milesdevis
commented
7 years ago Hello, Hope you're well. My name is Nishanth Devarajan, currently a fourth year student at the Indian Institute of Technology, Roorkee. I am from a networking background and although I'm familiar with the concepts of Shannon entropy, networks, etc. I haven't had prior experience with Cytoscape or CentiScaPe. That said, I must argue that I’m a fast learner and I'm keenly interested to work on this. I've downloaded CytoScape with CentiScaPe but it would be really helpful if I could get some suggestions on how to get comfortable with them. Any feedback would be of value, as I don't know where to start. I look forward to hearing from you.
giovanniscardoni
khanspers
Background
CentiScaPe is a Cytoscape app that allows, by using a very plain interface, to compute different network centrality parameters in single and in multiple networks at the same time. It allows to plot the results by using real and normalized values in different plots. Several centralities are available: Degree, Average Shortest Path, Eccentricity, Closeness, Betweenness, Centroid, Stress, Radiality, Eigenvector, Edge Betweenness, Bridging Centrality. Each one could be computed for directed and undirected networks; CentiScaPe gives the possibility to assign a weight to the edges and permits to assign a weight to each node by using an attribute.
Goal
Network Quantity Information is a new measure for network complexity, based on the Shannon Entropy. The measure calculates a sort of Shannon Entropy for each node and generates the complexity of the network as the sum of the information quantity that can be brought by each node. The measure can be used as a centrality measure but also as a measure to classify different kinds of networks. The goal is to implement such measure and to integrate it in Cytoscape. The implementation should also be able to compute it for several networks and produce graphical output to compare results in different networks.
Difficulty level 3:
Prior experience with Cytoscape, CentiScaPe and Java is required.
Technology and Skills
Cytoscape, CentiScaPe, Java
Potential Mentors
Giovanni Scardoni (CBMC, University of Verona)
Contact
cytoscape-discuss@googlegroups.com, giovanni.scardoni@gmail.com