Abstract
BackgroundOver the last years, several methods for the phenotype simulation of microorganisms, under specified genetic and environmental conditions have been proposed, in the context of Metabolic Engineering (ME). These methods provided insight on the functioning of microbial metabolism and played a key role in the design of genetic modifications that can lead to strains of industrial interest. On the other hand, in the context of Systems Biology research, biological network visualization has reinforced its role as a core tool in understanding biological processes. However, it has been scarcely used to foster ME related methods, in spite of the acknowledged potential.ResultsIn this work, an open-source software that aims to fill the gap between ME and metabolic network visualization is proposed, in the form of a plugin to the OptFlux ME platform. The framework is based on an abstract layer, where the network is represented as a bipartite graph containing minimal information about the underlying entities and their desired relative placement. The framework provides input/output support for networks specified in standard formats, such as XGMML, SBGN or SBML, providing a connection to genome-scale metabolic models. An user-interface makes it possible to edit, manipulate and query nodes in the network, providing tools to visualize diverse effects, including visual filters and aspect changing (e.g. colors, shapes and sizes). These tools are particularly interesting for ME, since they allow overlaying phenotype simulation results or elementary flux modes over the networks.ConclusionsThe framework and its source code are freely available, together with documentation and other resources, being illustrated with well documented case studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-014-0420-0) contains supplementary material, which is available to authorized users.
Highlights
Over the last years, several methods for the phenotype simulation of microorganisms, under specified genetic and environmental conditions have been proposed, in the context of Metabolic Engineering (ME)
Visualization layer features As stated previously, the visualization layer provides all the functionalities related with the visualization and editing of the metabolic layout
Some of them are the basic features that are typical in any visualization framework, Figure 3 Visualization framework interface examples
Summary
Several methods for the phenotype simulation of microorganisms, under specified genetic and environmental conditions have been proposed, in the context of Metabolic Engineering (ME). Within the field of Systems Biology, the analysis of different types of biological networks is an important task in understanding the underlying biological processes For this endeavour, a mathematical framework is provided by graph theory, which has allowed to verify that a multitude of organisms share relevant properties when analysing the topology of their networks [1]. In the pregenomic era, the analysis and visualization of these networks were approached as independent computational problems, it is desirable that these two levels are well integrated [2] Together with their regulatory [3] and signalling counterparts [4,5], metabolic networks represent a vastly studied class of biological networks. Metabolites can be converted by the cell into building blocks or decomposed to generate energy or other compounds
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