[Bioperl-l] Re: [Bioperl-guts-l] problems with Bio::DB::GenBank

[Jonathan Epstein]

I haven't made any progress on this recently, and am tied up with other stuff through the end of October, but I have some bad news: I found in my testing that in some cases the "netentrez" interface also suffers from dropped connections.  This is even though the NCBI is 500 yards from my office ;-)

-Jonathan

At 03:59 PM 9/20/2001 , Jason Eric Stajich wrote:
>Bio::DB::GenBank is always going to be problematic because of the way we
>connect to NCBI.  HTTP connections are frequently dropped and their site
>frequently fails to return proper data.  I am at a loss for a solution at
>this point other than building a netentrez wrapper/XS implementation
>(Johnathan Epstein has mentioned he might be able to lead this effort) as
>the problem is really on NCBI side dropping connections periodically. You
>can use the Bio::DB::EMBL which will be slower from California, but has
>typically been much more reliable.



Jonathan Epstein                                Jonathan_Epstein@nih.gov
Head, Unit on Biologic Computation              (301)402-4563
Office of the Scientific Director               Bldg 31, Room 2A47
Nat. Inst. of Child Health & Human Development  31 Center Drive
National Institutes of Health                   Bethesda, MD 20892