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Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules

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Deposition menu

FTP Upload Instructions

for NMR time-domain data

To deposit time-domain data, you need to use the File Transfer Protocol (FTP). FTP is a venerable, reliable method for transfering large amounts of data across networks. Since a web browser tends to limit the size of the files that can be transfered through FTP, we suggest that you do not use your browser to transfer time-domain data sets. There are software packages for using FTP, but if you are using a Windows, UNIX, Linux, or Mac OSX computer, FTP is a built in function of its command line interface.

First, please collate your files into one file using tar, the unix archiving software. After your data has been collated, it should also be compressed, preferably with gzip or bzip2. On Windows, winzip will collate your files and compress the archive.

If you have a BMRB accession number, please include it in the filename, e.g. bmr1234td.tar.gz, otherwise please name your file so that it is obvious it belongs to your deposition.

If you are using the command line interface, the next thing you need to do is navigate to the directory that contains the information you want to upload. Use the command 'cd' on UNIX and UNIX-like operating systms, and use the command 'CHDIR' on Windows. If you are not familiar with this, someone in your group probably is.

Next, connect to the BMRB FTP server by typing:

system prompt$ftp deposit.bmrb.wisc.edu

You should get a message that says

Connected to deposit.bmrb.wisc.edu
followed by some other information (number of users allowed, local time, etc.)

At the name prompt, enter anonymous and press Enter.

Name (deposit.bmrb.wisc.edu:your login): anonymous

You should get a message that says the login was ok. If the server request an email address or a password, enter your email address.

You should now see an 'ftp' prompt.

ftp>

Set ftp to binary mode by typing 'binary'.

ftp>binary

FTP navigation works the same way as navigation on UNIX. Use the command 'cd' (change directory) to move among directories. Typing 'cd subdirectory will move your position (present working directory, or pwd) to that directory. Typing 'cd ..' will move it to the directory containing your current position. Typing 'pwd' will tell you what your current position is. For a list of commands, type 'help'.

Navigate to the proper directory by typing, 'cd incoming/data_submission'.

ftp>cd incoming/data_submission

All that is left to do is to upload your data. Use the 'put' command to upload your file:

ftp>put bmr1234td.tar.gz

You're done! Type 'quit', and you are no longer using FTP.

If you've gone through all of these steps, and are sure you've done everything correctly, but have not been able to upload your data, contact bmrbhelp@bmrb.wisc.edu.

Important note:
You will not be able to look at the contents of the directory. After you upload your file, the directory will still appear to be empty if you examine it. This is not a bug and it does not indicate that your upload failed. It is a deliberate security measure so that nobody can see what files you are uploading. If the upload gave you no errors, then that does mean BMRB has received the file even though you will not see it in the directory.

Known problems:
Some users reported problems creating files over 2GB in size.

Solution: most archiver programs can create "multi-volume" archives with particular volume size. Set volume size to less than 2GB (2,000,000 bytes should work).
If you are using GNU tar, the command is

tar -M -L 2000000 -cf bmr1234td.tar
	
(if/when prompted for the next volume, type in "n bmr1234td1.tar", then "n bmr1234td2.tar", etc.)

For other software, follow instructions that accompany it.

If you are uploading multiple files, use 'mput' command instead of 'put':

ftp>mput bmr1234td.tar.gz bmr1234td1.tar.gz bmr1234td2.tar.gz
 
Contact bmrbhelp@bmrb.wisc.edu if you have any questions about this site

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Last Modified:    Monday, 06-Dec-2010 22:33:55 CST