[BioC] Genes2GO and suggestions to make it faster

Konika Chawla chawla at ntnu.no
Mon Aug 18 14:52:31 CEST 2014

I have created this webapp 
(http://norstore-trd-bio0.hpc.ntnu.no:8080/Genes2GO/clearpage.do) to 
makes a binary matrix between user specified genes and user selected GO 
term to represent the gene annotations by either 1 or 0. Users can also 
specify just some query terms and the program will find the related GO 
Its small and useful tool for biologists.

The tools uses annotation data from biomaRt and GO.DB to find GO terms.
1) The tool is bit slow sometimes.  Any suggestion to make it faster 
would be helpful.
A small part of code is
"ensembl = useMart("ensembl", dataset = organism)
godata<-getBM(attributes = c(list_type,"go_id","name_1006"), filters = 
list_type, values = genelist[,1], mart = ensembl)

2) Is it possible to show a progress bar on the webpage which could 
represent how much time is remaining to finish the process. That is if 
we can know how much time the process is going to take.

Thanks is advance.

With Regards,
Konika Chawla
NTNU, Norway
Phone +4772821344

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