Scientific Databases (once again)
Rob Harper CSC Finland
Rob.Harper at csc.fi
Tue May 26 07:16:03 EST 1992
About a week ago I posted a request to bionet.software asking about what
scientific databases people use and what they would like to have. I
received a few replies and as promised I will make a summary.
>From the replies it is obvious that there is no obvious line... everyone
is stearing their own course. I had hoped that I would get the big
picture, so that I would be able to say that this is the trend in
scientific computing at the moment. I would need more responses!!!
There is a wide range of solutions as to how people store and retrieve
data. The most used databases are Genbank/EMBL, PIR, SwissProt, PDB,
REbase, Prosite, Gosh's transcription factor DB, Vecbase. Other areas
where databases would be appreciated are HIV, Flybase, Database of
patents. One person was construction his own scientific database which
targets cancer causing mutations. So in general most people are supplied
with the well known databases, would like to have access to more exotic
databases, or if nothing is on hand then they roll their own.
There were two other aspects worthy of attention.
People are using the network for some of their computing problems, namely
FASTA searches at either Genbank or EMBL, NETSERV at EMBL for software,
GOS at GenBank, FTP to various molecular biology sites, and also getting
of PDB files. The biogopher services at Indiana, Basel, and Houston also
provide access to the major databases for searching and retrieving
In the PC world there is a trend to use CD-ROM for such things as MEDLINE
and SCI, and resources are being shared over university library LAN'S.
Both EMBL and NCBI are producing CD-ROM's of their data, with software for
searching included. Biological abstracts available via a library LAN was
considered a useful service.
I would like to receive more feedback about what you do at your
University. I will collect all the mail into one file and put it on
nic.funet.fi for downloading via anonymous ftp.
A few years ago Don Gilbert did a survey on what machines people used for
molecular biology. It was a very useful document because after reading it
you got a feel for what was going on in biocomputing. I would like to do
something similar for scientific databases. That is to say collect
information from the grass-roots user and make all the responses available
to biologists on the network, so they have a weighty document to help them
in their discussions with their administrations... (yes I need that
So if you have not already answered these question please take time to
drop me a short note if you would like to have your opinions included in
the scientific database document.
Here are the questions once again but in a modified form, taking into
consideration the feedback I have already received.
* What databases do you use at your work?
* What databases would you like to have access to?
* Do you have any databases on CD-ROM?
* Do you use the gopher servers for searching databases?
* Do you use NETSERV or anonymous ftp to molbio archives?
* Have you made any databases of your own?
* What network services would you like to see improved?
Thanks to all the people who have replied so far, and I hope that some
more people would take some time to make a response to me at
harper at convex.csc.fi
Rob Harper / E-mail: harper at convex.csc.fi
Finnish State Computer Centre / Molbio/software: harper at nic.funet.fi
P.O. Box 40, SF-02101 Espoo / Telephone: +358 0 457 2076
Finland / Fax: +358 0 457 2302
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