2014/09/02 by Daniel Bean, Joshua Heimbach, Lorenzo Ficorella +3 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Bioinformatics and Genomic Networks #Gene Regulatory Network Analysis #Gene expression and cancer classification #Computer science #Biological network #World Wide Web #Field (mathematics) #Network analysis #Simple (philosophy) #The Internet #Biological database #Data science #Bioinformatics
paper · pdf · doi:10.1371/journal.pone.0106035
openalex publication_date 2014/09/02 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
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.