Systems Biotechnology: Combined in Silico and Omics Analyses for the Improvement of Microorganisms for Industrial Applications - Systems Biology: Networks, Models, and Applications - page 208

enzymes, biochemical compounds, reactions, and pathways. In addition,
a robust systematic architecture of BioSilico is extended to a customized
web-start interface, the BioSilico Modeler, which provides the inte-
grated environment to enhance the construction of in silico metabolic
network models of interest.
In BioSilico, various querying logics and user-friendly web-accessible
interfaces are designed to efficiently retrieve the relevant information
on enzymes, compounds, reactions, and pathways from the integrated
database. Queries using Enzyme Commission (EC) number, name, for-
mula, CAS number, pathway, and organism simultaneously examine
all the classes of the database; the matched entries are collected and
a view page of query results is dynamically generated, allowing access
to more detailed information using the hyperlinks provided. Moreover,
a Java Applet for chemical structure search via the web interface
allows users to either draw the compound to be searched or enter its
SMILES string, giving rise to the list of matching compounds satisfying
the selected search type (similarity, substructure, or exact match).
Clicking on a returned structure of the compound from Chem DB,
which was developed using two Marvin Java applets (MarvinSketch
and MarvinView) and JChem libraries from ChemAxon (http://
chemaxon.com), leads to the corresponding BioSilico compound page
(figure 7.6). Consequently, one query renders it possible to efficiently
search for the entire classes of the integrated database, retrieve the
relevant information, and finally to display well-designed view pages
interactively for more detailed information.
In addition to the web-based interface, BioSilico provides a web-
client application, the BioSilico Modeler, which is launched with Java
Web Start independently of the web browser. Thus, users can compre-
hensively build reaction network models of their own. The model
composer supported in this application allows users to define com-
ponents (e.g., compounds or metabolites) and their interactions (e.g.,
reactions) after creating a model project. Furthermore, through the
customized client-server interface, a wide variety of queries retrieve
the list of reactions that can be imported from the BioSilico database
system on a remote server. Imported reactions are then mapped into
the current model project, thus leading to the construction of the
comprehensive model of a metabolic reaction network (figure 7.7).
The resultant model network can be automatically visualized by
several layout algorithms.
Integrated Environment for In Silico Modeling and
Simulation of Metabolic Networks
Considering the importance of metabolic flux analysis in systems
biotechnology, it will be extremely useful to have a user-friendly
computer program for quantitatively analyzing metabolic fluxes.