EMBL database availability

Reinhard Doelz doelz at comp.bioz.unibas.ch
Wed Jun 9 09:18:17 EST 1993


You might know that we maintain a very large molecular biology database 
server accessible via FTP, GOPHER, and HASSLE. Periodically, I receive 
messages like (original quote) 

>         My apologies for ftping some unwanted files. I wanted to get a 
> copy  of the recent embl and pir dbases for running blast. And I realized 
> I copied some outdated files. 
>        Once again my apologies for the apparent misuse of network 
> resources.
> I would appreciate if you can advise me how I can get the above mentioned
> dbases (and the updates) in an acceptable manner.

The reason for 'outdated files' is that he EMBL CD-ROM arrives usually 
a couple of days later than we install the magnetic version in the different 
formats.I won't describe PIR International Access, but will tell on EMBL 
databases. Several points to be made here: 

(1) Computer networks are extremely unsuited for transporting full database 
    releases. Unless there is a well-functioning data distribution schema, 
    ftp'ing databases of this size on transnational lines is not appreciated
    by the network providers and we  (Molecular Biology Users) can ruin 
    our image entirely if all end-users do this in uncoordinated fashion. 

(2) CD-ROMs are cheap and easy to ship. If you have the demand to get a 
    database not currently present in your portfolio, ask the database 
    providers to ship you the databases you want. 

(3) If you look for these issues in Europe, the European Molecular Biology
    network (EMBnet) is the umbrella organisation which keeps copies
    of the EMBL database in each country, on the so-called 'national node'
    in Norway, Sweden, Finnland, Denmark, UK, Netherlands, Belgium, France,
    Germany, Switzerland, Spain, Italy, Greece, Israel. Other nodes are 
    about being started in Portugal, Austria and more coutries. Inquiries 
    welcome! EMBL maintains also an ftp server with their current database, 
    and this archive is mirrored by the Israelian EMBnet node, and also 
    partially on others.

(4) If you look for the EMBL database in the US, Mike Cherry volunteered
    to make the EMBL database available on his machine, anonymous ftp 
    frodo.mgh.harvard.edu, in compressed form. 

(5) If you look for the _updates_ to the EMBL database, there are sevaral 
    possibilities. (1) The NCBI keeps collaborating with EMBL to incorporate
    the entries concerned into the GENBANK releases. (2) Mike Cherry 
    mirrors the updates on a weekly basis from Europe. (3) Various national
    EMBnet nodes provide the data to their community on demand or via 
    ftp archive. 
-- 
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|    Dr. Reinhard Doelz            | RFC     doelz at urz.unibas.ch         |
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