Stoichiometric modeling is a powerful in silico systems biology approach which enables rational analysis of metabolic components and interactions. Stoichiometric models are often built from a combination of omics data and experimental culturing data; the methodology can elucidate molecular-level phenomena including cellular phenotypes without requiring extensive knowledge of enzymatic kinetic parameters, data that is often difficult to acquire. Stoichiometric modeling of metabolic systems has been used to study physiologies of model systems ranging from viruses, to individual microbial cells, to microbial communities, to human tissues (Klamt and Stelling, 2003; Reed and Palsson, 2003; Trinh et al., 2009; Taffs et al., 2009; Orth et al., 2010).

The workshop material below focuses on the stoichiometric modelling approach known as elementary flux mode analysis (EFMA). Briefly, elementary flux modes (EFMs) are mathematically defined, minimal, non-divisible metabolic pathways which are ideal for bottom-up systems biology studies. Each EFM is comprised of a unique combination of biochemical steps (Schuster and Schuster 1993; Schuster et al. 2000). EFMs can be used to represent all steady state phenotypes in the model-defined physiological flux space through nonnegative linear combinations.


Klamt, S. and Stelling, J. (2003) Two approaches for metabolic pathway analysis? Trends Biotechnol. 21: 64–9.

Orth, J.D., Thiele, I., and Palsson, B.Ø. (2010) What is flux balance analysis? Nat. Biotechnol. 28: 245–8.

Reed, J.L. and Palsson, B.O. (2003) Thirteen years of building constraint-based in silico models of Escherichia coli. J. Bacteriol. 185: 2692–9.

Schuster R, Schuster S (1993) Refined algorithm and computer program for calculating all non–negative fluxes admissible in steady states of biochemical reaction systems with or without some flux rates fixed. Bioinformatics 9: 79-85.

Schuster S, Fell DA, Dandekar T (2000) A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 18: 326-332 .

Taffs, R., Aston, J.E., Brileya, K., Jay, Z., Klatt, C.G., McGlynn, S., et al. (2009) In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study. BMC Syst. Biol. 3: 114.

Trinh, C.T., Wlaschin, A., and Srienc, F. (2009) Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl. Microbiol. Biotechnol. 81: 813–26.


Workshop Files:

These files are designed to enable a researcher to build, run and analyze stoichiometric models using elementary flux mode analysis (EFMA).  


Link to workshop presentation, step-by-step instructions for EFMA, sample metabolic models and analysis templates.

Link to completed workshop exercises.

Link to publications relevant to the covered material.