Morning tutorial

The bigg_e_coli_core Escherichia coli K12 model is a simplified metabolic network model and is (almost) identical to the model published as supporting material in Orth et al. (2010). The following exercises are inspired by this document.

Warming up

  • Reset your session
  • Pick the bigg_e_coli_core E. coli model from the model and pathway repository
To get familiar with the website's interface, please answer the following questions about the bigg_e_coli_core model:
  • What is the total number of reactions?
  • What is the total number of external (boundary) reactions? Please distinguish between uptake and secretion reactions.
  • What are the total numbers of reversible/irreversible reactions?
  • Can you identify any reactions with a fixed reaction flux? If so, what does this mean?
  • What is the total number of metabolites?
  • What are the dimensions of the stoichiometric matrix for the considered model?
  • What compartments are considered in the model? Are there any compartments missing?
  • What additional compartments could be relevant for an eukaryotic model?
  • How many metabolites does the biomass reaction comprise? What does the biomass reaction represent? Are there potential extensions?
  • How many reactions are connected to the biomass reaction?
  • How many reactions occur in a single compartment only? What kind of reactions are the remaining reactions? What is their total number?
  • How many reactions are orphans, i.e. reactions without protein association? Which reaction comprises the most proteins or protein complexes?
  • Which protein imports malate into the cytoplasm? How is this import realized? Can you identify a homolog/homologs in Bacillus subtilis (e.g. use MyHits)?
  • What is the shortest path, i.e. number of reactions, between the external malate and the cytosolic phosphoenolpyruvate?
  • In which enzymatic complexes and reactions does the protein PT1_ECOLI participate?
  • In how many different subcellular locations and reactions does succinate(2-) occur? Can you identify its CHEBI and KEGG ID?

Model boundary

In the reac_list view, restrict the display to "external" reactions only by typing BOUNDARY in the Search field. Hint: consider the flux bounds in the Enzy column.
  • What can you tell about the growth conditions/environment of E. coli K12 as modelled by bigg_e_coli_core? What does it mean that some external reactions are unconstrained/unidirectional/bidirectional?


The model bigg_e_coli_core is an oversimplified metabolic network of Escherichia coli strain K12.
  • What can you tell about the biomass reaction of this model? Is it biologically relevant?
  • What can you tell about the biosynthesis of CoA, ADP, NAD+ and NADP+?
  • What can you tell about the sulfur metabolism?


Run CR and FBA analyses on the website.
  • Does the model grow?
  • Can you identify any reaction correlation groups? How do they relate to the flux distribution?
  • Can you identify any reaction incoherent correlation groups? Could you explain what's happening with them?