Advantages and disadvantages of aggregating fluxes into synthetic and degradative fluxes when modelling metabolic pathways.

Derivative processes for modelling metabolic fluxes

MOTIVATION One of the challenging questions in modelling biological systems is to characterize the functional forms of the processes that control and orchestrate molecular and cellular phenotypes. Recently proposed methods for the analysis of metabolic pathways, for example, dynamic flux estimation, can only provide estimates of the underlying fluxes at discrete time points but fail to capture ...

Strategies for representing metabolic pathways within biochemical systems theory: reversible pathways.

The search for systematic methods to deal with the integrated behavior of complex biochemical systems has over the past two decades led to the proposal of several theories of biochemical systems. Among the most promising is biochemical systems theory (BST). Recent comparisons of this theory with several others that have recently been proposed have demonstrated that all are variants of BST and s...

Modelling central metabolic fluxes by constraint-based optimization reveals metabolic reprogramming of developing Solanum lycopersicum (tomato) fruit

Modelling of metabolic networks is a powerful tool to analyse the behaviour of developing plant organs, including fruits. Guided by our current understanding of heterotrophic metabolism of plant cells, a medium-scale stoichiometric model, including the balance of co-factors and energy, was constructed in order to describe metabolic shifts that occur through the nine sequential stages of Solanum...

Influence of salinity on co2 fluxes stomatal conductance and specific leaf eeight of jojoba

Comparing metabolic pathways through potential fluxes: a selective opening approach

In our previous work we developed CoMeta, a tool for comparing metabolic pathways of different organisms, using the KEGG database as data source. The similarity measure adopted combines homology of reactions and functional aspects of the pathways. The latter are captured by T-invariants in the Petri net representation, which correspond to potential fluxes in the pathways. A Petri net can model ...