Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes.
The overarching ambition of kinetic metabolic modeling is to capture the dynamic behavior of metabolism to such an extent that systems and synthetic biology strategies can reliably be tested in silico. The lack of kinetic data hampers the development of kinetic models, and most of the current models use ad hoc reduced stoichiometry or oversimplified kinetic rate expressions, which may limit their predictive strength. There is a need to introduce the community-level standards that will organize and accelerate the future developments in this area. We introduce here a set of requirements that will ensure the model quality, we examine the current kinetic models with respect to these requirements, and we propose a general workflow for constructing models that satisfy these requirements.
Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
Ljubisa
L
Miskovic
Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
Milenko
M
Tokic
Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
Georgios
G
Fengos
Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland. Electronic address: vassily.hatzimanikatis@epfl.ch.
Vassily
V
Hatzimanikatis
D000818:Animals; D055598:Chemical Phenomena; D003198:Computer Simulation; D006801:Humans; D007700:Kinetics; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D010641:Phenotype