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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 interface examples. A network view where the network is displayed, and the user can interact with it; B side panel where filters, overlaps, information about the nodes and the zoom panel are displayed.
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Fig3: Visualization framework interface examples. A network view where the network is displayed, and the user can interact with it; B side panel where filters, overlaps, information about the nodes and the zoom panel are displayed.

Mentions: As stated previously, the visualization layer provides all the functionalities related with the visualization and editing of the metabolic layout. One of these features allows to change the default colours and shapes of the nodes. The graphical user interface (GUI) is composed of two major elements (Figure 3): the network view, where it is possible to edit the network and click/drag the nodes (Figure 3A), and the side panel where filters, overlaps and node information are available (Figure 3B). In this way, it is possible for the user to easily interact with the network, using all the features the interface has to offer.Figure 3


An integrated network visualization framework towards metabolic engineering applications.

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

Visualization framework interface examples. A network view where the network is displayed, and the user can interact with it; B side panel where filters, overlaps, information about the nodes and the zoom panel are displayed.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Visualization framework interface examples. A network view where the network is displayed, and the user can interact with it; B side panel where filters, overlaps, information about the nodes and the zoom panel are displayed.
Mentions: As stated previously, the visualization layer provides all the functionalities related with the visualization and editing of the metabolic layout. One of these features allows to change the default colours and shapes of the nodes. The graphical user interface (GUI) is composed of two major elements (Figure 3): the network view, where it is possible to edit the network and click/drag the nodes (Figure 3A), and the side panel where filters, overlaps and node information are available (Figure 3B). In this way, it is possible for the user to easily interact with the network, using all the features the interface has to offer.Figure 3

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