[Bioclusters] Local copy of NCBI

Joe Landman bioclusters@bioinformatics.org
Mon, 22 Sep 2003 01:49:30 -0400

Hi Josh:

  Last I checked, you had only the binary databases up there.  As a fair
number of users need to segment the databases for performance and other
reasons, it might help to have the FASTA formatted files there as
well.   It would save processing time (no additional steps).


On Mon, 2003-09-22 at 13:39, Josh Goodman wrote:
> 	In addition to the NCBI server you may want to take a look at our
> database mirroring service at http://www.bio-mirror.net.  We offer most of
> the NCBI dbs and other important dbs with mirrors all over the world.
> Most servers support ftp and http but the USA server also mirrors data via
> rsync.  If you don't see a database that you think we should have let us
> know and we will try to get it up there.
> Josh Goodman
> Indiana University
> ------------------------------------
> Subject: Re: [Bioclusters] Local copy of NCBI
> From: Nox <pheusion@snet.net>
> To: bioclusters@bioinformatics.org
> Cc: "Tang, Kevin" <kht7@cdc.gov>
> Date: Thu, 18 Sep 2003 13:16:38 -0400
> Reply-To: bioclusters@bioinformatics.org
> We are using in-house perl scripts, in crontab, that
> uses wget to pull updates from the DB.
> Perl is great for parsing, so thats what my developers are using.
> Unfortunatly I cant copy the script in here,
> but I can tell you it relies on the wget heavily,
> and  perl provides the transition  to populate our DB
> Hope that helps
> Nox
> GenMicro Systems
> On Thu, 2003-09-18 at 09:46, Osborne, John wrote:
> > Hi everyone,
> > What are people out there doing to get a local copy of NCBI's databases?  I
> > mean RefSeq, dbSNP, taxonomy, etc...  We've been updating our copy ad-hoc by
> > ftp, are most people just putting this into a cron job?
> >
> > I've heard that the NCBI tookkit offers something like this (to get daily
> > updates via web services or something) but I don't know where to look.
> > getseq looks suspicious but I need to configure it using entrez2, which
> > needs X Windows, which needs vibrant, which means RH dependency hell...  Is
> > there a simple commandline way to get get a seequence from NCBI and keep a
> > local copy of NCBI?

Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615