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Open Access Research article

Validation of a constraint-based model of Pichia pastoris metabolism under data scarcity

Marta Tortajada1, Francisco Llaneras2 and Jesús Picó2

Author Affiliations

1 Biopolis S.L., C/Catedrático Agustín Escardino Benlloch, 9, 46980, Paterna, Valencia, Spain

2 AI2, Universidad Politécnica de Valencia, Camino de Vera s/n, 46022, Valencia, Spain

BMC Systems Biology 2010, 4:115  doi:10.1186/1752-0509-4-115

Published: 17 August 2010



Constraint-based models enable structured cellular representations in which intracellular kinetics are circumvented. These models, combined with experimental data, are useful analytical tools to estimate the state exhibited (the phenotype) by the cells at given pseudo-steady conditions.


In this contribution, a simplified constraint-based stoichiometric model of the metabolism of the yeast Pichia pastoris, a workhorse for heterologous protein expression, is validated against several experimental available datasets. Firstly, maximum theoretical growth yields are calculated and compared to the experimental ones. Secondly, possibility theory is applied to quantify the consistency between model and measurements. Finally, the biomass growth rate is excluded from the datasets and its prediction used to exemplify the capability of the model to calculate non-measured fluxes.


This contribution shows how a small-sized network can be assessed following a rational, quantitative procedure even when measurements are scarce and imprecise. This approach is particularly useful in lacking data scenarios.