Reply to "Do genome-scale models need exact solvers or clearer standards?"

Abstract

In their Correspondence entitled, “Do genome‐scale models need exact solvers or clearer standards?”, Ebrahim et al (2015) suggest an unnecessary dichotomy. They discuss the findings of our paper, “An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models” (Chindelevitch et al, 2014), and suggest that our work highlights the need for better model encoding standards. Moreover, the authors dispute our claims that multiple previously published metabolic network models are unable to produce growth when analyzed with an exact arithmetic approach. They attribute discrepancies between their findings and ours solely to a misinterpretation of the formatting conventions used to encode these models. The authors conclude that genome‐scale metabolic network models need better standards, rather than the improvements in accuracy obtained with exact arithmetic. We argue here that improved standards and exact arithmetic are complementary advances that both benefit this field. Thus, the answer to the question posed by Ebrahim et al (2015) is “both.”