Tutorial- Building Biological Networks

I love networks! Nothing is better for visualizing complex multivariate relationships be it social, virtual or biological.

I recently gave a hands-on network building tutorial using R and Cytoscape to build large biological networks. In these networks Nodes represent metabolites and edges can be many things, but I specifically focused on biochemical relationships and chemical similarities. Your imagination is the limit.

If you are interested check out the presentation below.

Here is all the R code and links to relevant data you will need to let you follow along with the tutorial.

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#load needed functions: R package in progress - "devium", which is stored on github
source("http://pastebin.com/raw.php?i=Y0YYEBia")
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# get sample chemical identifiers here:https://docs.google.com/spreadsheet/ccc?key=0Ap1AEMfo-fh9dFZSSm5WSHlqMC1QdkNMWFZCeWdVbEE#gid=1
#Pubchem CIDs = cids
cids # overview
nrow(cids) # how many
str(cids) # structure, wan't numeric 
cids<-as.numeric(as.character(unlist(cids))) # hack to break factor

#get KEGG RPAIRS
#making an edge list based on CIDs from KEGG reactant pairs
KEGG.edge.list<-CID.to.KEGG.pairs(cid=cids,database=get.KEGG.pairs(),lookup=get.CID.KEGG.pairs())
head(KEGG.edge.list)
dim(KEGG.edge.list) # a two column list with CID to CID connections based on KEGG RPAIS
# how did I get this?
#1) convert from CID to KEGG using get.CID.KEGG.pairs(), which is a table stored:https://gist.github.com/dgrapov/4964546
#2) get KEGG RPAIRS using get.KEGG.pairs() which is a table stored:https://gist.github.com/dgrapov/4964564
#3) return CID pairs

#get EDGES based on chemical similarity (Tanimoto distances >0.07)
tanimoto.edges<-CID.to.tanimoto(cids=cids, cut.off = .7, parallel=FALSE)
head(tanimoto.edges)
# how did I get this?
#1) Use R package ChemmineR to querry Pubchem PUG to get molecular fingerprints
#2) calculate simialrity coefficient
#3) return edges with similarity above cut.off

#after a little bit of formatting make combined KEGG + tanimoto edge list
# https://docs.google.com/spreadsheet/ccc?key=0Ap1AEMfo-fh9dFZSSm5WSHlqMC1QdkNMWFZCeWdVbEE#gid=2

#now upload this and a sample node attribute table (https://docs.google.com/spreadsheet/ccc?key=0Ap1AEMfo-fh9dFZSSm5WSHlqMC1QdkNMWFZCeWdVbEE#gid=1)
#to Cytoscape 

You can also download all the necessary materials HERE, which include:

1. tutorial in powerpoint
2. R script
3. Network edge list and node attributes table
4. Cytoscape file

Happy network making!