Question: How to open the .BIN in the NCI DTP Data
1
gravatar for zero_hsy
4.0 years ago by
zero_hsy90
China
zero_hsy90 wrote:

Hello:

    I want to download the drug-response raw data on the NCI60. I found the url is 

https://wiki.nci.nih.gov/display/NCIDTPdata/NCI-60+Growth+Inhibition+Data. However, the data is .BIN data.When I open it with notepad++, it is messy code.

   Could anyone tell me how to open the .BIN file with new software?

   Thanks!

ADD COMMENTlink modified 4.0 years ago by Pierre Lindenbaum119k • written 4.0 years ago by zero_hsy90
3
gravatar for Pierre Lindenbaum
4.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

 

$ curl -Ls "https://wiki.nci.nih.gov/download/attachments/147193864/GI50_SEPT2014.BIN?version=1&modificationDate=1412702681000&api=v2" | file -
/dev/stdin: gzip compressed data, was "CANCER60GI50.csv", from Unix, last modified: Wed Oct  1 21:40:54 2014


$ curl -Ls "https://wiki.nci.nih.gov/download/attachments/147193864/GI50_SEPT2014.BIN?version=1&modificationDate=1412702681000&api=v2" | gunzip -c | more
NSC,CONCUNIT,LCONC,PANEL,CELL,PANELNBR,CELLNBR,NLOGGI50,INDN,TOTN,STDDEV        

1 ,M ,-4.00,Non-Small Cell Lung ,NCI-H23 ,1 ,1 ,4.575,1 ,1 , .                  

1 ,M ,-4.00,Non-Small Cell Lung ,NCI-H522 ,1 ,3 ,4.951,1 ,1 , .                 

1 ,M ,-4.00,Non-Small Cell Lung ,A549/ATCC ,1 ,4 ,4.100,1 ,1 , .                

1 ,M ,-4.00,Non-Small Cell Lung ,EKVX ,1 ,8 ,4.769,1 ,1 , .                     

1 ,M ,-4.00,Non-Small Cell Lung ,NCI-H226 ,1 ,13 ,4.691,1 ,1 , .                

1 ,M ,-4.00,Non-Small Cell Lung ,NCI-H322M ,1 ,17 ,4.000,1 ,1 , .               

1 ,M ,-4.00,Non-Small Cell Lung ,NCI-H460 ,1 ,21 ,4.484,1 ,1 , .                

1 ,M ,-4.00,Non-Small Cell Lung ,HOP-62 ,1 ,26 ,4.445,1 ,1 , .                  

1 ,M ,-4.00,Non-Small Cell Lung ,HOP-92 ,1 ,29 ,4.778,1 ,1 , .                  

1 ,M ,-4.00,Colon ,HT29 ,4 ,1 ,4.786,1 ,1 , .                                   

1 ,M ,-4.00,Colon ,HCC-2998 ,4 ,2 ,4.880,1 ,1 , .                   

 

so, it's a gzipped file... just 'g-unzip it' ; Under windows the best way(?) would be to change the extension '.BIN' to '.gz'

 

ADD COMMENTlink written 4.0 years ago by Pierre Lindenbaum119k

Thanks a lot!

I have opened it successfully in your method. And could I ask another question?

I have downloaded the NCI60 drug-response from CellMiner. It is the same with the .BIN. The difference is that it is somewhat processed.

What confused me is as the followings:

drug      cell_line_1_gi50    cell_line_2_gi50

A          **                 **

A (usan)   **                 **

What is the difference between A and A (usan) ?

ADD REPLYlink written 4.0 years ago by zero_hsy90

no idea, ask nci.ncbi.gov

ADD REPLYlink written 4.0 years ago by Pierre Lindenbaum119k
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