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

esyN: network building, sharing and publishing.

Author information

1
Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom; Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
2
Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.
3
Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom; Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom; Dipartimento di Biochimica, Universita' degli studi di Pisa, Pisa, Italy.
4
Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom.

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.

PMID:
25181461
PMCID:
PMC4152123
DOI:
10.1371/journal.pone.0106035
[Indexed for MEDLINE]
Free PMC Article

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