1. Amazon EC2 Cloud and Using R in EC2 instance Ishwor Thapa

2. Log in to: https://uno-biocloud.signin.aws.amazon.com/console username and password provided to you.

3. EC2Page

4. Selecting Instance (A)

5. Selecting Instance (B)

6. Instance Details

8. Create KEY PAIR (PASSWORD FILE)

9. Save the pem file

10. Security Definitions

11. Review Page

12. Launching……

13. What to see on EC2 console page

14. EC2 console page (right click on instance!!)

15. Instance is up and running Now how to connect to the machine and work in the ubuntu instance in cloud? Linux/ mac -> ssh (already installed) Windows -> putty (need to install) For Windows Users: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html Scroll Down to Binaries and download putty.zip and extract the files.

16. Instance Information from EC2 console Copy the public DNS value: ec2-50-17-17-23.compute-1.amazonaws.com

17. Connecting to ec2 instance using ssh (linux/ mac) chmod 700 ithapa.pem ssh -v -i ithapa.pem ubuntu@ec2-50-16-181-117.compute- 1.amazonaws.com Linux ip-10-117-89-77 2.6.35-24-virtual #42-Ubuntu SMP Thu Dec 2 05:15:26 UTC 2010 x86_64 GNU/Linux Ubuntu 10.10 Welcome to Ubuntu!

18. Connecting to ec2 instance using putty (Windows)

26. Linux ip-10-117-89-77 2.6.35-24-virtual #42-Ubuntu SMP Thu Dec 2 05:15:26 UTC 2010 x86_64 GNU/Linux Ubuntu 10.10 Welcome to Ubuntu! Login Name:ubuntu Connecting to ec2 instance using putty (Windows)

27. Installing / Using R ubuntu@ip-10-117-89-77:~$ R The program 'R' is currently not installed. You can install it by typing: sudo apt-get install r-base-core ubuntu@ip-10-117-89-77:~$ sudo apt-get update ubuntu@ip-10-117-89-77:~$ sudo apt-get install r-base-core

28. Installing iGraph in R R > install.packages("igraph") Warning in install.packages("igraph") : argument 'lib' is missing: using '/usr/local/lib/R/site-library' Warning in install.packages("igraph") : 'lib = "/usr/local/lib/R/site-library"' is not writable Would you like to create a personal library '~/R/x86_64-pc-linux-gnu-library/2.11' to install packages into? (y/n) y 69: USA (AZ) 70: USA (CA 1) 71: USA (CA 2) 72: USA (IA) 73: USA (MA) 74: USA (MI) 75: USA (MO) 76: USA (OH) 77: USA (OR) 78: USA (PA 1) 79: USA (PA 2) 80: USA (TX 1) 81: USA (TX 2) 82: USA (WA 1) 83: USA (WA 2) Selection: 72

29. Graph Basic Concepts Graph is defined by nodes/vertices and the connection between the nodes, called edges. directed/ undirected Weighted/ Unweighted  library(“igraph”)  G<-graph(c(0,1, 1,2, 3,4, 5,6)) Definition of the Graph:  G

30. iGraph Data model Vertices  V(G) Edges  E(G) Undirected Graph  G<-graph(c(0,1, 1,2, 3,4, 5,6), directed=F)

31. Network Structure Star Ring Lattice Tree

32. Network Structure  s<-graph.star(n=3)  s<-graph.star(n=4,mode=“in”, center=1)  r<-graph.ring(n=4)  Other parameters: directed, mutual, circular  l<-graph.lattice(c(5,5))  e<-graph.empty()  e<-graph.empty(n=5)  f<-graph.full(n=3)

33. Read network from a file  g<-read.graph(“sample.txt”, format=“ncol”)  g Big graphs  g<-read.graph(“ppi.mouse.uniprot”, format=“ncol”)  summary(g)  V(g)$[0]  E(g)$[2]

34. Sample and PPI network PPI : EBI intact page with mouse search key word. sample network

35. Analyzing a network Network Centrality ( the most central node in the network) PPI : proteins having many interactions with other proteins Degree Centrality, Closeness Centrality and Betweenness Centrality Degree: The number of edges coming to/from a vertex  d<-degree(g)  which.max(d)  V(g)[which.max(d) -1]

36. Closeness/ Betweenness Centrality Average Number of steps needed to travel to reach other vertices.  cl<-closeness(g)  V(g)[which.max(cl)-1] Betweenness: to which extent a vertex is “in between” other vertices  be<-betweenness(g)  V(g)[which.max(be)-1]

37. Community Detection Densely connected subgraphs  wtc<-walktrap.community(g)  through random walks (short random walks tend to stay in the same community)  memb<-community.to.membership(g, wtc$merges, steps=4)

38. References http://igraph.sourceforge.net/igraphbook/index.html http://igraph.sourceforge.net/doc/html/index.html http://geza.kzoo.edu/bionet/bioinf.pdf