[Gusdev-gusdev] Re: Fwd: [Gmod-schema] chado, Bio::DB::GFF, biosql

[Jessica K. <jki...@ug...>]

Chris,

	We have installed Gbrowse, but we do not=20
have it sitting on top of GUS. Sorry.

	Jessie


At 10:26 AM -0500 3/15/04, Chris Stoeckert wrote:
>Hi Jessie,
>You folks have hooked up Gbrowse to GUS haven't=20
>you? Do you know how the response time is for=20
>retrieving sequence?
>Chris
>
>Begin forwarded message:
>
>>From: "Vsevolod (Simon) Ilyushchenko" <si...@cs...>
>>Date: March 15, 2004 10:19:04 AM EST
>>To: Lincoln Stein <ls...@cs...>
>>Cc: Hilmar Lapp <hl...@gn...>, Scott Cain=20
>><ca...@cs...>, p.l...@me..., gmod=20
>>schema <gmo...@li...>
>>Subject: Re: [Gmod-schema] chado, Bio::DB::GFF, biosql
>>
>>Hi all,
>>
>>Here you go. Chart attached, full data below.
>>
>>I ran the comparison on intervals from 10 kbp=20
>>to 300 kbp. GFF has essentially constant access=20
>>time, Biosql's time grows pretty much linearly,=20
>>Chado's time grows even faster. Chado starts=20
>>off being almost twice as fast as Biosql, but=20
>>they even out around 150 Kbp and after that=20
>>Biosql is somewhat faster.
>>
>>Details: for all three methods. I used the same=20
>>1 Mbp snippet of chromosome II of Arabidopsis.=20
>>I ran wget 11 times consequetively for each=20
>>combination of storage methods and ranges, then=20
>>took the median value for each run. The machine=20
>>is a single-CPU 1.8 Ghz Pentium 4 with 256 MB=20
>>of RAM running Fedora Core 1 and apache 1.3.27.=20
>>I used bioperl-1.4, Genome-Browser 1.58 (I have=20
>>been warned against using its latest CVS=20
>>version, as it does not coexist with Chado yet)=20
>>and the current CVS snapshots of bioperl-db and=20
>>gmod.
>>
>>Simon
>>
>>The data in all columns except the first is access time in seconds.
>>
>>Range,	GFF 	Chado 	Biosql 
>>kbp
>>
>>10	1.61	1.77	3.24
>>20	1.63	1.96	3.59
>>30	1.63	2.13	3.8
>>40	1.66	2.23	3.96
>>50	1.65	2.33	4.17
>>60	1.66	2.36	4.26
>>70	1.68	2.44	4.44
>>80	1.71	3.01	4.93
>>90	1.78	4.37	5.74
>>
>>100	1.81	4.71	6.16
>>110	1.86	5.26	6.67
>>120	1.9	5.64	7.01
>>130	1.73	6.73	7.52
>>140	1.75	7.68	8
>>150	1.76	8.43	8.55
>>160	1.78	10.7	9.63
>>170	1.78	11.43	10.24
>>180	1.81	11.66	10.72
>>190	1.81	12.33	11.22
>>200	1.82	13.21	11.7
>>210	1.82	14.03	12.04
>>220	1.83	14.84	12.55
>>230	1.84	15.51	12.9
>>240	1.86	15.76	13.32
>>250	1.87	16.13	13.54
>>260	1.88	16.58	13.8
>>270	1.89	17.23	14.28
>>280	1.9	17.71	14.72
>>290	1.91	18.13	14.96
>>300	1.92	18.5	15.36
>>
>>Lincoln Stein wrote:
>>>-----BEGIN PGP SIGNED MESSAGE-----
>>>Hash: SHA1
>>>An easy thing to do would be to take a large=20
>>>GenBank record, such as an arabidopsis=20
>>>chromosome, import it into the three databases=20
>>>and then run gbrowse off them.  We could do=20
>>>simple page load timings using LWP.
>>>Does anyone reading this have a burning desire to run this test?
>>>Lincoln
>>
>>--
>>
>>Simon (Vsevolod ILyushchenko)   si...@cs...
>>				http://www.simonf.com
>>
>>The unknown is honoured, the known is neglected -
>>                              until all is known.
>>
>>               The C=FA Chulaind myth
>
>
>Content-Type: image/gif;
>	x-unix-mode=3D0666;
>	name=3D"gbrowse.gif"
>Content-Disposition: inline;
>	filename=3Dgbrowse.gif
>
>Attachment converted: ApiComputer:gbrowse.gif (GIFf/prvw) (0012A92B)


-- 
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
Jessica Kissinger                   
Center for Tropical & Emerging Global Diseases
& Department of Genetics
University of Georgia
422 Biological Sciences
Athens, GA 30602-2606		    

TEL: +1 (706) 542-6562/6563
=46AX: +1 (706) 542-3582
e-mail    jki...@ug...
http://www.ctegd.uga.edu/people_pages/kissinger.html
PGP-Key: http://www.arches.uga.edu/~jkissing/public_key.html
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++