Systems Biotechnology: Combined in Silico and Omics Analyses for the Improvement of Microorganisms for Industrial Applications - Systems Biology: Networks, Models, and Applications - page 210

Figure 7.7 Database query interface of the BioSilico Modeler. In this screen
capture, the list of metabolic reactions is retrieved as the result of a query, “Find
all reactions involved in the glycolysis pathway of E. coli K-12 strain.” The
resultant network is visualized and summarized in a tabular format.
MetaFluxNet allows users to set up their own metabolic network
models by registering information on two object classes, metabolites
and reactions . Each class consists of several fields describing biological
information. Users can freely edit and store the data contents in the
fields. A stoichiometric model can be built from the metabolic reaction
model under the steady-state assumption. The model system can be
classified by one of four possible cases according to determinacy and
redundancy [77]. In the case of the determined system, a unique solution
or a least-squares solution can be obtained if the system is observable.
In the case of the redundant system, the measured fluxes are reconciled
to remove the inconsistency, followed by inspecting calculable fluxes
which can be uniquely determined by the least-squares solution using
the pseudo-inverse. If the system is underdetermined, the constraints-
based flux analysis can be exploited to quantify the flux distribution
by maximizing or minimizing the objective function [59].
MetaFluxNet also allows users to compare the changes in flux
distribution under genetically or environmentally perturbed conditions,