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An integrated network visualization framework towards metabolic engineering applications.

Noronha A, Vilaça P, Rocha M - BMC Bioinformatics (2014)

Bottom Line: 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).The framework and its source code are freely available, together with documentation and other resources, being illustrated with well documented case studies.

View Article: PubMed Central - PubMed

Affiliation: Centre of Biological Engineering (CEB), School of Engineering, University of Minho, Campus de Gualtar, Braga, Portugal. bertonoronha@gmail.com.

ABSTRACT

Background: 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). 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.

Results: In 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.

Conclusions: The framework and its source code are freely available, together with documentation and other resources, being illustrated with well documented case studies.

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Related in: MedlinePlus

Visualization framework architecture overview. The Input/Output layer provides the reading and writing capabilities for several file formats. The visualization layer contains the layout representation, and provides the visualization capabilities. External sources can also provide filters and overlaps, being OptFlux one such example (through the visualization plugin).
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Fig2: Visualization framework architecture overview. The Input/Output layer provides the reading and writing capabilities for several file formats. The visualization layer contains the layout representation, and provides the visualization capabilities. External sources can also provide filters and overlaps, being OptFlux one such example (through the visualization plugin).

Mentions: The two main tasks of the software are to build these layouts from external sources (being able to export them as well), and to visually represent them. This leads to a two-layer architecture (Figure 2), where the first implements the capabilities to read and write metabolic layouts, while the other, the visualization layer, handles the visualization and edition of the metabolic layout. The main features of each are given below:Figure 2


An integrated network visualization framework towards metabolic engineering applications.

Noronha A, Vilaça P, Rocha M - BMC Bioinformatics (2014)

Visualization framework architecture overview. The Input/Output layer provides the reading and writing capabilities for several file formats. The visualization layer contains the layout representation, and provides the visualization capabilities. External sources can also provide filters and overlaps, being OptFlux one such example (through the visualization plugin).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4300605&req=5

Fig2: Visualization framework architecture overview. The Input/Output layer provides the reading and writing capabilities for several file formats. The visualization layer contains the layout representation, and provides the visualization capabilities. External sources can also provide filters and overlaps, being OptFlux one such example (through the visualization plugin).
Mentions: The two main tasks of the software are to build these layouts from external sources (being able to export them as well), and to visually represent them. This leads to a two-layer architecture (Figure 2), where the first implements the capabilities to read and write metabolic layouts, while the other, the visualization layer, handles the visualization and edition of the metabolic layout. The main features of each are given below:Figure 2

Bottom Line: 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).The framework and its source code are freely available, together with documentation and other resources, being illustrated with well documented case studies.

View Article: PubMed Central - PubMed

Affiliation: Centre of Biological Engineering (CEB), School of Engineering, University of Minho, Campus de Gualtar, Braga, Portugal. bertonoronha@gmail.com.

ABSTRACT

Background: 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). 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.

Results: In 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.

Conclusions: The framework and its source code are freely available, together with documentation and other resources, being illustrated with well documented case studies.

Show MeSH
Related in: MedlinePlus