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Computational Methods of Systems Biology Spring 2011 Exercise set 1 Return your answers to Leena (leena.salmela at cs.helsinki.) prior to the review session on Mon 24.1 All exercises refer to Chapter 2 to in the course book. A copy of the chapter is available on the course web page. 1. (Ex 2 page 27) Consider the undirected graph G = (VE) shown in Fig 2.2 (right). for each vertex v 2 V do the following (a) Compute the degree of v. (b) List all neighbors of v. (c) Find paths to all other vertices that are in the same connected com- ponent as the vertex v 2.

Computational Methods of Systems Biology Spring 2011 Exercise set 1 Return your answers to Leena (leena.salmela at cs.helsinki.) prior to the review session on Mon 24.1 All exercises refer to Chapter 2 to in the course book. A copy of the chapter is available on the course web page. 1. (Ex 2 page 27) Consider the undirected graph G = (VE) shown in Fig 2.2 (right). for each vertex v 2 V do the following (a) Compute the degree of v. (b) List all neighbors of v. (c) Find paths to all other vertices that are in the same connected com- ponent as the vertex v 2. (Ex 4 page 28) Take a graph with nine vertices four of them of degree 2 and four of degree 1. Is the graph connnected? 3. (Ex 6 page 28) Draw an undirected conected graph with 10 vertices and 20 edges. Construct two dierent spanning trees of G. 4. (Ex 7 page 28). Metabolite networks can be constructed from metabolic networks modeled as bipartite graphs by removing all vertices representing reactions and connecting substrates (vertices with an outgoing edge to the reaction) with products (vertices with an incoming edge from the reaction) directly. Construct a metabolite network from the metabolic network given in Fig. 2.11 (right). 5. (Ex 8 page 28). Apply the algorithms DFS and BFS to traverse the graph in Fig 2.2 (right). Start with vertex 1 and then apply the algorithms again starting from vertex 5. 1

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