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JUNG the Java Universal Network/Graph Framework--is a software library that provides a common and extendible language for the modeling, analysis, and visualization of data that can be represented as a graph or network. It is written in Java, which allows JUNG-based applications to make use of the extensive built-in capabilities of the Java API, as well as those of other existing third-party Java libraries. The JUNG architecture is designed to support a variety of representations of entities and their relations, such as directed and undirected graphs, multi-modal graphs, graphs with parallel edges, and hypergraphs. It provides a mechanism for annotating graphs, entities, and relations with metadata. This facilitates the creation of analytic tools for complex data sets that can examine the relations between entities as well as the metadata attached to each entity and relation. The current distribution of JUNG includes implementations of a number of algorithms from graph theory, data mining, and social network analysis, such as routines for clustering, decomposition, optimization, random graph generation, statistical analysis, and calculation of network distances, flows, and importance measures (centrality, PageRank, HITS, etc.). JUNG also provides a visualization framework that makes it easy to construct tools for the interactive exploration of network data. Users can use one of the layout algorithms provided, or use the framework to create their own custom layouts. In addition, filtering mechanisms are provided which allow users to focus their attention, or their algorithms, on specific portions of the graph.

MassBank of America (MoNA), is an auto curating repository for storing, comparing and querying mass spectra of chemical compounds. It is metadata centric and it was designed to allow easy integration into other tools by utilize its REST based application programming interface. At the current time it contains over 200k predicted and 40k unique experimental mass spectra and their associated metadata. The predicted spectra were obtained by utilizing the lipid blast library and the experimental spectra were acquired from 30 different facilities all over the world, including several major research facilities in the United States and Japan. MoNA is utilizing the InChI Key as unique identifier for chemicals and is designed for easy scalability and expendability. This is realized by utilizing common applications like nginx, grails, AngularJS, postgresSQL and tomcat. MoNA is currently integrated in applications like MSDial, BinBase, MZMine and the statistics package R. This was accomplished by utilizing its REST based API, which is also utilized by its main AngularJS based web interface. We consider MoNA to be highly useful for crosslinking mass spectra in publications, identification of unknowns and integration in data acquisition software. This package provides you with access to the REST api of the main MoNA installation.