Traversal-based graph algorithms are good at extracting “subgraphs of interest” when applied to large networks. However, applying known algorithms may not be enough every time to extract the useful information. Some specialized queries may be helpful in this sence to extract more useful or more specific information. Actually, these types of queries are already implemented inside the PATIKAweb software that is a result of the study done by Doğrusöz et al. in Java programming language. The aim of this project is to move these implementations into the common use of developers by making an extension to Cytoscape.js, which is a commonly used graph drawing library written in Javascript. Cytoscape.js already includes some basic graph traversal algorithms such as DFS, BFS, Dijkstra, Bellman-Ford, Kruskal etc., but I believe that these specialized queries will provide a good functionality to be used in not only in biological networks, but also in other types of networks. With the advantage of compound node support in Cytoscape.js, these specialized traversal algorithms will also be easily applied to the large networks with compound node content.


Hasan Balcı


  • Ugur Dogrusoz
  • Ozgun Babur