Table of Contents

Lab 11

First Hour

  • Return and go over exam 2.
  • In-Lab problem
    • In Project 4, you will be required to manipulate graphs using the networkX package. In the in-lab problem, you need to fill in the body of the function replace_scc which replace all the strongly connected components of a graph with single nodes that you read in using import_edge_list(filename). You can use the following sample input. It's suggested that you use the strongly_connected_components function on the graph that you read in, which will return a list of components. Each list of components is a list of nodes. Thus, we suggest you create a new graph, and add the edges that go between components. You can check your graph by using pylab to draw it. Here is a template to start you off.
      def replace_scc(G):
          components = strongly_connected_components(G)
       
          c = {}                                      # figure out which 
          for i in xrange(len(components)):           # component each node
              for node in components[i]:                  # belongs to
                  c[node] = i + 1
       
          H = networkx.DiGraph()                           # create a new graph
          for u,v in G.edges_iter():                 # replace endpoints with
              H.add_edge(c[u], c[v])                 # new component numbers
       
          return H

Second Hour

  • Introduce and discuss project 4, part 1.
  • Demonstration of using Cytoscape
  • Note: the lecture on Monday will provide the background.
  • Part 2 will be finished when the data sets finish generation. (Some of them are very large.)
 
cs190c/lab11.txt · Last modified: 2008/04/01 21:40 by alint
 
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