From zhaow at cshl.edu  Fri Jan 10 12:46:52 2003
From: zhaow at cshl.edu (Wei Zhao)
Date: Fri, 10 Jan 2003 12:46:52 -0500 (EST)
Subject: Gramene Presentations at the PAG-XI Conference
Message-ID: <Pine.GSO.4.05.10301101240001.8475-100000@phage.cshl.org>



Gramene will be at the Plant and Animal Genome XI Conference, January 11 -
15, 2003. Please come to visit us in the following sessions:


Workshops & Computer Demos:
    
  .W91    Gramene: A Tool for Comparative Grass Genomics 
          Comparative Genomics. Jan 12 (Sun) 9 am-12:30 pm 
  .W294B  New Module on Phenotypic Variants within the Gramene Database
          Rice. Jan 12 (Sun) 1-3:45 pm 
  .W64    Development of Plant Ontologies for Oryza, Arabidopsis and
          Zea: An Overview 
          Bioinformatics Interfaces, Ontologies and Interoperability.
          Jan 12 (Sun) 4-6:15 pm 
  .W59    CMap: A Comparative Mapping Tool 
          Bioinformatics - Genomic Computing Techniques and Applications.
          Jan 14 (Tue) 4-6:30 pm 
  .C7     Gramene: Comparative Genomics for Rice and Other Cereals 
          Computer Demos (Part 2). Jan 14 (Tue) 8-10:30 pm 
                                                 

Posters: 

  .P888   Gramene: Comparative Genomics for Rice and Other Cereals 
  .P297   New Module on Phenotypic Variants within the Gramene Database 


For more information, please visit Gramene at http://www.gramene.org




From motallebi2002 at yahoo.com  Sat Jan 11 00:50:59 2003
From: motallebi2002 at yahoo.com (A. Motallebi)
Date: Fri, 10 Jan 2003 21:50:59 -0800 (PST)
Subject: information
Message-ID: <20030111055059.78550.qmail@web40705.mail.yahoo.com>



Dear Prof.
I am working with haploid techniques in several tomato species.
I am currently doing some initial experiments in tomato anther
and microspore culture.  I will appreciate if you send me  your

papers and information about pollen and anther culture techniques.

    Sincerely Yours
A.   Motallebi
Department of Horticulture
Faculty of Agriculture
Tabriz University
Tabriz 51664
IRAN
e-mail :
motallebi2002 at yahoo.com
 
motallebi at tabrizu.ac.ir







---------------------------------
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From ren at cshl.edu  Fri Jan 17 17:09:05 2003
From: ren at cshl.edu (Liya Ren)
Date: Fri, 17 Jan 2003 17:09:05 -0500
Subject: Gramene User Survey
Message-ID: <39FDE54A4920D411AE0C0090274602F201FB78A7@exch01.cshl.org>

Hi everyone,

In order to make the information contained on our Gramene website as useful
as possible, your feedback is very import to us. We thank those people who
have already submitted the user survey form. If you haven't submitted the
survey form, may you take a few minutes to fill out and submit it? We really
appreciate your help.

The user survey form is on: http://www.gramene.org/survey/survey.html

Thank you!    


From jn66 at cornell.edu  Wed Jan 22 10:04:50 2003
From: jn66 at cornell.edu (Jun Jian Ni)
Date: Wed, 22 Jan 2003 10:04:50 -0500
Subject: [Re: Feedback Submission from the Live Site]
Message-ID: <3E2EB312.B0997F02@cornell.edu>

Dear Pailin Nieuwenhuis,

Although the methods to determine water absorbing capacity have not
clearly
mentioned in original note
(http://www.gramene.org/newsletters/rice_genetics/rgn4/v4p95.html), it
should be
done like as follows:
1. Putting certain amount of culture solution or water in the container
(pot);
2. Planting mutant plant and wild-type plant in separate containers, and
placing
containers under normal growth condition, usually in greenhouse;
3. After 6 hours and 16 hours, determining culture solution amount left
in the
containers and calculate absorbed amount by plant; (For total roots this
time)
4. Cutting short roots and only keeping longest root for both mutant and
wild-type
plants, repeating above procedure (1 to 3), you can get water uptake
amount for
longest root.

I hope this info helpful to you.

Regards.

Junjian Ni
Curator in Gramene


feedback_submission at brie.cshl.org wrote:

>     *** Feedback from the Live Site ***
>
> refer_to_url:
http://www.gramene.org/newsletters/rice_genetics/rgn4/v4p95.html
>
> comments: May I know how to determine water absorbing capacity? Thanks

>
> name: Pailin Nieuwenhuis
>
> email: pailinnieuwenhuis at yahoo.com
>
> organization: Department of Agriculture, Thailand
>
> send_feedback: Send your feedback





From jn66 at cornell.edu  Wed Jan 22 17:07:19 2003
From: jn66 at cornell.edu (Jun Jian Ni)
Date: Wed, 22 Jan 2003 17:07:19 -0500
Subject: Feedback Submission from the Live Site
References: <200301222145.QAA08951@stein.cshl.org>
Message-ID: <3E2F1617.1C38CAF6@cornell.edu>

Dear Siavash Sal,

The gene for aroma in rice was mapped on chromosome 8. For more details, please see
reference in Gramene:
http://www.gramene.org/perl/pub_search?ref_id=49

Hope this info helpful to you.

Junjian Ni
Curator in Gramene

feedback_submission at brie.cshl.org wrote:

>     *** Feedback from the Live Site ***
>
> refer_to_url: http://www.gramene.org/newsletters/rice_genetics/rgn15/v15p123.html
>
> comments: I want some information about chromosomes that control rice aroma trait.
>
> name: Siavash Sal
>
> email: ssrizi at myway.com
>
> organization: Rice breeding project of Tabriz university
>
> send_feedback: Send your feedback



From chauser at duke.edu  Wed Jan 29 10:29:39 2003
From: chauser at duke.edu (Charles Hauser)
Date: 29 Jan 2003 10:29:39 -0500
Subject: blast.cgi
Message-ID: <1043854179.14399.22.camel@pandorina.biology.duke.edu>

Hi,

I am working on a Chlamydomonas EST project and have put up an web-based
blast utility which I would like to upgrade.  I am a molec biologist by
training, but am decent w/perl. 

I like how you parse the blast results on the gramene site.  Are you
using BioPerl? Any chance I could look at your scripts for ideas?

regards,

Charles





From teytelma at cshl.edu  Wed Jan 29 11:22:25 2003
From: teytelma at cshl.edu (Lenny Teytelman)
Date: Wed, 29 Jan 2003 11:22:25 -0500 (EST)
Subject: blast.cgi
In-Reply-To: <1043854179.14399.22.camel@pandorina.biology.duke.edu>
Message-ID: <Pine.GSO.4.05.10301291118360.2438-100000@phage.cshl.org>

Dear Charles,

Of course, you can look at the scripts.   As a matter of fact, all of the
software/scripts used for the Gramene web site are open-source and
available for download.  But, in this case, you don't need everything, and
I will email you the scripts shortly.

Lenny

> Hi,
> 
> I am working on a Chlamydomonas EST project and have put up an web-based
> blast utility which I would like to upgrade.  I am a molec biologist by
> training, but am decent w/perl. 
> 
> I like how you parse the blast results on the gramene site.  Are you
> using BioPerl? Any chance I could look at your scripts for ideas?
> 
> regards,
> 
> Charles
> 
> 
> 
> 

-- 
Lenny Teytelman
Cold Spring Harbor Laboratory
516-367-8864
teytelman at cshl.org



From jtchieu at sdsc.edu  Wed Jan 29 16:48:27 2003
From: jtchieu at sdsc.edu (Jason Tchieu)
Date: Wed, 29 Jan 2003 13:48:27 -0800 (PST)
Subject: blast
Message-ID: <Pine.GSO.4.30.0301291346290.2278-100000@lenny.sdsc.edu>

hello,

i was trying to use your blast interface but all i seem to be getting is a
message saying that there was no response from this (i'm guessing) server.

i wanted to download your information for the IRGSP Clones but didn't know
which file to grab.  Could you point me to this database so that I can run
the blast locally?

thank you for your time

jason

==========================================
Department of Biological Sciences
University of California, San Diego

http://plantst.sdsc.edu/
http://www.biology.ucsd.edu/~jtchieu/



From matthews at greengenes.cit.cornell.edu  Wed Jan 29 17:05:40 2003
From: matthews at greengenes.cit.cornell.edu (Dave Matthews)
Date: Wed, 29 Jan 2003 17:05:40 -0500 (EST)
Subject: blast.cgi
Message-ID: <200301292205.h0TM5df01929@greengenes.cit.cornell.edu>

Hi Lenny,

> I will email you the scripts shortly.

Me too me too?  There might be something there I could use too.

cheers,
- Dave


From teytelma at cshl.edu  Wed Jan 29 17:09:39 2003
From: teytelma at cshl.edu (Lenny Teytelman)
Date: Wed, 29 Jan 2003 17:09:39 -0500 (EST)
Subject: blast.cgi
In-Reply-To: <200301292205.h0TM5df01929@greengenes.cit.cornell.edu>
Message-ID: <Pine.GSO.4.05.10301291709230.7899-100000@phage.cshl.org>

Certainly.

Lenny

> Hi Lenny,
> 
> > I will email you the scripts shortly.
> 
> Me too me too?  There might be something there I could use too.
> 
> cheers,
> - Dave
> 

-- 
Lenny Teytelman
Cold Spring Harbor Laboratory
516-367-8864
teytelman at cshl.org



From a.price at abdn.ac.uk  Thu Jan 30 04:35:17 2003
From: a.price at abdn.ac.uk (Adam Price)
Date: Thu, 30 Jan 2003 09:35:17 +0000
Subject: Data for a mapping population
Message-ID: <5.1.0.14.0.20030130092914.00b19b08@mailms.abdn.ac.uk>

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------------
Adam Price
Lecturer in Plant Molecular Genetics
School of Biological Sciences
(Department of Plant and Soil Science)
University of Aberdeen
Aberdeen AB24 3UU, UK
Tel; 01224 272690 Fax; 01224 272703
e.mail a.price at abdn.ac.uk

From iyalcin at adu.edu.tr  Thu Jan 30 23:01:42 2003
From: iyalcin at adu.edu.tr (İbrahim Yalçın)
Date: Thu, 30 Jan 2003 23:01:42 EET
Subject: (no subject)
Message-ID: <BasiliX-1.1.0-10439605023e3992b60aa54@mail2>

Dear Sir,

Will you please send me the web and e-mail address of "Indian Journal of Agronomy". 

Sincerely,

Assist.Prof.?brahim Yal??n
Adnan Menderes University
Agriculture Faculty
Agricultural Machinery Department

Phone:  9 0 256 7727023
Fax:  9 0 256 7727233


From srm4 at cornell.edu  Thu Jan 30 11:58:03 2003
From: srm4 at cornell.edu (Susan McCouch)
Date: Thu, 30 Jan 2003 11:58:03 -0500
Subject: Data for a mapping population
In-Reply-To: <5.1.0.14.0.20030130092914.00b19b08@mailms.abdn.ac.uk>
References: <5.1.0.14.0.20030130092914.00b19b08@mailms.abdn.ac.uk>
Message-ID: <p05100316ba5f0799e7b8@[128.253.184.76]>

Hi Adam,

It was nice to catch site of you at PAGXI, however briefly.

Thank you very much for this communication about the mapping data 
from your drought QTL work on the Bala x Azucena population.  We are 
currently altering our data models and database schema to be able to 
store and provide access to raw mapping data files.

Do you still have the raw data that was used to map the QTLs?  If so, 
we are interested in offering it a home within Gramene.  If you agree 
to donate that data, it would be one of the first submissions of raw 
marker and phenotype data to a public database.  We aim to establish 
collaborations with authors of QTL papers so that they can help 
annotate their work for submission to our database in the future.  We 
have only begun to develop the process that will facilite this kind 
of relationship, but we would be interested in working with you to 
improve and streamline a mechanism for:

a) submission of raw data
b) author-based extraction of information from your published work to 
be integrated into Gramene
c) final quality-check on curated information that you have donated, 
once the Gramene curators have made all the internal and external 
links required for full functionality to query the information you 
have donated.

Please let us know if you are interested in working with us on these 
points, and if you have the original, raw mapping scores for both 
markers and phenotypes (in each environment), please let us know if 
you are willing to make those public.

We are very happy to hear from you and look forward to working with 
you to get your data integrated into our database.

Best regards,
Susan




>Dear Gramene,
>
>Contained below this email and as a Word attachment are details of 
>mapping data on the Bala x Azucena mapping population of rice that I 
>have been using for QTL mapping drought traits.  I email it to you 
>in the hope that it might be interesting for you to include it in 
>the web site.  Please let me know if it is interesting, if you will 
>use it, if you need it in another format or if there is other 
>information regarding the population tht would be useful.
>
>Yours sincerely,
>
>
>Adam Price
>
>------------------------------------------------
>The mapping population is an F6 recombinant inbred population 
>derived from a cross between rice (Oryza sativa) varieties Bala and 
>Azucena. 205 lines were evaluated, using a LOD threshold of 3.0. The 
>map now contains 102 (RGP and Cornell) RFLP, 35 AFLP and 17 
>microsatellites markers. The original  version of the map was 
>published in Price et al. (2000) TAG 100:49-56 (2000). To date the 
>population has been used to identify QTLs for root penetration 
>ability (Price et al. 2000, TAG 100:49-56), root morphological 
>traits (Price et al. 2002, Field Crops Research 76: 25-43) and 
>drought avoidance in the field (Price et al. 2002 Plant Molecular 
>Biology 48: 683-695).
>
>The map as produced in mapmaker is given below.  Note:
>1/ Here are presented the distance between markers (3rd column) and 
>the distance from the top of the chromosome. 
>2/ Chromosome 12 is split into two linkage groups (12t and 12b).
>3/ AFLP markers are named by the EcoR1 primer (e.g. E12) followed by 
>the Mse primer (e.g. M36) followed by a full stop and a number 
>representing the order of the polymorphic bands from the top of the 
>gel; e.g. E18M43.7 was the 7th polymorphic band from the top of the 
>gel using the EcoR1 primer 18 and Mse primer 43.
>4/ Two gaps exceed the 40 cM threshold (on chromosomes 2 and 6) but 
>these markers are linked due to reasonably high LOD scores and known 
>marker positions.
>
>=====================================================================
>c1	framework:
>
>		Markers		Distance
>	23	RG532		28.4	0
>	8	RG173		8	28.4
>	37	RZ995		11.1	36.4
>	160	E18M43.7	12.3	47.5
>	159	E18M43.6	7.6	59.8
>	146	E12M45.4	1.9	67.4
>	45	C178		22	69.3
>	249	RM5		2.7	91.3
>	106	R2635		33.5	94
>	239	RM246		14.9	127.5
>	63	C1370		6.8	142.4
>	81	G393		1.4	149.2
>	105	R2417		23.8	150.6
>	241	RM212		23.6	174.4
>	43	C86		19.3	198
>	60	C949		0.7	217.3
>	30	RZ14		32.8	218
>	90	R117	----------	250.8
>	250.5	cM	18	markers	log-likelihood=	-597.94
>
>
>c2	framework:
>
>		Markers		Distance
>	21	RG509		20.1	0
>	3	RG83		34.4	20.1
>	7	RG171		42.5	54.5
>	68	G45		18.9	97
>	161	E18M43.8	16.4	115.9
>	66	G39		0	132.3
>	5	RG139		3.2	132.3
>	254	RM221		5.3	135.5
>	69	G57		11.4	140.8
>	250	RM6		5	152.2
>	54	C601		35.7	157.2
>	13	RG256	----------	192.9
>	192.8	cM	12	markers	log-likelihood=	-432.44
>
>c3	framework:
>
>		Markers		Distance
>	132	E12M37.4	26.5	0
>	56	C643		2.7	26.5
>	19	RG409		11.7	29.2
>	11	RG191		33.1	40.9
>	143	E12M45.1	18	74
>	28	RG745		10	92
>	118	E12M36.10	5.1	102
>	75	G144		12.2	107.1
>	125	E12M36.16	22.6	119.3
>	34	RZ474		14.1	141.9
>	44	C136		32.9	156
>	101	R1618		25.5	188.9
>	76	G164	----------	214.4
>	214.6	cM	13	markers	log-likelihood=	-525.89
>
>c4	framework:
>
>		Markers		Distance
>	169	E18M43.17	14.6	0
>	10	RG190		12	14.6
>	58	C734		6.7	26.6
>	20	RG449		37	33.3
>	53	C513		13.6	70.3
>	235	RM252		10.7	83.9
>	6	RG163		39	94.6
>	61	C1016		5.3	133.6
>	237	RM349		1.3	138.9
>	236	RM348		13.2	140.2
>	26	RG620	----------	153.4
>	153.5	cM	11		log-likelihood=	-400.88
>
>c5	framework:
>
>		Markers		Distance
>	33	RZ390		30.1	0
>	104	R2232			14.9	30.1
>	93	R569		28.3	45
>	2	RG13		17.3	73.3
>	55	C624		12	90.6
>	41	C43		13	102.6
>	31	RZ70		14.8	115.6
>	251	RM26		24.1	130.4
>	4	RG119		5.3	154.5
>	16	RG346	----------	159.8
>	159.8	cM	10		log-likelihood=	-426.4
>
>c6 framework:
>              
>  	     Markers	Distance
>  	 42  C76  	       2.4		 0
>  	 35  RZ516        30.1		 2.4
>  	110  E12M36.1     12.0		 32.5
>  	 12  RG213         7.3		 44.5
>  	248  MRG6488      41.9		 51.8
>  	127  E12M36.18     8.4		 93.7
>  	107  R2654        26.3		102.1
>  	135  E12M37.7      4.0		128.4
>  	134  E12M37.6      1.6		132.4
>   	 29  RG778         3.4		134.0
>   	 36  RZ682      ----------
>                    137.4 cM   11 markers   log-likelihood= -360.56
>
>c7	framework:
>
>		Markers		Distance
>	62	C1057		17.8	0
>	247	L538T7		26.7	17.8
>	218	E12M39.11	6.5	44.5
>	79	G338		4	51
>	40	C39		5.8	55
>	71	G89b		4.4	60.8
>	100	R1440		2.4	65.2
>	64	G20		22.3	67.6
>	50	C451		22.9	89.9
>	99	R1357		19	112.8
>	27	RG650		18.9	131.8
>	238	RM234		14.5	150.7
>	52	C507		14.5	165.2
>	142	E12M37.14	2.5	179.7
>	120	E12M36.12	3.8	182.2
>	17	RG351	----------	186
>	185.9	cM	16	markers	log-likelihood=	-531.39
>
>c8	framework:
>
>		Markers		Distance
>	97	R902		15.4	0
>	116	E12M36.7	7.1	15.4
>	83	G1010b		6.6	22.5
>	48	C225		1.7	29.1
>	138	E12M37.10	2.6	30.8
>	156	E18M43.4	11.3	33.4
>	88	G2132		11.7	44.7
>	84	G1073		19.7	56.4
>	77	G187		2	76.1
>	108	R2676		13.4	78.1
>	91	R202		20.4	91.5
>	25	RG598		2.5	111.9
>	96	R662	----------	114.4
>	114.2	cM	13	markers	log-likelihood=	-380.4
>
>c9	framework:
>
>		Markers		Distance
>	98	R1164		8.6	0
>	102	R1687		19.2	8.6
>	89	R79		26.2	27.8
>	80	G385		9.7	54
>	209	E12M39.1	5.4	63.7
>	246	RM242		15.3	69.1
>	181	E18M43.26	21.5	84.4
>	122	E12M36.13	3.2	105.9
>	86	G1085		4.1	109.1
>	180	E18M43.25	5.4	113.2
>	113	E12M36.4	17.2	118.6
>	51	C506	----------	135.8
>	136	cM	12		log-likelihood=	-406.24
>
>c10	framework:
>
>		Markers		Distance
>	57	C701		7.9	0
>	73	G89d		33.8	7.9
>	14	RG257		16.1	41.7
>	130	E12M37.2	9.2	57.8
>	85	G1082		40.4	67
>	39	C16		35.7	107.4
>	47	C223	----------	143.1
>	143.2	cM	7		log-likelihood=	-321.71
>
>c11	framework:
>
>	Markers	Distance
>	95	R642		26.1	0
>	32	RZ141		11.5	26.1
>	175	E18M43.z	5.1	37.6
>	111	E12M36.2	3.5	42.7
>	78	G320		8.8	46.2
>	230	E15M35.14	2.5	55
>	67	G44		2.7	57.5
>	124	E12M36.15	3.8	60.2
>	149	E12M45.y	10.5	64
>	255	RM229		0	74.5
>	1	RG2		20.1	74.5
>	253	RM206		2.8	94.6
>	46	C189		10.2	97.4
>	115	E12M36.6	5.4	107.6
>	87	G1465		5.7	113
>	140	E12M37.12	----------	118.7
>	118.9	cM	16	markers	log-likelihood=	-439.99
>
>c12t	framework:
>
>		Markers		Distance
>	244	RM20A		4.9	0
>	65	G24		9.4	4.9
>	38	CDO127		6.7	14.3
>	141	E12M37.13	4	21
>	240	RM247		4.9	25
>	74	G124	----------	29.9
>	30	cM	6	markers	log-likelihood=	-183.87
>
>c12b	framework:
>
>		Markers		Distance
>	94	R617		3.7	0
>	15	RG341		3.7	3.7
>	123	E12M36.14	8.6	7.4
>	103	R1933		9.9	16
>	49	C449		19.5	25.9
>	24	RG543		28.9	45.4
>	9	RG181		0	74.3
>	59	C901	----------	74.3
>	74.4	cM	8	markers	log-likelihood=	-257.02
>
>
>Attachment converted: Macintosh HD:Bala x Azucena.doc (WDBN/MSWD) (0003D642)
>
>------------
>Adam Price
>Lecturer in Plant Molecular Genetics
>School of Biological Sciences
>(Department of Plant and Soil Science)
>University of Aberdeen
>Aberdeen AB24 3UU, UK
>Tel; 01224 272690 Fax; 01224 272703
>e.mail a.price at abdn.ac.uk


-- 
******************************************
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

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From D.F.Marshall at scri.sari.ac.uk  Fri Jan 31 04:30:30 2003
From: D.F.Marshall at scri.sari.ac.uk (David Marshall)
Date: Fri, 31 Jan 2003 09:30:30 -0000
Subject: Data for a mapping population
In-Reply-To: <5.1.0.14.0.20030130092914.00b19b08@mailms.abdn.ac.uk>
Message-ID: <LPBBJODAJBOJBAADMEEMOEIPCPAA.D.F.Marshall@scri.sari.ac.uk>

Hi Adam.

I picked this up through my involvement with Gramene and got your E-mail
address.

I hoped to see you at PAG. I though it might be nice for you to visit here
and chat about any areas of common interest.


Best wishes


David

David Marshall
Computational Biology
Scottish Crop Research Institute
Invergowrie
Dundee
DD2 5DA

E-mail: D.F.Marshall at scri.sari.ac.uk
Tel (SwitchB): 44(0)1382 562731
     (Direct): 44(0)1382 568583
Fax          : 44(0)1382 562426



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