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Network modeling is important in many areas of biological research, from tissue-based gene networks to systems-level analyses, and as such it is an emerging field in network biology. There is a need for network modeling tools that are easy-to-use, have a powerful underlying feature set and are accessible via a web browser. To this end, we have developed a web-based modeling tool (NetMiner) for the analysis of biological network data. NetMiner is a Java-based, web-based, standalone Java application that allows for the analysis of biological networks such as gene regulatory and protein-protein interaction networks. NetMiner has extensive functionality including the ability to extend the data by adding genes and proteins, extracting the topology of a network using either a set of nodes or a set of edges, analyzing the structure of a network using a wide range of centrality measures, plotting the network using graph visualization and network abstraction algorithms, and comparing the results to known biological knowledge. NetMiner is currently available for use and download along with the supporting documentation at https://www.bioinf.ed.ac.uk/netminer/ .
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