amazon ec2 cloud and using r in ec2 instance ishwor thapa
Post on 19-Dec-2015
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Amazon EC2 Cloud and Using R in EC2 instanceIshwor Thapa
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Log in to: • https://uno-biocloud.signin.aws.amazon.com/console• username and password provided to you.
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EC2Page
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Selecting Instance (A)
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Selecting Instance (B)
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Instance Details
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Instance Details
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Create KEY PAIR (PASSWORD FILE)
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Save the pem file
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Security Definitions
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Review Page
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Launching……
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What to see on EC2 console page
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EC2 console page (right click on instance!!)
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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.
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Instance Information from EC2 console
Copy the public DNS value:ec2-50-17-17-23.compute-1.amazonaws.com
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Connecting to ec2 instance using ssh (linux/ mac)
• chmod 700 ithapa.pem • ssh -v -i ithapa.pem [email protected]
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!
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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Connecting to ec2 instance using putty (Windows)
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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/LinuxUbuntu 10.10Welcome to Ubuntu!
Login Name:ubuntu
Connecting to ec2 instance using putty (Windows)
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Installing / Using R
ubuntu@ip-10-117-89-77:~$ RThe program 'R' is currently not installed. You can install it by typing:sudo apt-get install r-base-coreubuntu@ip-10-117-89-77:~$ sudo apt-get update
ubuntu@ip-10-117-89-77:~$ sudo apt-get install r-base-core
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Installing iGraph in RR> 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 writableWould 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
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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
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iGraph Data model
VerticesV(G)
EdgesE(G)
Undirected GraphG<-graph(c(0,1, 1,2, 3,4, 5,6), directed=F)
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Network Structure• Star• Ring• Lattice• Tree
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Network Structures<-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)
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Read network from a fileg<-read.graph(“sample.txt”, format=“ncol”)g
Big graphsg<-read.graph(“ppi.mouse.uniprot”, format=“ncol”)summary(g)V(g)$[0]E(g)$[2]
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Sample and PPI network• PPI : EBI intact page with mouse search key word.• sample network
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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]
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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 verticesbe<-betweenness(g)V(g)[which.max(be)-1]
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Community Detection• Densely connected subgraphswtc<-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)
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References• http://igraph.sourceforge.net/igraphbook/index.html• http://igraph.sourceforge.net/doc/html/index.html• http://geza.kzoo.edu/bionet/bioinf.pdf