[Bioclusters] requested summary (genbank)

[bioclusters@bioinformatics.org]

 >Hi, I am really sorry, but I have been deleting all the genbank posts.
 >
 >I don't suppose you could summarise the mails in one final post to the
 >list?
 >
 >Else I can just check the archives.
 >
 >cheers,
 >
 >Dan.


Dan,

Sure.  Here is a summary of all replies to my initial question:


  -------------------------------------------
Nick Brockner wrote:

> Hi All,
>
> I am brand new to this list (and bio clusters in general. . . ).  Just  
> wondering if anybody has any experience downloading and housing  
> GenBank locally.


http://www.bio-mirror.net/  Not that hard, just need disk space :)



> Any info related to he process used to get the database and store it  
> would be greatly appreciated.


See the link.




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

-------------------------------------------

You might want to try MyGenBank.  Information is at

http://homepage.mac.com/iankorf/mygenbank.html  and code can be  
downloaded at
http://mgb.sourceforge.net/download/

It uses MySQL and is fairly easy and lightweight.  We've been using it  
for a couple of years.  Good luck.

Paul


--------------------------------------------

Hi Nick,

We are offering a Product/Service that creates and maintains a mirror of
EMBL-Genbank in a Postgres Database. The Installation also comes with a
WebGui and Java API.
Let me know if you want to know more.

Best Regards

Guenther


----------------------------------------------

Hi Nick,

We are using SRS with great success. It can also maintain dozens of  
other databases, integrates tools such as EMBOSS and BLAST, and  
supports Sun Grid Engine. It is *not* lightweight or easy to  
administer, though. The upside is that you are getting a heavyweight  
commercial product that is free for academia.
SRS is from Lion: http://www.lionbioscience.com . The reference  
implementation is at EBI: http://srs.ebi.ac.uk

I'll be happy to answer any other questions.

Regards,

Ran Rubinstein
Center for Bioinformatics Infrastructure, Hebrew University, Jerusalem,  
Israel.

------------------------------------------------

I have a few shell scripts and C programs that can download GenBank and  
sort according to organism. I'll be happy to post them.

--  
Kenneth Geisshirt, M.Sc., Ph.D.   --   http://kenneth.geisshirt.dk/

------------------------------------------------


************************************************************************ 
************************









On Tue, 22 Jun 2004, Nick Brockner wrote:

> Hi All,
>
> Just wanted to thank everybody who replied with great info on genBank.
>  It was very helpful.
>
> Thanks again,
>
> ************************************
> Nick Brockner
> System Administrator, Biology Computing Facility
> Hamilton College
> nbrockne@hamilton.edu
> (315) 859-4137
>
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>


************************************
Nick Brockner
System Administrator, Biology Computing Facility
Hamilton College