BMRB

Biological Magnetic Resonance Data Bank


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

The BMRB Metabolomics website is being developed as a repository for public-domain metabolomics/metabonomics standard compound NMR data.

Contents of a BMRB standard compound(s) deposition

And at least one or more of the following:

Creating a BMRB standard compound(s) deposition

Since the data sets can become quite large, we ask that you archive your files with the tar utility and then compress them with zip or gzip. Refer to your operating system's instructions for more information about tar, zip, and gzip.

Submitting a deposition to BMRB

FTP instructions

To deposit time-domain data, you need to use the File Transfer Protocol (FTP). 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.

If you have more than five files, please collate them into one large file using tar, the text archiving format software. After your data has been collated, it should also be compressed, preferably with zip or gzip.

If you are using software with a graphical user interface, follow the instructions that accompany it.

If you are using the command line interface, the first 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 ftp.bmrb.wisc.edu

You should get a message that says

Connected to ftp.bmrb.wisc.edu (your network address).
220 BMRB FTP server ready
Name (ftp.bmrb.wisc.edu:cfschulte):

At the name prompt, enter anonymous and press Enter.

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

You should get a message that says the login was ok, and a request for an email address or a password. Because you are logging in anonymously, enter your email address.

Name (ftp.bmrb.wisc.edu:cfschulte): anonymous
331 Anonymous login ok, send your complete email address as your password.
Password: you@institution.org

You should now see an 'ftp' prompt.

ftp>

If you are transfering a zipped or gzipped file, there is one more thing you must do at this point: set ftp to binary mode by typing 'binary'.

ftp>binary

Don't bother doing this, however, if you are sending plain text.

FTP navigation works the same way as navigation on UNIX. Use the command 'cd' (change directory) to move among directories, and ls (list) to view the contents of a directory. 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/metabolomics'.

ftp>cd incoming/metabolomics

All that is left to do is to upload your data files. Create a new subdirectory, and give it a name that will be obvious that it belongs to your deposition (include your name or the name of your organization and the date). Move (cd) to that directory and upload the data. Use the 'put' command, if you only have one file, otherwise use 'mput' to upload all of your files.

ftp>mkdir jane_doe_20070612
ftp>cd jane_doe_20070612
ftp>mput file1.tar file2.tar.gz etc.str

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

If your data upload failed, first try repeating the steps above. If you have gone through all of these steps, and are confident that everything was carried out correctly, but have not been able to upload your data, contact bmrbhelp@bmrb.wisc.edu.