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. 2014 Sep 2;9(9):e106035.
doi: 10.1371/journal.pone.0106035. eCollection 2014.

esyN: network building, sharing and publishing

Daniel M Bean  1 , Joshua Heimbach  2 , Lorenzo Ficorella  3 , Gos Micklem  4 , Stephen G Oliver  1 , Giorgio Favrin  1
Affiliations

esyN: network building, sharing and publishing

Daniel M Bean et al. PLoS One. .

Erratum in

Abstract

The construction and analysis of networks is increasingly widespread in biological research. We have developed esyN ("easy networks") as a free and open source tool to facilitate the exchange of biological network models between researchers. esyN acts as a searchable database of user-created networks from any field. We have developed a simple companion web tool that enables users to view and edit networks using data from publicly available databases. Both normal interaction networks (graphs) and Petri nets can be created. In addition to its basic tools, esyN contains a number of logical templates that can be used to create models more easily. The ability to use previously published models as building blocks makes esyN a powerful tool for the construction of models and network graphs. Users are able to save their own projects online and share them either publicly or with a list of collaborators. The latter can be given the ability to edit the network themselves, allowing online collaboration on network construction. esyN is designed to facilitate unrestricted exchange of this increasingly important type of biological information. Ultimately, the aim of esyN is to bring the advantages of Open Source software development to the construction of biological networks.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Screenshot of the esyN Model-building tool.
The left panel is the menu for the network building tool, with options e.g saving, uploading and exporting projects. The central blue panel is the window in which the network is displayed, in this case a model. This window is used for node and edge creation and selection. The right panel contains tools for editing individual nodes and edges. The lower yellow panel displays options to create parent-child relationships for the selected node. The lower right panel is the interface to the supported InterMine databases, allowing interaction data to be automatically retrieved for the selected node. The page layout is identical for the Graphs tool, which the exception of the node hierarchy panel (yellow), which is absent for graphs.
Figure 2
Figure 2. Schematic representation of Kinase-Substrate interaction in a graph (left) and Petri Net (right).
Additional nodes and edges are required to represent the process in the Petri Net framework.
See this image and copyright information in PMC

References

    1. Chatr-Aryamontri A, Breitkreutz BJ, Heinicke S, Boucher L, Winter A, et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res 41: D816–823. - PMC - PubMed
    1. Razick S, Magklaras G, Donaldson IM (2008) iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics 9: 405. - PMC - PubMed
    1. Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, et al. (2013) The MIntAct project–IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. - PMC - PubMed
    1. Ben-Zvi A, Miller EA, Morimoto RI (2009) Collapse of proteostasis represents an early molecular event in Caenorhabditis elegans aging. Proc Natl Acad Sci U S A 106: 14914–14919. - PMC - PubMed
    1. Balch WE, Morimoto RI, Dillin A, Kelly JW (2008) Adapting proteostasis for disease intervention. Science 319: 916–919. - PubMed

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