[Bioclusters] Local copy of NCBI

[Tim Harsch]

I also wanted to cast my vote inline with Joe's.  I'd like to figure out the
best, or even a very reasonable, algorithm for doing the downloads/formats
etc.  I you're site giving the Rsync method is most welcomed.  But, I may
need those FASTA files for updates and would have to have them in order to
develop a method that would use your site.

Thanks much for providing the mirror with or without the FASTA files!!

----- Original Message ----- 
From: "Joe Landman" <landman@scalableinformatics.com>
To: "biocluster" <bioclusters@bioinformatics.org>
Sent: Sunday, September 21, 2003 10:49 PM
Subject: Re: [Bioclusters] Local copy of NCBI


> 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).
>
> Joe
>
> 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
>
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