Hello, I'm experiencing enormous delays when attempting to query any of the databases @ genome-mysql.cse.ucsc.edu.
I'm using version 1.2.17 of MySQL's Query Browser and connect to genome-mysql.cse.ucsc.edu using the information provided here http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 <http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29> I can successfully connect to the server and can see a listing of all databases in the Query Browser window. When attempting to view the tables of a database via Query Browser's GUI the application either hangs completely or takes approximately (more than) 10 minutes just to display the tables under a schema. I'm experiencing similar side effects when trying to retrieve table information from a schema using a simple Java class (MySQL JDBC version 5.1.2). Any suggestions/hints on how to overcome this issue are welcome. Thanks in advance. Kind Regards, Michael On Fri, Oct 30, 2009 at 12:25 AM, Brooke Rhead <[email protected]> wrote: > Hello Michael, > > I cannot tell you why your tools are not working for all databases, but I > can point out a few things that may be helpful to you: > > 1. You should be able to access genome-mysql.cse.ucsc.edu without a > password. Instructions are here: > http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 > > 2. The only mouse databases that are available in full on the public server > are mm7, mm8 and mm9. Earlier mouse browsers have been archived ( > http://genome-archive.cse.ucsc.edu/) and are no longer available on the > public mysql server, except for a single "chromInfo" table in the mm5 and > mm6 databases. > > > > Are schemas mm8 and mm9 not public? > > All of the data on genome-mysql.cse.ucsc.edu should be publicly > accessible. > > I hope this information is helpful. If you have further questions, please > feel free to write back to the mailing list at [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 10/29/09 01:06, Michael Zouberakis wrote: > >> Hello, >> >> I'm writing on behalf of BSRC Al. Fleming Institute's BioIT Unit. >> >> We have developed an online database containing mouse related web >> resources >> called the Mouse Resource Browser a.k.a. MRB (http://bioit.fleming.gr/mrb >> ). >> >> One of the recorded resources is UCSC's Genome Browser ( >> http://bioit.fleming.gr/mrb/Controller?workflow=ViewModel&eid=238). >> >> On the "Technical Tab" of your resource's view you'll notice a section >> entitled "Direct Database Access". >> >> Under that section MRB provides a tool called "wsGenerator" which parses a >> database's schema and generates Java SOAP API classes and schema >> descriptive >> XML and PNG files. >> >> In Genome Browser's case we provide links to mm5 and mm8 databases located >> @ >> genome-mysql.cse.ucsc.edu using genomep as username and password as >> password. >> >> wsGenerator can successfully parse the mm5 schema but fails to parse your >> mm8 schema. Even with various MySQL clients schema mm8 and mm9 seem not to >> be accessible. Is there a reason for that? Are schemas mm8 and mm9 not >> public? >> >> Also could you point out other databases on your publicly available server >> that might be of interest to bench scientists working with mice? >> >> Thank you in advance. >> >> Kind regards, >> Michael Zouberakis >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
