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PHYS 597A, CMPSC 497E: Graphs and networks in sys-tems biology
 

Summary: PHYS 597A, CMPSC 497E: Graphs and networks in sys-
tems biology
Homework assignment 5, due Tuesday Oct. 6
1. The Sept. 24 lecture surveyed a number of graph processing and visu-
alization tools. Install one of them and use it to draw and analyze a graph.
Provide a screenshot of your work and a two-three paragraph overview of
what the software/library can do, what you did with it, and your assessment
of the process of accomplishing the desired outcome.
URLs to the tools discussed in the lecture:
GraphViz: http://www.research.att.com/sw/tools/graphviz/
Pajek: http://vlado.fmf.uni-lj.si/pub/networks/pajek/
Yed: http://www.yworks.com/en/products yed about.htm
NetworkX: https://networkx.lanl.gov/
Cytoscape: http://www.cytoscape.org/
UCINET: http://www.analytictech.com/ucinet/
igraph: http://igraph.sourceforge.net/
2. Answer the following questions:
a) At what connection probability you expect the existence of (i) a tree
with six nodes, (ii) a cycle with six nodes, and (iii) a completely connected
subgraph with six nodes in a large (N ) random graph?

  

Source: Albert, Réka - Departments of Biology & Physics, Pennsylvania State University

 

Collections: Biology and Medicine