From pj37 at cornell.edu  Wed Feb  5 12:02:29 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 05 Feb 2003 12:02:29 -0500
Subject: Changes to molecular function term names in Gene Ontology
Message-ID: <3E4143A5.67415469@cornell.edu>

Please note the following changes recommended by Gene Ontology Consortium. 
Gramene will include the changes in its next Ontology updates.

Sincerely,

-Pankaj
Gramene Database
________________________

Subject: Changes to molecular function term names



Following the latest GO meeting, the GO Consortium has decided that all 
GO molecular function term names are to be appended with the word 'activity'. 
This is to improve the operability of the GO in other systems, and should 
help enhance the general understanding of this part of the GO. 

These changes will be implemented on March 1 2003. Versions of the 
ammended flat files can be found here:

http://www.ebi.ac.uk/~jane/newfunction.ontology
http://www.ebi.ac.uk/~jane/newGO.defs

For further information please email me,

thanks,

Jane Lomax
jane at ebi.ac.uk



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From bioinformatics at interbaun.com  Fri Feb  7 00:57:07 2003
From: bioinformatics at interbaun.com (Paul McCourt)
Date: Thu, 6 Feb 2003 22:57:07 -0700
Subject: Your Ontology browser vs DAG-EDIT
Message-ID: <FD4CB0A3-3A60-11D7-B820-0050E4D0A74A@interbaun.com>

Hi...

Is it possible to install only your Ontology Browser which shows an 
integrated view of the various ontologies (Gene, Plant, and Trait) as a 
stand alone product? And if so does it require Oracle or can another DB 
be used (or does it use the flat files)?

Appreciate any help you can provide. thanks


... Paul McCourt

bioinformatics at interbaun.com
Edmonton, Alberta
Canada



From irfanemre at hotmail.com  Thu Feb  6 14:05:45 2003
From: irfanemre at hotmail.com (Irfan Emre)
Date: Thu, 06 Feb 2003 19:05:45 +0000
Subject: have nice day
Message-ID: <F1627gC2DWpmy20h08x00000d8f@hotmail.com>




    hi sir;
I m a research assistant in turkey(university of firat;elazig).I m 
interested in purifications of seed proteins, therefore I need to your 
helping.Would you please send me a few article about this tissue,
and would you send me purification steps of seed proteins with sds poly 
acrylamide gel electrophoresis. I want to you how I use electrophoresis 
process(step by step) for  purification of seed proteins. you can help me Im 
very glad. Good bye. good luck with your research.










_________________________________________________________________
Add photos to your messages with MSN 8. Get 2 months FREE*. 
http://join.msn.com/?page=features/featuredemail



From pj37 at cornell.edu  Fri Feb  7 13:23:57 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 07 Feb 2003 13:23:57 -0500
Subject: have nice day
References: <F1627gC2DWpmy20h08x00000d8f@hotmail.com>
Message-ID: <3E43F9BD.8CA8D5A5@cornell.edu>

Dear Irfan,

At this moment Gramene does not carry information on the lab protocols. Perhaps
you would like to go to PubMed/Agricola/BIOSIS databases to search for the query
terms you mentioned in your mail and ask the authors directly for the protocols
and reprints.

A PubMed listing at the following URL might help to start with.

http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12166980&dopt=Abstract

Sincerely,

Pankaj
Gramene Database

Irfan Emre wrote:
> 
>     hi sir;
> I m a research assistant in turkey(university of firat;elazig).I m
> interested in purifications of seed proteins, therefore I need to your
> helping.Would you please send me a few article about this tissue,
> and would you send me purification steps of seed proteins with sds poly
> acrylamide gel electrophoresis. I want to you how I use electrophoresis
> process(step by step) for  purification of seed proteins. you can help me Im
> very glad. Good bye. good luck with your research.
> 
> _________________________________________________________________
> Add photos to your messages with MSN 8. Get 2 months FREE*.
> http://join.msn.com/?page=features/featuredemail


From pj37 at cornell.edu  Thu Feb 13 11:14:33 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 13 Feb 2003 11:14:33 -0500
Subject: [Fwd: Gene identifier synonym table standard and/or repository?]
Message-ID: <3E4BC469.C8ADAFED@cornell.edu>

FYI and feedback
-Pankaj

-------- Original Message --------
From: Fritz Roth <froth at hms.harvard.edu>
Subject: Gene identifier synonym table standard and/or repository?
To: go-friends at genome.stanford.edu

Greetings GOphiles,

We are working on some new software that uses GO annotation, and we would 
really like it to support all GO-annotated organisms.  Our chief barrier to 
doing this is the lack of gene identifier synonym tables for each organism 
(so that users can enter gene names rather than being restricted to MOD 
IDS, e.g., SGD or MGI IDs).

Is there an agreed GO Consortium standard for gene identifier synonym 
tables (could be as simple as tab-delimited text with a synonym-uniqueID 
pair on each line).  If so, is there a repository for such files?  Or is 
this a GMOD question?

Thanks!
Fritz Roth

-------------------------------------------------
Frederick P. Roth, Asst. Professor
Harvard Medical School
Dept. of Biological Chemistry and Molecular Pharmacology
250 Longwood Avenue, SGMB-322, Boston, MA 02115
(617) 432-3551 phone            (617) 432-3557 FAX
froth at hms.harvard.edu           http://llama.med.harvard.edu
-------------------------------------------------


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Problems with the list?           E-mail: owner-gofriends at geneontology.org
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Web:          http://www.geneontology.org/


From zhaow at cshl.edu  Thu Feb 13 15:37:29 2003
From: zhaow at cshl.edu (Wei Zhao)
Date: Thu, 13 Feb 2003 15:37:29 -0500 (EST)
Subject: Your Ontology browser vs DAG-EDIT
In-Reply-To: <FD4CB0A3-3A60-11D7-B820-0050E4D0A74A@interbaun.com>
Message-ID: <Pine.GSO.4.05.10302090219510.20735-100000@phage.cshl.org>


Dear Paul,

Yes, the Gramene Ontology Browser requires a database as the back end. We
use Oracle, but other relational databases should work too (you might need
to make some minor modifications).

All of the software/scripts used for the Gramene web site are open-source
and available for download at our ftp site:
ftp://ftp.gramene.org/pub/gramene/software/website/

If you download gramene_ensembl-live.tgz and untar it, you can find the
Ontology Browser (including a couple of cgi scripts and a module) in the
perl/ontology directory. You will also need a couple of static pages, 
which can be found in the gramene-live.tgz tar-ball.

Hope this helps,

Wei


On Thu, 6 Feb 2003, Paul McCourt wrote:

> Hi...
> 
> Is it possible to install only your Ontology Browser which shows an 
> integrated view of the various ontologies (Gene, Plant, and Trait) as a 
> stand alone product? And if so does it require Oracle or can another DB 
> be used (or does it use the flat files)?
> 
> Appreciate any help you can provide. thanks
> 
> 
> ... Paul McCourt
> 
> bioinformatics at interbaun.com
> Edmonton, Alberta
> Canada
> 
> 


--
Wei Zhao
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977




From leroy at clermont.inra.fr  Mon Feb 17 06:02:28 2003
From: leroy at clermont.inra.fr (Philippe LEROY)
Date: Mon, 17 Feb 2003 12:02:28 +0100
Subject: Rice Unigene
Message-ID: <5.1.0.14.0.20030217115855.0246ceb0@valmont>

Dear All,

         I am looking for a Rice Unigene set.
         I have been on Gramene Web site : http://www.gramene.org/
and on Downloads Sequence Databases : 
ftp://ftp.gramene.org/pub/gramene/blast_databases/

         I can see a Corn_Unigene.gz and a Sorghum_Unigene.gz.

         Don't you have a rice_Unigene. gz ???

Thank you very much for answering

Looking Forward

Thank you very much for your help

Philippe


Institut National de la Recherche Agronomique
UMR INRA-UBP  ASP
Groupe Annotation & Cartographie In Silico
Philippe LEROY
234 Avenue du Brezet
Domaine de Crouelle
63039 CLERMONT-FERRAND CEDEX 2 - FRANCE

         Tel: +33 4 73 62 43 37
         Fax: +33 4 73 62 44 53
         mailto:leroy at clermont.inra.fr
         http://grain.jouy.inra.fr



From info at amprox.com  Fri Feb 14 17:26:54 2003
From: info at amprox.com (General Information)
Date: Fri, 14 Feb 2003 14:26:54 -0800
Subject: Request for permission to post your web site as a link.
Message-ID: <PIEGKMJJJGPPNPNEKDLLMEEOCAAA.info@amprox.com>

Dear Colleagues:

We would like to request your permission for us to post your web site
(http://www.gramene.org/) as a link on one of AmProx?s web pages
(http://www.amprox.com/links.htm) which has not been made public yet. Your
prompt reply will be greatly appreciated and we look forward to your
permission.


Sincerely,

AmProx, Inc.
2120 Las Palmas Drive, Suite F
Carlsbad, CA 92009
Phone: (888) 326-7769, (760) 918-0585
Fax: (760) 918-0586
Eamil: info at amprox.com
URL: www.amprox.com



From plsudarshana at ucdavis.edu  Tue Feb 18 16:14:04 2003
From: plsudarshana at ucdavis.edu (Padmalatha Sudarshana)
Date: Tue, 18 Feb 2003 13:14:04 -0800 (PST)
Subject: Map Viewer
Message-ID: <200302182114.h1ILE4T09153@cucujus.ucdavis.edu>


Dear Sir/Madam,

I am Padma Sudarshana, curator of Compositdb.  We have been using Acedb 
software for archiving and retreving data from Compositdb.  We like to 
adopt "Map Viewer" for displaying our genetic maps.  Would you please 
write me if the Map Viewer software is available for download and where 
to find.  Thank you very much,

Looking forward to hearing from you,

Sincerely,
Padma Sudarshana 


From kclark at stein.cshl.org  Wed Feb 19 14:10:40 2003
From: kclark at stein.cshl.org (Ken Y. Clark)
Date: Wed, 19 Feb 2003 14:10:40 -0500 (EST)
Subject: Map Viewer
In-Reply-To: <200302182114.h1ILE4T09153@cucujus.ucdavis.edu>
Message-ID: <Pine.LNX.4.44.0302191408420.22031-100000@formaggio.cshl.org>

On Tue, 18 Feb 2003, Padmalatha Sudarshana wrote:

> 
> Dear Sir/Madam,
> 
> I am Padma Sudarshana, curator of Compositdb.  We have been using Acedb 
> software for archiving and retreving data from Compositdb.  We like to 
> adopt "Map Viewer" for displaying our genetic maps.  Would you please 
> write me if the Map Viewer software is available for download and where 
> to find.  Thank you very much,
> 
> Looking forward to hearing from you,
> 
> Sincerely,
> Padma Sudarshana 

Padma,

We are please that you like our comparative map viewer.  The source
code is publicly available through the GMOD project:

    http://www.gmod.org/cmap

There is a mailing list for support of CMap.  If you have any
questions, please join the list and let's talk there!

ky



From lstein at stein.cshl.org  Sat Feb 22 23:12:09 2003
From: lstein at stein.cshl.org (Lincoln Stein)
Date: Sat, 22 Feb 2003 23:12:09 -0500
Subject: Map Viewer
In-Reply-To: <200302182114.h1ILE4T09153@cucujus.ucdavis.edu>
References: <200302182114.h1ILE4T09153@cucujus.ucdavis.edu>
Message-ID: <200302222312.09725.lstein@cshl.org>

You can find it at www.gmod.org.  Look for the links to the "CMap" program.

Lincoln

On Tuesday 18 February 2003 04:14 pm, Padmalatha Sudarshana wrote:
> Dear Sir/Madam,
>
> I am Padma Sudarshana, curator of Compositdb.  We have been using Acedb
> software for archiving and retreving data from Compositdb.  We like to
> adopt "Map Viewer" for displaying our genetic maps.  Would you please
> write me if the Map Viewer software is available for download and where
> to find.  Thank you very much,
>
> Looking forward to hearing from you,
>
> Sincerely,
> Padma Sudarshana

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
	1 Bungtown Road, Cold Spring Harbor, NY 11724
========================================================================



From pj37 at cornell.edu  Mon Feb 24 17:36:48 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 24 Feb 2003 17:36:48 -0500
Subject: [Fwd: Fwd: CCGI Website]
Message-ID: <3E5A9E80.EFB271B2@cornell.edu>

FYI.  Some of you might be interested.

Best

Pankaj


Susan McCouch wrote:
> 
> Hi Pankaj,
> 
> FYI.  Please forward to Gramene-dev if you think people will be interested.
> 
> Thanks, Susan
> 
> --- begin forwarded text
> 
> Status: U
> From: "Robert Zeigler" <rzeigler at ksu.edu>
> To: "'Susan McCouch'" <srm4 at cornell.edu>,
> Subject: CCGI Website
> Date: Mon, 24 Feb 2003 15:38:57 -0600
> X-Priority: 3 (Normal)
> Importance: Normal
> We have put up a Website for the Cereals Comparative Genomics initiative.
>  I've been trying to send this message for the last week; but there are some
> glitches in my e-mail address book.  It seems to go; but then it does not
> appear in my outbox.  So, if you have received this message more than once,
> please accept my apologies.
> 
> The address is www.cerealsgenomics.org
> 
> Cheers,
> 
> Bob
> 
> Robert S. Zeigler
> Professor and Head
> Department of Plant Pathology
> Director
> Plant Biotechnology Center
> 4024 Throckmorton Plant Sciences Center
> Kansas State University
> Manhattan, KS 66506-5502
> 
> Tel: 785-532-6176
> Fax: 785-532-5692
> e-mail: rzeigler at ksu.edu
> 
> 
> --- end forwarded text
> 
> --
> 
> ******************************************
> Susan McCouch
> Dept of Plant Breeding
> 418 Bradfield Hall
> Cornell University
> Ithaca, NY  14853-1901
> Phone: 607-255-0420
> Fax: 607-255-6683
> E-Mail: srm4 at cornell.edu
> 
> ******************************************

-- 
******************************************
Pankaj Jaiswal, Ph.D.                                   
Research Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************


From moussaz2003 at yahoo.com  Fri Feb 28 14:08:26 2003
From: moussaz2003 at yahoo.com (Zein Moussa)
Date: Fri, 28 Feb 2003 11:08:26 -0800 (PST)
Subject: No subject
Message-ID: <20030228190826.65885.qmail@web80404.mail.yahoo.com>


Dear Sir,

I 'd be grateful when receiving copies of the Symposium articles dealing with the production of drought-tolerant lines of Rice via cell and tissue culture techniques either to the address at the end of this message or as an e-mail attachment.

Thank you in advance.


Dr. Zein El-Abedin A. Mohamed
Dept. of Agric. Botany
Fac. of Agriculture
Mansoura University
35516, El-Mansoura, Egypt.


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