors like CoA and ATP are set based on measurements from E. coli and other model organisms (see Noor et al., PloS Comp. Bio 2014). You can edit these defaults by modifying the SBtab file (e.g. in Excel) before performing the analysis below.

Step 2: Verify & Edit Pathway Model
  1. Check relative fluxes for all reactions in the SBtab file.
  2. Check KEGG IDs for all reactants in the model.
  3. Check and/or edit bounds on metabolite concentrations.
  4. If using ECM, change the default kinetic parameters to the relevant values.

Step 3: Perform Pathway Analysis
Pathway SBtab
(examples MDF, ECM)
Output
HTML       SBtab