From evelyne.james at bayercropscience.com  Mon Apr  5 07:38:26 2004
From: evelyne.james at bayercropscience.com (evelyne.james at bayercropscience.com)
Date: Mon, 5 Apr 2004 13:38:26 +0200
Subject: Interest in Gramene 
Message-ID: <OF2BC553F7.949E7C99-ONC1256E6D.0036FED6-C1256E6D.003FF1C5@bayer.de>





Dear M. Stein,

We are interested within Bayer CropScience by your Gramene Web site environment.
As you offer the possibility  to download your web site, we have tried to do
that in order to implement it internally.

One of my collaborators, Laurent Viau, has downloaded and tried to install the
release 11 and more recently the release 13. He has encountered  a lot of
difficulties to make running this environment. It seems like there is
inconsistencies between the Oracle schema and the Perl Scripts.

For example :
   some DBI SQL requests don't work because the selected table doesn't exist
   anymore.
   inconsistencies between the Oracle shema and the TSV files (differences
   between the number of columns in the TSV files and the number of fields in
   the Oracle tables).
   problems to execute some perl/bioperl scripts (compilation errors due to some
   uninitialized values and some access to scripts that don't exist...).

Is there any possibilities for you to help us in this process of installation ?
Maybe something is wrong in the release offered for downloading ... Could you be
so kind to check if it is the case ?

We would be ready if necessary to initiate a collaboration with you in order to
help us to implement efficiently within Bayer CropScience your Gramene
environment. Is this proposal conceivable for you ?

Thank you in advance to tell us what would be the conditions of such a
collaboration.

For information, we are located in France (in Evry near Paris) and our
informatics configuration is : Unix SUN servers with BioPerl, Perl, PHP, Oracle
8.1.7, Apache server.

Best regards,

___________________________________
Dr. Evelyne James
Bioinformation Manager
Bayer CropScience SA / BioScience
4, rue Pierre Fontaine
91058 Evry Cedex, France
Phone: 33 (0) 1 69 47 61 50
Fax: 33 (0) 1 69 47 61 42
GSM: 33 (0) 6 86 42 69 61
e-mail: evelyne.james at bayercropscience.com




From linedelbosc at yahoo.com  Mon Apr  5 05:37:37 2004
From: linedelbosc at yahoo.com (line delbosc)
Date: Mon, 5 Apr 2004 02:37:37 -0700 (PDT)
Subject: Gramene EnsEMBL
Message-ID: <20040405093737.23607.qmail@web40503.mail.yahoo.com>

Hello,

I would like to know if it is possible to integrate
the gramene database on an existing EnsEMBL database
build on MySQL?
thanks

Regards

Line

__________________________________
Do you Yahoo!?
Yahoo! Small Business $15K Web Design Giveaway 
http://promotions.yahoo.com/design_giveaway/


From schmidt at cshl.edu  Wed Apr  7 16:13:37 2004
From: schmidt at cshl.edu (Steven Schmidt)
Date: Wed, 7 Apr 2004 16:13:37 -0400
Subject: Gramene EnsEMBL
In-Reply-To: <20040405093737.23607.qmail@web40503.mail.yahoo.com>
References: <20040405093737.23607.qmail@web40503.mail.yahoo.com>
Message-ID: <200404071613.37917.schmidt@cshl.edu>

Hello Line,

Gramene is using version 13 of the Ensembl schema, with a few added tables, 
columns and indexes.  I believe and will soon verify that it would work with 
MySQL, except that we've customized unisearch in a way that needs to be 
fixed.

CMap and the QTL module should work under MySQL  with no changes.

Ontology, Protein, and Literature modules currently work only with Oracle.

We are working on making everything MySQL-friendly, but haven't set a release 
date.

-Steve

On Monday 05 April 2004 05:37 am, line delbosc wrote:
> Hello,
>
> I would like to know if it is possible to integrate
> the gramene database on an existing EnsEMBL database
> build on MySQL?
> thanks
>
> Regards
>
> Line
>
> __________________________________
> Do you Yahoo!?
> Yahoo! Small Business $15K Web Design Giveaway
> http://promotions.yahoo.com/design_giveaway/

-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977
Maybe someday I'll start following my own advice.



From gerard.second at mpl.ird.fr  Thu Apr  8 09:36:45 2004
From: gerard.second at mpl.ird.fr (=?iso-8859-1?Q?G=E9rard?= Second)
Date: Thu, 8 Apr 2004 15:36:45 +0200
Subject: SSAHA in Oryza
Message-ID: <a06010204bc9b0569491f@[195.220.160.207]>

Dear Colleague,

I am very much interested to use SSAHA to search 
for SNP in Oryza sativa genomic sequence. While 
the Ensemble SSAHA search server seems to be 
specialized in certain genomes, I was unable to 
locate a server to do my search online for Oryza 
sativa.

I would like to ask you for any information on SSAHA servers on line for rice.

Thank you very much.

With my best regards,

G?rard Second
-- 
G?rard Second

UMR DGPC
Centre IRD, BP 64501
911 Av Agropolis
F-34394 Montpellier Cedex 5
France

Tel (direct): 0467416309
Fax (indiquer mon nom): 0467416222
Courriel: <gerard.second at mpl.ird.fr>

http://www.dgpc.org



From neo at mbone.petra.ac.id  Tue Apr  6 09:08:32 2004
From: neo at mbone.petra.ac.id (Sirius_Black)
Date: Tue, 6 Apr 2004 20:08:32 +0700
Subject: Oracle 9i
Message-ID: <001601c41bd8$42fbca60$28140f0a@sirius>

Hiiii everyone I have an oracle problem especially about Oracle Text, here is my problem :)

When I want to create index in my Oracle using indextype ctxsys.context it always appear some messages error :

Here is my PL/SQL formula :

> create or replace directory MY_DIR as 'E:\Project\Tugas Akhir\Jurnal_pdf';

> create table oscar (
      nomer number primary key,
      namadoc varchar2(80),
      dok clob
   );

> DECLARE 
      f_lob BFILE;
      c_lob CLOB;
  
    BEGIN
      INSERT INTO oscar(nomer,namadoc,dok)
      VALUES (1,'coba.txt',EMPTY_CLOB())
      RETURN dok into c_lob;
      
      f_lob := BFILENAME('MY_DIR','coba.txt');
      dbms_lob.fileopen(f_lob,dbms_lob.file_readonly);
      dbms_lob.loadfromfile(c_lob,f_lob,dbms_lob.getlength(f_lob));
      dbms_lob.fileclose(f_lob);
      commit;
    END;

>  create index coba on oscar(dok)
    indextype is ctxsys.context;

When I execute the last formula Oracle displayed some message error :

create index coba on oscar(dok)
*
ERROR at line 1:
ORA-29855: error occurred in the execution of ODCIINDEXCREATE routine
ORA-20000: Oracle Text error:
DRG-50857: oracle error in drixtab.create_index_tables
ORA-00955: name is already used by an existing object
ORA-06512: at "CTXSYS.DRUE", line 157
ORA-06512: at "CTXSYS.TEXTINDEXMETHODS", line 186

Can someone helps me n this is very emergency question thanx 4 all :)
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From loic.rajjou at bayercropscience.com  Wed Apr  7 09:15:22 2004
From: loic.rajjou at bayercropscience.com (loic.rajjou at bayercropscience.com)
Date: Wed, 7 Apr 2004 15:15:22 +0200
Subject: Meeting
Message-ID: <OF16EA53AA.B1407EAE-ONC1256E6F.0048C22A-C1256E6F.0048D1B4@bayer.de>





Hello

I Would like to suggest you to add on "Gramene" Web site in the section
"Conference" the 3th Plant Genomics European Meetings (Plant GEMs)
http://www.plant-gems.org which will be organized in the city of Lyon in france.
Thank you
best regards

Lo?c RAJJOU
Laboratoire mixte CNRS/BAYER Cropscience
14-20 rue Pierre Baizet
BP 9163
69263 LYON Cedex 9
FRANCE
TEL : (+33) 4 72 85 21 75
FAX : (+33) 4 72 85 22 97
http://seed.proteome.free.fr




From schmidt at cshl.edu  Thu Apr  8 14:17:29 2004
From: schmidt at cshl.edu (Steven Schmidt)
Date: Thu, 8 Apr 2004 14:17:29 -0400
Subject: Interest in Gramene
In-Reply-To: <OF2BC553F7.949E7C99-ONC1256E6D.0036FED6-C1256E6D.003FF1C5@bayer.de>
References: <OF2BC553F7.949E7C99-ONC1256E6D.0036FED6-C1256E6D.003FF1C5@bayer.de>
Message-ID: <200404081312.50732.schmidt@cshl.edu>

Hello E. James,

If you send me the details of these problems, I will investigate them.

-Steve

On Monday 05 April 2004 07:38 am, evelyne.james at bayercropscience.com 
wrote:
> Dear M. Stein,
>
> We are interested within Bayer CropScience by your Gramene Web site
> environment. As you offer the possibility  to download your web 
site, we
> have tried to do that in order to implement it internally.
>
> One of my collaborators, Laurent Viau, has downloaded and tried to 
install
> the release 11 and more recently the release 13. He has encountered  
a lot
> of difficulties to make running this environment. It seems like 
there is
> inconsistencies between the Oracle schema and the Perl Scripts.
>
> For example :
>    some DBI SQL requests don't work because the selected table 
doesn't
> exist anymore.
>    inconsistencies between the Oracle shema and the TSV files 
(differences
>    between the number of columns in the TSV files and the number of 
fields
> in the Oracle tables).
>    problems to execute some perl/bioperl scripts (compilation errors 
due to
> some uninitialized values and some access to scripts that don't 
exist...).
>
> Is there any possibilities for you to help us in this process of
> installation ? Maybe something is wrong in the release offered for
> downloading ... Could you be so kind to check if it is the case ?
>
> We would be ready if necessary to initiate a collaboration with you 
in
> order to help us to implement efficiently within Bayer CropScience 
your
> Gramene environment. Is this proposal conceivable for you ?
>
> Thank you in advance to tell us what would be the conditions of such 
a
> collaboration.
>
> For information, we are located in France (in Evry near Paris) and 
our
> informatics configuration is : Unix SUN servers with BioPerl, Perl, 
PHP,
> Oracle 8.1.7, Apache server.
>
> Best regards,
>
> ___________________________________
> Dr. Evelyne James
> Bioinformation Manager
> Bayer CropScience SA / BioScience
> 4, rue Pierre Fontaine
> 91058 Evry Cedex, France
> Phone: 33 (0) 1 69 47 61 50
> Fax: 33 (0) 1 69 47 61 42
> GSM: 33 (0) 6 86 42 69 61
> e-mail: evelyne.james at bayercropscience.com

-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977
Maybe someday I'll start following my own advice.




From laurent.viau at bayercropscience.com  Wed Apr 14 04:30:18 2004
From: laurent.viau at bayercropscience.com (laurent.viau at bayercropscience.com)
Date: Wed, 14 Apr 2004 10:30:18 +0200
Subject: =?ISO-8859-1?Q?R=E9f=2E_=3A_Re=3A_Interest_in_Gramene?=
Message-ID: <OFD9E595EA.72D4E860-ONC1256E76.002D73EE-C1256E76.002EB82B@bayer.de>






Dear Steve,

As you mentioned in your last mail to my collaborator Evelyne James, I send you
the details of the problems we encountered during the installation of Gramene.
You will find attached a Word document containing the problems which occurs in
the Gramene interface and what are the associated error messages.

(See attached file: Errors.doc.zip)


Thank you again for your help.
Best regards,

Laurent
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From schmidt at cshl.edu  Wed Apr 14 18:16:50 2004
From: schmidt at cshl.edu (Steven Schmidt)
Date: Wed, 14 Apr 2004 18:16:50 -0400
Subject: Interest in Gramene
In-Reply-To: <OFD9E595EA.72D4E860-ONC1256E76.002D73EE-C1256E76.002EB82B@bayer.de>
References: <OFD9E595EA.72D4E860-ONC1256E76.002D73EE-C1256E76.002EB82B@bayer.de>
Message-ID: <200404141811.01650.schmidt@cshl.edu>

Hi Laurent,

0. As you probably noticed, gramene.org doesn't accept .doc and 
Lincoln 
doesn't accept .zip.  This is because they can carry viruses. It's 
best to 
send us plain text, or, if the formatting is important, rtf or html.

1. I've fixed some obsolete things in gramene_installation.html 
bioperl version should be 1.+, not 0.7
Use gramene_ensembl/conf, not gramene_ensembl/conf.ensembl

1a.  This document needs some more changes relating to the 
configuration.
We use two web servers - the EnsEMBL, protein, ontology, and phenotype 
pages 
are proxied to a backend server.  CMap & qtl modules can be on either.
The front-end config is in gramene/conf, the backend in 
gramene_ensembl/conf.
You probably want to use one server.  The installation instructions 
say to use 
the gramene_ensembl configuration and edit it in certain ways.  But 
probably 
there are more edits not contained in these instructions.  Maybe Alex 
Li can 
provide information on what he did.  I will look into merging the 
configs and 
using parameters to make it work with one or two servers.
Note that EnsEMBL does not play well with other sites on the same 
server.  
Also, the server startup takes a while because it checks the database 
for 
each species to see what features exist.  If you restart apache while 
the 
database is down or inacessible then EnsEMBL will not work.

2.  ACTION :
Click on "Genome Browser" link 
(www.bayer-gramene.org/japonica/mapview?chr=1)                                                                     
Error :
"File does not exist: 
/data/private/Gramene_files/htdocs/japonica/mapview"

This looks like a web server configuration problem.
initHandler in gramene_ensembl/modules/Apache/EnsEMBL/Handlers.pm 
should 
direct /japonica/mapview  to  /perl/default/mapview
with the environment variable ENSEMBL_SPECIES set to japonica, 
assuming 
japonica is one of the values or keys in $ENSEMBL_SPECIES_ALIASES in 
SIteDefs.pm
This line in gramene_ensembl/conf/httpd.conf does it:
@PerlPostReadRequestHandler     = 
('Apache::EnsEMBL::Handlers::initHandler');

3. ACTION :
Click on "Marker" link (www.bayer-gramene.org/db/markers/marker_view) 
:
Error :
"File does not  exist: 
/data/private/Gramene_files/htdocs/db/markers/marker_view"
...
"[Wed Apr 14 09:53:16 2004] [error] (2)No such file or directory: exec 
of 
/data/private/Gramene_files/cgi-bin/markers/marker_view failed

I think this is because /cgi-bin should be Apache::Registry or 
Apache::PerlRun, not really a cgi-bin.  I added this to the install 
docs


4. ACTION :
Click on a chromosome link (www.bayer-gramene.org/perl/mapview?chr=1) 
:
Error :
"[Tue Apr 13 16:54:10 2004] [error] Global symbol 
"$ENSEMBL_CONFIG_FILENAME" 
requires explicit package name at 
/data/private/Gramene_files/lib/modules/SpeciesDefs.pm line 47.
etc.

Thise variables are declared in SiteDefs.pm which Species.pm uses.
And httpd.conf already does a require of SiteDefs.pm and puts the conf 
directory into @INC.
Assuming that httpd.conf is ok, maybe you should put
BEGIN { print STDERR $INC{'SiteDefs.pm'},"\n" } into Species.pm to see 
if 
something has gone astray.

5. Error :
"[Tue Apr 13 17:05:54 2004] [error] Storable binary image v17.33 more 
recent 
than I am (v2.6) at blib/lib/Storable.pm (autosplit into 
blib/lib/auto/Storable/thaw.al) line 363, <FH> chunk 1, at 
/data/private/Gramene_files/lib/modules/SpeciesDefs.pm line 74
Compilation failed in require at 
/data/private/Gramene_files/cgi-bin/mapview 
line 25, <FH> line 1.
BEGIN failed--compilation aborted at 
/data/private/Gramene_files/cgi-bin/mapview line 25, <FH> line 1."
                                                                    
Remove conf/config.packed and restart the server.
Do you have two versions of Storable on your system?

6. ACTION :
Quick Search (with the number ap004078)                                                                 
Error :
"[Tue Apr 13 17:20:00 2004] browser: Can't locate object method 
"request" via 
package "Apache" at 
/data/private/Gramene_files/cgi-bin/searches/browser line 
54."

You have 
use Apache;
in perl.startup, right?
Assuming this script is invoked by Apache::Registry or 
Apache::PerlRun, this 
should not happen.  So fixing the config in that way should fix this 
problem.

-Steve

On Wednesday 14 April 2004 04:30 am, laurent.viau at bayercropscience.com 
wrote:
> Dear Steve,
>
> As you mentioned in your last mail to my collaborator Evelyne James, 
I send
> you the details of the problems we encountered during the 
installation of
> Gramene. You will find attached a Word document containing the 
problems
> which occurs in the Gramene interface and what are the associated 
error
> messages.
>
> (See attached file: Errors.doc.zip)
>
>
> Thank you again for your help.
> Best regards,
>
> Laurent

-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977
Maybe someday I'll start following my own advice.




From brigitte.courtois at cirad.fr  Mon Apr 19 02:15:01 2004
From: brigitte.courtois at cirad.fr (brigitte.courtois at cirad.fr)
Date: Mon, 19 Apr 2004 14:15:01 +0800
Subject: i don't think so.
Message-ID: <200404190614.i3J6EgnE028683@brie4.cshl.org>

i am speachless about your document!
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From kksabu at yahoo.com  Tue Apr 20 02:39:38 2004
From: kksabu at yahoo.com (Sabu)
Date: Mon, 19 Apr 2004 23:39:38 -0700 (PDT)
Subject: e-PCR to align SSRs to the Rice Gramene - TIGR Assembly 2003
Message-ID: <20040420063938.84383.qmail@web12002.mail.yahoo.com>

Hi,
Which e-PCR program has been used to align SSRs to the
Rice Gramene - TIGR Assembly 2003? Is it availble
through Gramene or NCBI site? 

Reference:
http://www.gramene.org/documentation/Alignment_docs/rice_ssr.html

Thanks
Sabu

=====
Dr. Sabu, K.K.
Postdoctoral Fellow
School of Environmental and Natural Resource Sciences
Faculty of Science and Technology
Universiti Kebangsaan Malaysia
43600 Bangi, Selangor
Malaysia 
Tel: +6012 6889124


	
		
__________________________________
Do you Yahoo!?
Yahoo! Photos: High-quality 4x6 digital prints for 25?
http://photos.yahoo.com/ph/print_splash


From sc167 at cornell.edu  Fri Apr 23 20:32:37 2004
From: sc167 at cornell.edu (sc167 at cornell.edu)
Date: Sat, 24 Apr 2004 08:32:37 +0800
Subject: hello
Message-ID: <200404240033.i3O0XKnE013305@brie4.cshl.org>



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From boston at unity.ncsu.edu  Sat Apr 24 13:53:52 2004
From: boston at unity.ncsu.edu (Rebecca Boston)
Date: Sat, 24 Apr 2004 13:53:52 -0400
Subject: error message
Message-ID: <6.0.1.1.1.20040424134937.01ba9a48@pop-in.ncsu.edu>



When I try to click on the maize high cot cluster to get the sequence, I 
get an error page.

This is the info and page I had.  Thanks for any help you can give.
Becky Boston

Please note that this is an alignment to a 0-bp subsequence of the rice 
chromosome 11, from bp 4906412to 4906412 There may be other, potentially 
better, matches on other regions

Rice region: 11 : 4906612 - 4906612


http://www.gramene.org/perl/blast/show_alignment.pl?chr=11&chr_start=4906612&chr_end=4906612&feature_id=&blastdb=Maize_meth_filt_hi_cot_cluster.fa&species=japonica


The error was:


unknown (no specific information available)





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From laurent.viau at bayercropscience.com  Fri Apr 30 11:46:23 2004
From: laurent.viau at bayercropscience.com (laurent.viau at bayercropscience.com)
Date: Fri, 30 Apr 2004 17:46:23 +0200
Subject: Problem with Apache Web Server
Message-ID: <OF0F4E7646.A22DFBCD-ONC1256E86.0055070D-C1256E86.0056A51C@bayer.de>





Dear Gramene,

We installed Gramene internally (Database schemas, data loading and Apache Web
server configuration), and we have an error when we are trying to access to the
index page of our internal Gramene Web Page.

On the web page, this error is :

"HTTP/1.1 500 Internal Server Error Date: Fri, 30 Apr 2004 15:33:41 GMT Server:
Apache/1.3.28 (Unix) mod_perl/1.29 Ensembl-Error: Problem in module
Apache::EnsEMBL::SendDecPage Connection: close Transfer-Encoding: chunked
Content-Type: text/html X-Pad: avoid browser bug"

"Problem in module Apache::EnsEMBL::SendDecPage"

In the error log file, the error comment is :

"Undefined subroutine &Apache::EnsEMBL::NavTrail::make_nav_trail called at
/data/private/GrameneCode//lib/modules/Apache/EnsEMBL/SendDecPage.pm line 111,
<_GEN_0> line 1."

We don't know why we have this error, because the package "NavTrail.pm" exists
and the subroutine "make_nav_trail" exists too.
The line "use Apache::EnsEMBL::NavTrail;" was commented out in the package
SendDecPage. We activated this line, but it doesn't work. The same error occurs.

Could you help us ?
Best regards,

Laurent

Laurent VIAU
Bayer CropScience
1 rue Pierre Fontaine
91058 EVRY - France
mail : laurent.viau at bayercropscience.com



