From pj37 at cornell.edu  Fri Jul  5 12:34:00 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 05 Jul 2002 12:34:00 -0400
Subject: [Fwd: Rice 14-3-3]
Message-ID: <3D25CA78.9F444DC9@cornell.edu>



"Ferl, Robert J." wrote:
> 
> Dear Pankaj,
> 
> Thank you for your note. Give us some time to look things over and we will
> see if we have any suggestions for you. I agree that good curation of
> nomenclature is important at the very least. But the understanding of the
> evolutionary paths is even more important. So give us a couple of days to
> look at your alignments and compare them to ours (we keep an alignment of
> all the 14-3-3s in the databases). Also, I should mention even before I look
> at your data that alignments can vary (especially in noise) depending upon
> which areas of the proteins are included or excluded from the alignment.
> 
> Take care, talk to you later,
> Rob
> 
> -----Original Message-----
> From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
> Sent: Friday, July 05, 2002 12:05 PM
> To: robferl at ufl.edu
> Subject: Rice 14-3-3
> 
> Dear Rob,
> 
> I was going through your excellent review article that just appeared in
> Genome
> Biology 3(7) and tried to classify the 14-3-3 family of proteins from rice.
> I am
> having some difficulty as you would see in the attached powerpoint file
> (rice_14-3-3_tree.ppt), showing the phylogenetic tree drawn from the clustal
> alignment of Arabidopsis and rice proteins . The non-epsilons from
> Arabidopsis
> (G14kappa, lambda, chi omega and phi) referred in your review appear to be
> with
> the epsilons (epsilon, omicron, mu and iota). Even if I take the Arabidopsis
> proteins the situation does not change. I don't know if the situation will
> change if I take all the sequences from other organisms, referred in your
> review, I haven't given it a try. Anyhow, the problem is how should I
> classify
> the rice 14-3-3 proteins as I am doing the curation of the rice protein
> database
> at Gramene
> 
> http://www.gramene.org/perl/protein_search
> 
> specific URL for members of 14-3-3 family
> http://www.gramene.org/perl/protein_advanced?pfam=PF00244
> 
> Also there is inconsistency of nomenclature in rice 14-3-3. I would like to
> get
> it fixed and it will be great if you could help me in curation of the
> 14-3-3s
> from rice.
> 
> Looking forward to your suggestions.
> 
> Best regards
> 
> Pankaj
> 
> ******************************************
> Pankaj Jaiswal, Ph.D.
> Postdoctoral 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
> ******************************************

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral 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 nabi_babu at rediffmail.com  Thu Jul  4 12:27:53 2002
From: nabi_babu at rediffmail.com (nabi  babu)
Date: 4 Jul 2002 16:27:53 -0000
Subject: REQUEST FOR REPRINTS
Message-ID: <20020704162753.3699.qmail@webmail25.rediffmail.com>

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From pj37 at cornell.edu  Fri Jul  5 12:38:00 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 05 Jul 2002 12:38:00 -0400
Subject: [Fwd: Rice Growth Stages]
Message-ID: <3D25CB68.8ED3C7@cornell.edu>

FYI and E mail from Paul Counce

pcounce wrote:
> 
> Pankaj,
>    Dr. Karen Moldenhauer forwarded your email to me and asked me to reply.
> Here are my thoughts:
>     The rice growth staging system provides an objective, adaptive and uniform
> system for expressing rice development.   The system is authentic.
>         The system was developed at the impetus of the Rice Technical Working Group
> beginning with committee formation in 1994.  In 1998 a special discussion
> session for the proposed system was held at the RTWG meeting in Reno, Nevada
> (Counce, P.A. 1998. Rice growth staging committee report. pp. 9-10 In
> Proceedings of the Twenty Seventh Rice Technical Working Group Meeting in
> Reno, Nevada).   This session was attended by approximately 150 scientists
> from all over the world.  Later in 1998 (August 30 - September 3) the
> International Symposium on Rice Germplasm Evaluation and Enhancement at
> Stuttgart, Arkansas,  a workshop was held and input was obtained from
> scientists there.     Later in 1998, the system was presented to scientists in
> the People's Republic of China (Seminar presented to the faculty of the
> Chengdu Institute of Biology, Chengdu, People?s Republic of China on September
> 12).  In 1999, the system was presented to scientists at the Temperate Rice
> Conference in Sacramento, California (Counce, P.A., T.C. Keisling , and A.J.
> Mitchell. 1999. An adaptive, objective rice growth staging system.  Paper
> presented to the Temperate Rice Conference held at Sacramento, CA, June 13-17,
> 1999).   In 2000, the completed system was presented to scientists at the Rice
> Technical Working Group at Biloxi, Mississippi.  Also in that year, the system
> was published in Crop Science (Counce, P.A., T.C. Keisling, and A.J. Mitchell.
> 2000. A uniform, objective and adaptive system for expressing rice
> development. Crop Science 40:436-443).  Crop Science is an international
> journal with a high citation impact and a large number of subscribers.
> Reprints have been distributed to scientists all over the world by request
> since 2000.  In addition, posters with the illustrations have also been
> distributed widely by request.  The article provides precise definition for
> the stages.  The system has been cited in several international journals and
> will be cited in many more in the future.
>         The system is based on the uniform application of objective criteria for
> determining a growth stage so that 2 people examining the same plant will
> arrive at the same answer.  The defined growth stages are specific and keyed
> to the main stem.  The system is consistent with the proposed universal plant
> growth staging system (Keisling, T.C., and P.A. Counce. 1999. Universal plant
> growth staging revisited.  Agronomy Abstracts pp. 110 and Counce, P.A., T.C.
> Keisling, and D.C. Annis. 2000. Framework for an objective, universal plant
> growth staging system adapted to plant development.  Presented at the Annual
> meeting of the American Society of Agronomy in Minneapolis, Minnesota.)  In
> addition, the rice growth staging system?s Vstages are consistent with  the
> corn growth staging system.  The nomenclature (R1, R2, V1, V2) is the same as
> the corn and soybean growth staging system nomenclature.
>         The system is especially well suited to the needs of the Gramene database
> because it is based on objective, biologically based criteria rather than
> subjective, non-biological criteria.  All of the stages you mentioned are
> accomodated by the system except imbibition and tillering.  Imbibition is
> intermediate between Stages S0 and S1.  Tillering is not a stage but it is
> related to the stage.  Most modern rice varieties can tiller at the V4 Growth
> Stage with the first tiller arising from Node 2.    Tillering, however, does
> not necessarily occur at the V4 Stage because conditions, particularly light
> and nitrogen fertility, can delay tillering until much later.  Consequently,
> one plant may tiller at V4 and another at V7 depending upon environmental
> conditions.  One way, spelled out in the rice growth staging article, would be
> to note tillering as (V5tillering or V6tillering etc.).
>         A website with some more material is:
> 
>    http://www.uaex.edu/nerec/RTWG.htm
> 
>      Also on my faculty website is information on how to growth stage a rice
> plant:
>         http://www.uark.edu/depts/agronomy/index.html
> 
>         For these reasons the rice growth staging system I think the would work
> extremely well for for the Gramene Database vocabulary to enhance the
> usefulness of that database and its meaninfulness to scientists.
> 
>      I would be happy to discuss any aspects of the system for your gramene
> database vocabulary.  I will gladly send you a reprint of the rice growth
> staging system article and the poster.  Just let me know and send me your
> mailing or shipping address.
> 
>         Sincerely,
>         Paul Counce

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral 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 pj37 at cornell.edu  Fri Jul  5 13:06:33 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 05 Jul 2002 13:06:33 -0400
Subject: REQUEST FOR REPRINTS
References: <20020704162753.3699.qmail@webmail25.rediffmail.com>
Message-ID: <3D25D219.FB85F6F1@cornell.edu>

Dear Dr. Nabi,

The article requested by you is not authored by us, however Gramene
does carry full text of articles published in Rice Genetics Newsletters from
previous years. They are available at 
http://www.gramene.org/newsletters/rice_genetics/

Full text of the reference you requested is available at 
http://www.gramene.org/newsletters/rice_genetics/rgn11/v11p137.htm


Sincerely

Pankaj
www.gramene.org 

nabi babu wrote:
> 
> Dear sir,
>         I would appreciate receiving the reprint of yours
> entitled"34. Restriction fragment length polymorphism and linkage
> analysis of rice alpha-amylase gene family "and published in" ".I
> will be thankful if you kindly send this to my address which will
> be helpful for my ongoing research.
> Thanking you,
> B.Nabi,
> Research scholar,
> School of life sciences,
> Pondicherry university,
> Pondicherry 605 014
> INDIA
> _________________________________________________________
> There is always a better job for you at Monsterindia.com.
> Go now http://monsterindia.rediff.com/jobs


From jde22 at cornell.edu  Mon Jul  8 09:52:19 2002
From: jde22 at cornell.edu (Jeremy Darwin Edwards)
Date: Mon, 08 Jul 2002 09:52:19 -0400
Subject: obtaining sequences
In-Reply-To: <5.1.0.14.2.20020708083447.00baefb8@postoffice2.mail.cornel
 l.edu>
Message-ID: <5.1.0.14.2.20020708091902.00bad600@postoffice2.mail.cornell.edu>

Steve,

With regard to the proposed batch sequence extraction feature, I think the 
input should look something like the following, perhaps in an uploadable 
tab-delimited file:

AB023482.2      23683   24028
AF161269.1      136842  137041
AP000492.1      25885   26232

The output should be in a single FASTA formatted file as follows:

 >AB023482.2_23683_24028
GGCTGTGTTTAGTTGGGGAAAAGAAAATTTTTGGGTGTCACATCAGACGTTTGACCGGAT 
GTCGGAAGGGGTTTTTGGACACGAATGAAAAAACTAATTTCAGAACTCGCCTGGAAACCG 
CGAGACGAATCTTTTGAGTCTACTTAAGCCGTCATTAGCACATGTGGGGTTACTGTAGCA 
CTTATGGCTAATCATGGCCTAATTAGGCTCAAAAGATTCGTCTCGCGATTTATAGCTAAA 
CTGTGCAATTGGTTTTTCTTTTTGTCCACATTTAATGCTCCATGCATGTGTCCAAAGATT 
CGATGTGACAGGTGAAGGGGAAAATTTTTGGGAACTAAACTAGCCC

 >AF161269.1_136842_137041
GGCCTAATTAGTACATGATTAGCCATAATTGCTACAATAACCCACATGTGCTAATGACGGATTAATTAGGTTCAAAAGATTCGTCTCGCGGTTTCCAGACGAGTTATGAAATTAGTTTTTTCATTCGTCTCCGAAAACTCCTTCCGGTTAAACATCCGATGTGACACCCAAATTTTTTTTTTCGCGAACTAAATAGGCCC

 >AP000492.1_25885_26232
GGCCCCGTTTAGTTCCCCAAAATTTTTTCTCAAAAACATCACATCGAATCTTTGGACACATGCACAAAACATTAAATATAGATAAATGAAAAAACTAATTGCACAGTTAGGGATGAAATCGCGAGACAAATCTTTTGAGCATAATTAGTCCATGATTAGCCATAAAGTGCTATAGTAACCCACATGTGCTAATGACGGATTAATTAGGCTCAAAAGATCCGTCTCGCGGTTTCCAGACGAGTTATGAAAATATTTTTTTTTCATTCGTGTCCGAAAAGCCCTTCCGACATCCGGTCAAACATCCAATGTGACACTCTAAATTTTTCTTTTCTCGAACTAAACAGGCCC

I realize that Gramene doesn't currently keep sequences, but it might be a 
good idea to at least keep a current copy of the rice genome 
sequence.   This will be a nice feature for users to extract multiple 
sequences corresponding to their query results.  If this batch sequence 
extraction feature is implemented, I'm sure that it will very popular.

Jeremy Edwards



At 08:34 AM 7/8/2002 -0400, you wrote:
>I support this idea.
>
>Lincoln
>
>On Thursday 27 June 2002 04:09 pm, jde22 at cornell.edu wrote:
> > I have an idea for Gramene that I think will be very useful for many
> > users.  It would be great if there was a way to download specific
> > pieces of sequences by submitting a list of BACs
> > (or any other sequences) and regions within those sequences.  So, the
> > user would specify the BAC and the beginning and end of the sequences of
> > interest and the sequences would be returned, perhaps in FASTA format.
> > This is something that Genbank should do, but doesn't, and most of us spend
> > too much time cutting out the sequences that we want.  A batch option would
> > also be really great.  I typically write scripts and have a few other
> > tricks to do this, but for the typical user, it is a real chore.
> >
> > Jeremy Edwards
>
>--
>========================================================================
>Lincoln D. Stein                           Cold Spring Harbor Laboratory
>lstein at cshl.org                                   Cold Spring Harbor, NY
>========================================================================



From schmidt at cshl.edu  Mon Jul  8 16:17:33 2002
From: schmidt at cshl.edu (Steven Schmidt)
Date: Mon, 8 Jul 2002 16:17:33 -0400
Subject: obtaining sequences
In-Reply-To: <5.1.0.14.2.20020708091902.00bad600@postoffice2.mail.cornell.edu>
References: <5.1.0.14.2.20020708091902.00bad600@postoffice2.mail.cornell.edu>
Message-ID: <200207082017.QAA02312@cshl.org>

Jeremy,

this looks good except that I would leave out the blank line between the 
name of the sequence  (>accession.version_start_end) and the sequence itself.

It will be in the next major update of the gramene sequence viewer.

We have the rice genomic sequence in the database.
We could put other sequences in.  We'd probably want to be selective, not
put in all ESTs for all grains.

-Steve


On Monday 08 July 2002 09:52, Jeremy Darwin Edwards wrote:
> Steve,
>
> With regard to the proposed batch sequence extraction feature, I think the
> input should look something like the following, perhaps in an uploadable
> tab-delimited file:
>
> AB023482.2      23683   24028
> AF161269.1      136842  137041
> AP000492.1      25885   26232
>
> The output should be in a single FASTA formatted file as follows:
>  >AB023482.2_23683_24028
>
> GGCTGTGTTTAGTTGGGGAAAAGAAAATTTTTGGGTGTCACATCAGACGTTTGACCGGAT
> GTCGGAAGGGGTTTTTGGACACGAATGAAAAAACTAATTTCAGAACTCGCCTGGAAACCG
> CGAGACGAATCTTTTGAGTCTACTTAAGCCGTCATTAGCACATGTGGGGTTACTGTAGCA
> CTTATGGCTAATCATGGCCTAATTAGGCTCAAAAGATTCGTCTCGCGATTTATAGCTAAA
> CTGTGCAATTGGTTTTTCTTTTTGTCCACATTTAATGCTCCATGCATGTGTCCAAAGATT
> CGATGTGACAGGTGAAGGGGAAAATTTTTGGGAACTAAACTAGCCC
>
>  >AF161269.1_136842_137041
>
> GGCCTAATTAGTACATGATTAGCCATAATTGCTACAATAACCCACATGTGCTAATGACGGATTAATTAGGTTCAA
>AAGATTCGTCTCGCGGTTTCCAGACGAGTTATGAAATTAGTTTTTTCATTCGTCTCCGAAAACTCCTTCCGGTTAA
>ACATCCGATGTGACACCCAAATTTTTTTTTTCGCGAACTAAATAGGCCC
>
>  >AP000492.1_25885_26232
>
> GGCCCCGTTTAGTTCCCCAAAATTTTTTCTCAAAAACATCACATCGAATCTTTGGACACATGCACAAAACATTAA
>ATATAGATAAATGAAAAAACTAATTGCACAGTTAGGGATGAAATCGCGAGACAAATCTTTTGAGCATAATTAGTCC
>ATGATTAGCCATAAAGTGCTATAGTAACCCACATGTGCTAATGACGGATTAATTAGGCTCAAAAGATCCGTCTCGC
>GGTTTCCAGACGAGTTATGAAAATATTTTTTTTTCATTCGTGTCCGAAAAGCCCTTCCGACATCCGGTCAAACATC
>CAATGTGACACTCTAAATTTTTCTTTTCTCGAACTAAACAGGCCC
>
> I realize that Gramene doesn't currently keep sequences, but it might be a
> good idea to at least keep a current copy of the rice genome
> sequence.   This will be a nice feature for users to extract multiple
> sequences corresponding to their query results.  If this batch sequence
> extraction feature is implemented, I'm sure that it will very popular.
>
> Jeremy Edwards
>
> At 08:34 AM 7/8/2002 -0400, you wrote:
> >I support this idea.
> >
> >Lincoln
> >
> >On Thursday 27 June 2002 04:09 pm, jde22 at cornell.edu wrote:
> > > I have an idea for Gramene that I think will be very useful for many
> > > users.  It would be great if there was a way to download specific
> > > pieces of sequences by submitting a list of BACs
> > > (or any other sequences) and regions within those sequences.  So, the
> > > user would specify the BAC and the beginning and end of the sequences
> > > of interest and the sequences would be returned, perhaps in FASTA
> > > format. This is something that Genbank should do, but doesn't, and most
> > > of us spend too much time cutting out the sequences that we want.  A
> > > batch option would also be really great.  I typically write scripts and
> > > have a few other tricks to do this, but for the typical user, it is a
> > > real chore.
> > >
> > > Jeremy Edwards
> >
> >--
> >========================================================================
> >Lincoln D. Stein                           Cold Spring Harbor Laboratory
> >lstein at cshl.org                                   Cold Spring Harbor, NY
> >========================================================================

-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977


From xytang at iastate.edu  Thu Jul 11 01:05:47 2002
From: xytang at iastate.edu (Xiaoyun Tang)
Date: Thu, 11 Jul 2002 00:05:47 -0500 (CDT)
Subject: Comparative Map Viewer
Message-ID: <200207110505.AAA32156@mailhub-1.iastate.edu>

Hi:

I am trying to download the Comparative map Viewer from your site. Could you
please tell me where and how to download this tool?

Thanks for any help from you,
Xiaoyun Tang











From srm4 at cornell.edu  Thu Jul 11 10:34:11 2002
From: srm4 at cornell.edu (Susan McCouch)
Date: Thu, 11 Jul 2002 10:34:11 -0400
Subject: Fwd: Re: information sharing and biology
Message-ID: <p05100304b953454172f0@[128.253.184.76]>

Hi folks,

I have just looked at the article cited below.  Gramene is mentioned 
in a one-liner in the 4th paragraph from the bottom.  It's short but 
sweet- they cut most of the info that was in the original article, 
which is too bad, but we've already been slashdotted and inquiries 
are coming in.

I suggest we consider putting this up in our "NEW" category on the 
web page, though it's a bit heavy on the salesmanship.

Susan


--- begin forwarded text


Status: U
From: "Nicholas Thompson" <thompson at newamerica.net>
To: "Susan McCouch" <srm4 at cornell.edu>
Subject: Re: information sharing and biology
Date: Wed, 10 Jul 2002 21:10:54 -0400
X-Priority: 3

Susan:
Alas, the story we emailed about ended up getting nixed by the 
Atlantic Monthly (after they accepted and edited it --- but so it 
goes). So, I sent it to the Washington Monthly, and they have just 
published it. They did shorten it substantially and make it more 
tendentious than the original, but at least it's out.

<http://www.washingtonmonthly.com/features/2001/0207.thompson.html>http://www.washingtonmonthly.com/features/2001/0207.thompson.html

thank you very much for your help and time, and please let me know if 
you come across any other interesting stories that I should cover * 
Nick

-- 
******************************************
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 liuxx175 at tc.umn.edu  Thu Jul 11 13:28:26 2002
From: liuxx175 at tc.umn.edu (Sixin Liu)
Date: Thu, 11 Jul 2002 10:28:26 -0700
Subject: suggestions about BLAST search
Message-ID: <l03130300b9536c4d53bb@[134.84.43.63]>

Hello,

I have a few suggestions about BLAST search in the Gramene web site.

1. For results of summary section of blast search with database of Rice
IRGSP clones, the description column is empty . It would be helpful if the
chromosomal location of the BAC clone is listed in this column. Or, you can
indicate the chromosomal location of the sequences in the detailed
alignment section.

2. Reset button doe not work when using Search Again option after the
previous BLAST search.

Thanks for your help.





From CoeE at missouri.edu  Thu Jul 11 21:41:49 2002
From: CoeE at missouri.edu (Ed Coe)
Date: Thu, 11 Jul 2002 20:41:49 -0500
Subject: Fwd: Re: information sharing and biology
References: <p05100304b953454172f0@[128.253.184.76]>
Message-ID: <3D2E33DD.D0E0685E@missouri.edu>

Susan,
Thank you for passing along the article.  Its message is clear and
visionary.
By coincidence today, my daughter sent the following, which hits the
same target.
Best wishes.
Ed

Growing Good Corn

There was a farmer who grew award-winning corn. Each year he entered his
corn in the state fair where it won a blue ribbon. One year a newspaper
reporter interviewed him and learned something interesting about how he
grew it.

The reporter discovered that the farmer shared his seed corn with his
neighbors. ?How can you afford to share your best seed corn with your
neighbors when they are entering corn in competition with yours each
year?? the reporter asked.

?Why sir,? said the farmer, ?didn?t you know? The wind picks up pollen
from the ripening corn and swirls it from field to field. If my
neighbors grow inferior corn, cross-pollination will steadily degrade
the quality of my corn. If I am to grow good corn, I must help my
neighbors grow good corn.?

He is very much aware of the connectedness of life. His corn cannot
improve unless his neighbor?s corn also improves.

So it is in other dimensions. Those who choose to be at peace must help
their neighbors to be at peace. And those who choose to be happy must
help others to find happiness. While one can certainly be happy by
oneself, maintaining happiness is difficult when those around you are
unhappy, for the welfare of each is bound up with the welfare of all.




From pj37 at cornell.edu  Fri Jul 12 16:29:58 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 12 Jul 2002 16:29:58 -0400
Subject: Feedback Submission from brie2 (fwd)
References: <Pine.GSO.4.05.10207121604090.18768-100000@phage.cshl.org>
Message-ID: <3D2F3C46.3F7BC0DD@cornell.edu>

Dear Manju,

Gramene database simply stores the information on sequences and markers. We do
not have the stocks of clones.
In order to get the clones, you need to contact the source person/lab. The
address of source can be found either from GenBank / SWISSPROT links on
the protein page or via the publication referring that data set.

For example in this instance the clone for GA-20 Oxidase gene 

http://www.gramene.org/perl/protein_search?protein_id=79131

can be requested from the authors of following publication.
  
http://www.gramene.org/perl/pub_search?ref_id=3793

Sincerely

Pankaj
www.gramene.org


Wei Zhao wrote:
> 
> ---------- Forwarded message ----------
> Date: Fri, 12 Jul 2002 15:54:38 -0400
> From: feedback_submission at gramene.org
> To: Wei Zhao <zhaow at cshl.edu>
> Subject: Feedback Submission from brie2
> 
>     *** Feedback for Gramene ***
> 
> refer_to_url: http://brie2.cshl.org:8082/gramene/searches/browser
> 
> comments: do you supply clones of any specific genes?
> if so i need the clone for GA-2-Oxidase gene from rice
> (Q9AVA5)
> 
> name: Manju George
> 
> email: mgeorge at tc.umn.edu
> 
> organization: University of Minnesota
> 
> send_feedback: Send your feedback

--


From pj37 at cornell.edu  Fri Jul 12 12:30:49 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 12 Jul 2002 12:30:49 -0400
Subject: [Fwd: download the physical map viewer]
Message-ID: <3D2F0439.1FA190A6@cornell.edu>

Hi,

This is just a copy of Ken's reply to Xiaoyun Tang's e. mail  asking for comparative map viewer.

Pankaj


"Ken Y. Clark" wrote:
> 
> ---------- Forwarded message ----------
> Date: Tue, 9 Jul 2002 11:23:16 -0400
> From: feedback_submission at gramene.org
> To: Wei Zhao <zhaow at cshl.edu>
> Subject: Feedback Submission from brie2
> 
>     *** Feedback for Gramene ***
> 
> refer_to_url: http://brie2.cshl.org:8082/maps/viewer
> 
> comments: Hi:
> 
> Would you like to tell me that how  I can download the physical map viewer for local use, please?
> Thanks.
> 
> name: Xiaoyun Tang
> 
> email: xytang at iastate.edu
> 
> organization: ISU
> 
> send_feedback: Send your feedback
> 
> Xiaoyun,
> 
> Thank you for inquiring about the comparative mapping code.  We have
> made two tarballs available here:
> 
>     ftp://ftp.gramene.org/pub/software/website/
> 
> Please view the README file to learn about the two versions of the
> code.
> 
> ky


From jn66 at cornell.edu  Sun Jul 14 08:55:29 2002
From: jn66 at cornell.edu (Jun Jian Ni)
Date: Sun, 14 Jul 2002 08:55:29 -0400
Subject: Mutagen Rice
References: <20020713093410.97178.qmail@web14408.mail.yahoo.com>
Message-ID: <3D3174C1.5AAAC762@cornell.edu>

Dear Mr. Dinh Chi Hieu,

Maybe you can get some info from Rice Genetics Newsletters
(http://www.gramene.org/newsletters/rice_genetics/). You also can get
some useful info from publications on TAG, MGG, Breeding Science and
other related journals. Please let's know if you have further questions.

With best regards.

Junjian Ni
gramene at gramene.org

Chi Hieu Dinh wrote:

> Dear Sir,
>  I am Hieu Dinh Chi. I come from Vietnam. Now I am
> working in Rice Breeding Laboratory. My main working
> is anther rice tissue culture and mutagent of rice for
> breeding. Because lack of information and
> documentation about these problems , please help me if
> you has any possiblities. I am hope to get your help
> soon to develope my job.
> Thank you in advance and looking forward to hearing
> from you.
> Sincerely yours
> Dinh Chi Hieu
> Rice Breeding Laboratory
> Vietnam Agricuture Science Institute
> Vandien Town, Thanhtri District, Hanoi Vietnam
>
> __________________________________________________
> Do You Yahoo!?
> Yahoo! Autos - Get free new car price quotes
> http://autos.yahoo.com



From jn66 at cornell.edu  Tue Jul 16 09:34:11 2002
From: jn66 at cornell.edu (Jun Jian Ni)
Date: Tue, 16 Jul 2002 09:34:11 -0400
Subject: ask for information
References: <3C551727.000042.27952@smtp2>
Message-ID: <3D3420D3.E250C390@cornell.edu>

Hi Mr. Chuanxiao Xie,

You can find rice genetics newsletter on Gramene website:

http://www.gramene.org/newsletters/rice_genetics/

Dr. N. Kurata is the editor for RGN. You can contact with him through
following address:

Dr. N. Kurata
Plant Genetics Lab, Genetics Strains Research Center,
National Institute of Genetics, Mishima, 441-8540 Japan
Tel: 81-559-81-6808, Fax: 81-559-81-6879
e-mail: nkurata at lab.nig.ac.jp

Hope this info helpful and let's know if you need more info.

Regards.

Junjian Ni
gramene at brie.cshl.org
gramene at gramene.org




XXXXXX wrote:

> Dear Sir or Madam,
> May you let me have the idea of the web site of the journal Rice
> Genetics newsletter.
> I can see the content of vol.5 of the magzine. How can i contact with
> this journal editors.
> Thank you!
>
> Xie, Chuanxiao From P.R.China
>
>
>
>
>
> __________________________________________
>
> ??????????????????????????????MP3
> http://shopping.263.net/category21.htm
> ????????,????????! http://stock19.263.net/download/borntowin.htm



From srm4 at cornell.edu  Tue Jul 16 20:39:03 2002
From: srm4 at cornell.edu (Susan McCouch)
Date: Tue, 16 Jul 2002 20:39:03 -0400
Subject: Fwd: Re: information sharing and biology
In-Reply-To: <3D2E33DD.D0E0685E@missouri.edu>
References: <p05100304b953454172f0@[128.253.184.76]>
 <3D2E33DD.D0E0685E@missouri.edu>
Message-ID: <p05100312b95a6cfd1041@[128.253.184.76]>

Ed,

Thanks for sending that note along.  I enjoyed it very much.

Susan


>Susan,
>Thank you for passing along the article.  Its message is clear and
>visionary.
>By coincidence today, my daughter sent the following, which hits the
>same target.
>Best wishes.
>Ed
>
>Growing Good Corn
>
>There was a farmer who grew award-winning corn. Each year he entered his
>corn in the state fair where it won a blue ribbon. One year a newspaper
>reporter interviewed him and learned something interesting about how he
>grew it.
>
>The reporter discovered that the farmer shared his seed corn with his
>neighbors. ?How can you afford to share your best seed corn with your
>neighbors when they are entering corn in competition with yours each
>year?? the reporter asked.
>
>?Why sir,? said the farmer, ?didn?t you know? The wind picks up pollen
>from the ripening corn and swirls it from field to field. If my
>neighbors grow inferior corn, cross-pollination will steadily degrade
>the quality of my corn. If I am to grow good corn, I must help my
>neighbors grow good corn.?
>
>He is very much aware of the connectedness of life. His corn cannot
>improve unless his neighbor?s corn also improves.
>
>So it is in other dimensions. Those who choose to be at peace must help
>their neighbors to be at peace. And those who choose to be happy must
>help others to find happiness. While one can certainly be happy by
>oneself, maintaining happiness is difficult when those around you are
>unhappy, for the welfare of each is bound up with the welfare of all.


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

******************************************


From xytang at iastate.edu  Fri Jul 19 13:14:26 2002
From: xytang at iastate.edu (Xiaoyun Tang)
Date: Fri, 19 Jul 2002 12:14:26 -0500 (CDT)
Subject: No subject
Message-ID: <200207191714.MAA05029@mailhub-2.iastate.edu>

Ken:

I am sorry to bother you again. I tried to install CSHL::CMap 0.02 according to 

the INSTALL instruction. After it passed "Perl Makefile.PL", I typed "make" and 

got the error message:
"Where would you like the HTML templates installed?  my_t
Where would you like the command-line scripts installed?  my_c
Copying templates from ./templates to my_t
Checking if your kit is complete...
Looks good
Warning: prerequisite File::MkTemp 1.06 not found at
/usr/lib/perl5/5.6.1/ExtUtils/MakeMaker.pm line 352.
Writing Makefile for CSHL::CMap
Change CSHL::CMap::Constants TEMPLATE_DIR => my_t
To load your data, run 'my_c/cmap_admin.pl'
==> Your Makefile has been rebuilt. <==
==> Please rerun the make command.  <==
false
make: *** [Makefile] Error"

Actually I did install File::MkTemp 1.06 already. I guess something wrong. 

Another problem is there is no CSHL::CMap::Apache::RelationalMapViewer module 
in the new release.

I appreciate your help.

Have a nice day,
Xiaoyun  













From timothy.close at ucr.edu  Mon Jul 22 17:13:54 2002
From: timothy.close at ucr.edu (TJ Close)
Date: Mon, 22 Jul 2002 14:13:54 -0700
Subject: HarvEST to Gramene
Message-ID: <000201c231c5$88bc8610$cebe178a@TJCOFFICE>

If you would like to make use of the information that we have in HarvEST Triticeae for Gramene, please let me know.  For example, we could provide you with a tab delimited file listing each barley unigene and its best rice hit (using the TIGR annotated rice genome).  A new version of HarvEST Triticeae will be posted on our website in the very near future.  If you wish to view HarvEST to see what might be useful to Gramene, then please have a look at a temporary version http://harvest.ucr.edu/HarvEST085.exe.  Of course, we are always interested in feedback, so if anything is not obvious about the software, or you see any errors, then please let us know.

Thanks.

Timothy J Close
Botany & Plant Sciences
University of California
Riverside, CA  92521-0124
USA
Phone: 909-787-3318
FAX: 909-787-4437
http://cnas.ucr.edu/~bps/close.html
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From lstein at stein.cshl.org  Tue Jul 23 15:50:42 2002
From: lstein at stein.cshl.org (Lincoln Stein)
Date: Tue, 23 Jul 2002 12:50:42 -0700
Subject: HarvEST to Gramene
In-Reply-To: <000201c231c5$88bc8610$cebe178a@TJCOFFICE>
References: <000201c231c5$88bc8610$cebe178a@TJCOFFICE>
Message-ID: <200207231250.42997.lstein@cshl.org>

Hi Tim,

We most certainly would like to use this information.  Thank you!

Lincoln

On Monday 22 July 2002 02:13 pm, TJ Close wrote:
> If you would like to make use of the information that we have in HarvEST
> Triticeae for Gramene, please let me know.  For example, we could provide
> you with a tab delimited file listing each barley unigene and its best rice
> hit (using the TIGR annotated rice genome).  A new version of HarvEST
> Triticeae will be posted on our website in the very near future.  If you
> wish to view HarvEST to see what might be useful to Gramene, then please
> have a look at a temporary version http://harvest.ucr.edu/HarvEST085.exe. 
> Of course, we are always interested in feedback, so if anything is not
> obvious about the software, or you see any errors, then please let us know.
>
> Thanks.
>
> Timothy J Close
> Botany & Plant Sciences
> University of California
> Riverside, CA  92521-0124
> USA
> Phone: 909-787-3318
> FAX: 909-787-4437
> http://cnas.ucr.edu/~bps/close.html


From kclark at stein.cshl.org  Tue Jul 23 16:33:41 2002
From: kclark at stein.cshl.org (Ken Y. Clark)
Date: Tue, 23 Jul 2002 16:33:41 -0400 (EDT)
Subject: Installing comparative maps
In-Reply-To: <200207191714.MAA05029@mailhub-2.iastate.edu>
Message-ID: <Pine.LNX.4.44.0207231630120.29951-100000@formaggio.cshl.org>

On Fri, 19 Jul 2002, Xiaoyun Tang wrote:

> Ken:
> 
> I am sorry to bother you again. I tried to install CSHL::CMap 0.02
> according to the INSTALL instruction. After it passed "Perl
> Makefile.PL", I typed "make" and got the error message:
>
> "Where would you like the HTML templates installed?  my_t
> Where would you like the command-line scripts installed?  my_c
> Copying templates from ./templates to my_t
> Checking if your kit is complete...
> Looks good
> Warning: prerequisite File::MkTemp 1.06 not found at
> /usr/lib/perl5/5.6.1/ExtUtils/MakeMaker.pm line 352.
> Writing Makefile for CSHL::CMap
> Change CSHL::CMap::Constants TEMPLATE_DIR => my_t
> To load your data, run 'my_c/cmap_admin.pl'
> ==> Your Makefile has been rebuilt. <==
> ==> Please rerun the make command.  <==
> false
> make: *** [Makefile] Error"
> 
> Actually I did install File::MkTemp 1.06 already. I guess something wrong. 
> 
> Another problem is there is no CSHL::CMap::Apache::RelationalMapViewer module 
> in the new release.
> 
> I appreciate your help.
> 
> Have a nice day,
> Xiaoyun  

Xiaoyun,

I'm very sorry it's taken me a while to get back with you.  I'm in San
Diego this whole week.  I won't be able to fix these problems (and I'm
sure they're mine, not yours!) until next week.  My sincerest
apologies.

ky



From ueno at chanko.lab.nig.ac.jp  Wed Jul 24 04:18:07 2002
From: ueno at chanko.lab.nig.ac.jp (Shingo Ueno)
Date: Wed, 24 Jul 2002 17:18:07 +0900
Subject: Error occurred
Message-ID: <002a01c232ea$a3e95870$524b2785@shigenet.local>

Error occurred.

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

Gramene EnsEMBL Server Error
Sorry, an error occurred while the Ensembl server was processing your
request.

Please email a report , quoting any additional information given below,
along with the URL, to gramene at gramene.org.

The error was:


unknown (no specific information available)
 last modified : Wed Dec 31 19:00:00 1969


http://www.gramene.org/perl/ontology/search_term?id=TO:0000387

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

Shingo Ueno




From changku at stein.cshl.org  Wed Jul 24 10:30:28 2002
From: changku at stein.cshl.org (Kuan Y. Chang)
Date: Wed, 24 Jul 2002 10:30:28 -0400 (EDT)
Subject: Error occurred
In-Reply-To: <002a01c232ea$a3e95870$524b2785@shigenet.local>
Message-ID: <Pine.GSO.4.05.10207241023230.29520-100000@phage.cshl.org>

Hi Shingo,

The error does not occur.  The reason why the error occurred is still not
certain.  We will pay more attention to it.   

Meanwhile please go ahead to do your search and let us know if any
problem.  Thanks!

Kuan



On Wed, 24 Jul 2002, Shingo Ueno wrote:

> Error occurred.
> 
> ----------------------------------------------------------------------------
> -------
> 
> Gramene EnsEMBL Server Error
> Sorry, an error occurred while the Ensembl server was processing your
> request.
> 
> Please email a report , quoting any additional information given below,
> along with the URL, to gramene at gramene.org.
> 
> The error was:
> 
> 
> unknown (no specific information available)
>  last modified : Wed Dec 31 19:00:00 1969
> 
> 
> http://www.gramene.org/perl/ontology/search_term?id=TO:0000387
> 
> ----------------------------------------------------------------------------
> -------
> 
> Shingo Ueno
> 
> 
> 



From pan at stein.cshl.org  Thu Jul 25 14:33:11 2002
From: pan at stein.cshl.org (Xiaokang Pan)
Date: Thu, 25 Jul 2002 14:33:11 -0400 (EDT)
Subject: Error occurred
In-Reply-To: <Pine.GSO.4.05.10207241023230.29520-100000@phage.cshl.org>
Message-ID: <Pine.GSO.4.05.10207251426070.3366-100000@phage.cshl.org>


Hi Kuan,

     Last morning from 3:30 to 9: 00 am, the Oracle database on
Raclette was shutdown automatically due to some reasons I am still
checking. If someone used http://www.gramene.org during that time period,
he/she could get this kind errors. 

     Xiaokang 


On Wed, 24 Jul 2002, Kuan Y. Chang wrote:

> Hi Shingo,
> 
> The error does not occur.  The reason why the error occurred is still not
> certain.  We will pay more attention to it.   
> 
> Meanwhile please go ahead to do your search and let us know if any
> problem.  Thanks!
> 
> Kuan
> 
> 
> 
> On Wed, 24 Jul 2002, Shingo Ueno wrote:
> 
> > Error occurred.
> > 
> > ----------------------------------------------------------------------------
> > -------
> > 
> > Gramene EnsEMBL Server Error
> > Sorry, an error occurred while the Ensembl server was processing your
> > request.
> > 
> > Please email a report , quoting any additional information given below,
> > along with the URL, to gramene at gramene.org.
> > 
> > The error was:
> > 
> > 
> > unknown (no specific information available)
> >  last modified : Wed Dec 31 19:00:00 1969
> > 
> > 
> > http://www.gramene.org/perl/ontology/search_term?id=TO:0000387
> > 
> > ----------------------------------------------------------------------------
> > -------
> > 
> > Shingo Ueno
> > 
> > 
> > 
> 
> 



From teytelma at cshl.edu  Tue Jul 30 15:27:06 2002
From: teytelma at cshl.edu (Lenny Teytelman)
Date: Tue, 30 Jul 2002 15:27:06 -0400 (EDT)
Subject: suggestions about BLAST search
In-Reply-To: <l03130300b9536c4d53bb@[134.84.43.63]>
Message-ID: <Pine.GSO.4.05.10207301429570.9460-100000@phage.cshl.org>

Dear Sixin,


> 1. For results of summary section of blast search with database of Rice
> IRGSP clones, the description column is empty . It would be helpful if the
> chromosomal location of the BAC clone is listed in this column. Or, you can
> indicate the chromosomal location of the sequences in the detailed
> alignment section.

We will put the GenBank titles/summaries in the headers of the fasta files
(downloadable on the ftp site), and that will show up in the summaries.
Is that fine?  These should display the assigned chromosome of each clone.

As for chromosomal locations, we don't have a pseudomolecule for rice, so
we don't have the locations.  We wish we did!

 
> 2. Reset button doe not work when using Search Again option after the
> previous BLAST search.

Fixed.  Thanks.

Regards,

Lenny



From ajitpal at nrcpb.org  Tue Jul 30 06:10:09 2002
From: ajitpal at nrcpb.org (ajitpal)
Date: Tue, 30 Jul 2002 18:10:09 +0800
Subject: N/A
Message-ID: <20020730181009.M88751@nrcpb.org>

Hello Sir,
this is to tell u that, ur ssrtool for finding sequence(motif) repeats in a
nucleotide sequence is giving some output repeated i.e. same results r
repeated several times within the same table of output.Can u check it and
suggest.

Regards

Ajit kumar Pal.
RA, Rice Genome Sequencing;
NRC on Plant Biotechnology.
IARI,New Delhi-12, India.




From noelyap at ascus.plbr.cornell.edu  Tue Jul 30 18:14:43 2002
From: noelyap at ascus.plbr.cornell.edu (Immanuel Yap)
Date: Tue, 30 Jul 2002 18:14:43 -0400
Subject: N/A
In-Reply-To: <20020730181009.M88751@nrcpb.org>
References: <20020730181009.M88751@nrcpb.org>
Message-ID: <20020730221443.GB4101@ascus.plbr.cornell.edu>

On Tue, Jul 30, 2002 at 06:10:09PM +0800, ajitpal wrote:
> Hello Sir,
> this is to tell u that, ur ssrtool for finding sequence(motif) repeats in a
> nucleotide sequence is giving some output repeated i.e. same results r
> repeated several times within the same table of output.Can u check it and
> suggest.

Could you please send us the parameters or settings that gave you the
repeated output?  This will help us in debugging.

Thank you,
Noel
-- 
Immanuel V. Yap <ivy1 at cornell.edu>
Department of Plant Breeding and Biometry, Cornell University
G15 Bradfield Hall, Ithaca, NY 14853
Phone: 1-607-255-3103
http://www.gramene.org


From shibo at nature.Berkeley.EDU  Wed Jul 31 13:45:49 2002
From: shibo at nature.Berkeley.EDU (Shibo Zhang)
Date: Wed, 31 Jul 2002 10:45:49 -0700 (PDT)
Subject: Swissprot/Trembl Rice Proteins Database?
Message-ID: <Pine.GSO.4.44.0207311033400.8159-100000@nature.Berkeley.EDU>

Dear Gramene,

I have a question regarding the rice protein db used in your blast page.

How often is updated? It has covered >95% rice protein sequences in public
sector? The TIGR rice protein DB covered more than this rice DB?

Thank you in advance,

regards,


Shibo



From rhee at acoma.Stanford.EDU  Wed Jul 31 15:03:29 2002
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Wed, 31 Jul 2002 12:03:29 -0700 (PDT)
Subject: Important Plant Journals into PubMed--Attached
In-Reply-To: <3D48252E.1030305@missouri.edu>
Message-ID: <Pine.GSO.4.44.0207311203060.24591-100000@acoma.Stanford.EDU>

Ed,

I still have all the maize db tallies, so no worries.

sue

On Wed, 31 Jul 2002, Ed Coe wrote:

> Hi, Pankaj.
> The list you sent to Sue has left out many tallies for MaizeDB -- not
> sure what happened, but while you are re-visiting the journal list for
> PubMed access, per Sue's suggestion, please use the attached list, which
> incorporates all the MaizeDB tallies.  Thanks.
> Best,
> Ed
>
> Pankaj Jaiswal wrote:
> > Dear Sue,
> >
> > We have gone through the list of journals you provided. Based on it and one from
> > PubMed, we have added a few more to the list (marked in red) and updated the
> > numbers from Gramene. I hope this will help in mobolizing the PubMed to cover a
> > variety of plant journals.
> >
> > The updated list is attached both in excel and tab delimited file format
> >
> > Best
> > Pankaj
> >
> > Susan McCouch wrote:
> >
> >>Sue,
> >>
> >>We will look at the list you sent and get back to you shortly with
> >>any additional journals of interest to Gramene.  It's a great idea to
> >>go forward together on this and it sure would make our jobs easier.
> >>
> >>Best,
> >>Susan
> >>
> >>
> >>>Thanks Ed!
> >>>
> >>>I think backfilling would be harder than future additions, but it seems
> >>>like this is a reasonable number of new journals to support. I hope we can
> >>>get them all in. I will wait until Friday to see if there are any
> >>>more feedback from others to send the list to NCBI.
> >>>
> >>>Cheers,
> >>>Sue
> >>>
> >>>
> >>>On Mon, 29 Jul 2002, Ed Coe wrote:
> >>>
> >>>
> >>>> Updated list attached, ...29jul02.
> >>>> The tallies for MaizeDB sometimes extend back as far as 1900.
> >>>> If most or all of these journals can be covered in PubMed, we will be
> >>>> greatly aided!!!
> >>>> Ed
> >>>>
> >>>
> >>>
> >>
> >>
> >>------------------------------------------------------------------------
> >>
> >>JOURNAL TITLE	TAIR	PubMed	MaizeDB	Gramene
> >>ACTA BOTANICA NEERLANDICA	5	0	20	1
> >>ACTA BOTANICA SINICA	15	0	55	111
> >>AMERICAN JOURNAL OF BOTANY	37	11		14
> >>ANNALS OF BOTANY	47	8		12
> >>ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY	17	0		0
> >>AUSTRALIAN JOURNAL OF PLANT PHYSIOLOGY	85	1		24
> >>BIOCHEMICAL SOCIETY TRANSACTIONS	56	0		6
> >>BIOLOGIA PLANTARUM	24	0	59	15
> >>BIOLOGY OF THE CELL	22	1		4
> >>BOTANICA ACTA	13	0		3
> >>BOTANICAL BULLETIN OF ACADEMIA SINICA	10	0		54
> >>BOTANICHESKII ZHURNAL	13	0	0	0
> >>CANADIAN JOURNAL OF BOTANY	22	1		7
> >>CEREAL CHEMISTRY	0	0	231	49
> >>CROP SCIENCE				174
> >>CURRENT PLANT SCIENCE AND BIOTECHNOLOGY IN AGRICULTURE	18	0	0	0
> >>CURRENT TOPICS IN PLANT BIOCHEMISTRY AND PHYSIOLOGY	90	0	25	0
> >>CURRENT TOPICS IN PLANT PHYSIOLOGY	11	0	7
> >>CYTOL GENET (ENGL TRANSL OF TSITOLOGIA I GENETIKA)			21	1
> >>DAI	69	0
> >>DOKLADY : BIOLOGICAL SCIENCES - AKADEMIIA NAUK SSSR	16	0		13
> >>EXPERIENTIA	12	0		7
> >>FIZIOLOGIYA RASTENII	16	0	94	19
> >>INTERNATIONAL JOURNAL OF PLANT SCIENCES	18	2		2
> >>INTERNATIONALE ZEITSCHRIFT FUER THEORETISCHE UND ANGEWANDTE GENETIK	21	0		0
> >>JOURNAL OF PLANT BIOLOGY	16	0	5	14
> >>JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE	64			15
> >>JOURNAL OF PLANT PHYSIOLOGY	55	1		93
> >>JOURNAL OF PLANT RESEARCH	41	5		4
> >>MOLECULAR BREEDING	16	0		45
> >>PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON. SERIES B: BIOLOGICAL SCIENCES	33	0		1
> >>PHOTOCHEMISTRY AND PHOTOBIOLOGY	16	0		7
> >>PHOTOSYNTHESIS RESEARCH	19	0		6
> >>PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY	15	0	17	15
> >>"PHYSIOLOGY, BIOCHEMISTRY, AND MOLECULAR BIOLOGY OF PLANT LIPIDS"	14	0	0	0
> >>PHYTOPATHOLOGY	24	0		103
> >>PLANT AND CELL PHYSIOLOGY	191	0		204
> >>PLANT AND SOIL	16	0		22
> >>PLANT BIOLOGY	11	0	5	23
> >>PLANT CELL AND ENVIRONMENT	78	0		5
> >>PLANT CELL REPORTS	59	1		59
> >>PLANT GROWTH REGULATION	18	2		16
> >>PLANT MOLECULAR BIOLOGY REPORTER	33	0		3
> >>PLANT PHYSIOLOGY AND BIOCHEMISTRY	45	0		17
> >>PLANT SCIENCE	92	29	0	113
> >>PLANT SCIENCE LETTERS	13	0	62	3
> >>PROTOPLASMA	53	19		7
> >>RADIATION BOTANY	12	0	12	3
> >>RUSSIAN JOURNAL OF GENETICS	0	0	10	0
> >>RUSSIAN JOURNAL OF PLANT PHYSIOLOGY (ENGL TRANSL OF FIZIOLIYA RASTENII)	0	0	62	0
> >>SEED SCIENCE TECHNOLOGY	0	0	35	0
> >>SEXUAL PLANT REPRODUCTION	33	0	51	5
> >>SOVIET GENETICS	15	15		0
> >>THE NEW PHYTOLOGIST	24	0		1
> >>THEORETICAL AND APPLIED GENETICS	66	0	481	394
> >>WEED SCIENCE	11	0		1
> >>TSITOLOGIYA I GENETIKA	7	0	68	0
> >>ZEITSCHRIFT FUER PFLANZENPHYSIOLOGIE	23	10		4
> >>rice genetics newsletter				269
> >>japanese journal of breeding				248
> >>breeding science				374
> >>plant breeding				57
> >>International Rice Research Notes				51
> >>Photosynthetica				4
> >>Journal of Plant Nutrition				15
> >>Plant Pathology				42
> >>Euphytica				91
> >>Journal of Bioscience and Bioengineering				10
> >>"Memoirs of the Faculty of Agriculture, Hokkaido University"				82
> >>Genes and Genetic Systems				23
> >>Zeitschrift fuer Naturforschung				5
> >>Japanese Journal of Crop Science				57
> >>Chinese Journal of Rice Science				44
> >>Biochemical Genetics				13
> >>Biologia Plantarum Prague				12
> >>"Bioscience, Biotechnology and Biochemistry"				73
> >>"CRRN, Chinese Rice Research Newsletter"				25
> >>Hereditas Landskrona				5
> >>Hereditas				13
> >>Indian Journal of Agricultural Sciences				28
> >>Indian Journal of Biochemistry and Biophysics				31
> >>Indian Journal of Experimental Biology				33
> >>Indian Journal of Genetics and Plant Breeding				36
> >>Indian Journal of Plant Physiology				10
> >>International Rice Research Newsletter				25
> >>Japanese Journal of Genetics				78
> >>"JARQ, Japan Agricultural Research Quarterly"				18
> >>Molecular plant-microbe interactions :  MPMI				33
> >>Oryza				27
> >>Pakistan Journal of Agricultural Research				4
> >>Science in China Series C Life Sciences				21
> >
>
>

-----------------------------------------------------------------------------
Sue Rhee                         	rhee at acoma.stanford.edu
The Arabidopsis Information Resource	URL: www.arabidopsis.org
Carnegie Institution of Washington	FAX: +1-650-325-6857
Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
260 Panama St.
Stanford, CA 94305
U.S.A.
-----------------------------------------------------------------------------



From rhee at acoma.Stanford.EDU  Wed Jul 31 12:40:17 2002
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Wed, 31 Jul 2002 09:40:17 -0700 (PDT)
Subject: Important Plant Journals into PubMed--Attached
In-Reply-To: <3D47FF3C.ABAC46CE@cornell.edu>
Message-ID: <Pine.GSO.4.44.0207310935040.24591-100000@acoma.Stanford.EDU>

Pankaj

Thanks for the list. For the additional journals you added, I need more
information. 1. Are they in the NLM database? (search through Journal
Browser, http://www.ncbi.nlm.nih.gov:80/entrez/jrbrowser.cgi). 2. For
those that are in the NLM database, how many rice articles PubMed
currently contains. It looks like some of the journals you added are
already handled by PubMed.

Cheers,
Sue

rice genetics newsletter
japanese journal of breeding
breeding science
plant breeding
International Rice Research Notes
Photosynthetica
Journal of Plant Nutrition
Plant Pathology
Euphytica
Journal of Bioscience and Bioengineering
Memoirs of the Faculty of Agriculture, Hokkaido University
Genes and Genetic Systems
Zeitschrift fuer Naturforschung
Japanese Journal of Crop Science
Chinese Journal of Rice Science
Biochemical Genetics
Biologia Plantarum Prague
Bioscience, Biotechnology and Biochemistry
CRRN, Chinese Rice Research Newsletter
Hereditas Landskrona
Hereditas
Indian Journal of Agricultural Sciences
Indian Journal of Biochemistry and Biophysics
Indian Journal of Experimental Biology
Indian Journal of Genetics and Plant Breeding
Indian Journal of Plant Physiology
International Rice Research Newsletter
Japanese Journal of Genetics
JARQ, Japan Agricultural Research Quarterly
Molecular plant-microbe interactions :  MPMI
Oryza
Pakistan Journal of Agricultural Research
Science in China Series C Life Sciences




On Wed, 31 Jul 2002, Pankaj Jaiswal wrote:

> Dear Sue,
>
> We have gone through the list of journals you provided. Based on it and one from
> PubMed, we have added a few more to the list (marked in red) and updated the
> numbers from Gramene. I hope this will help in mobolizing the PubMed to cover a
> variety of plant journals.
>
> The updated list is attached both in excel and tab delimited file format
>
> Best
> Pankaj
>
> Susan McCouch wrote:
> >
> > Sue,
> >
> > We will look at the list you sent and get back to you shortly with
> > any additional journals of interest to Gramene.  It's a great idea to
> > go forward together on this and it sure would make our jobs easier.
> >
> > Best,
> > Susan
> >
> > >Thanks Ed!
> > >
> > >I think backfilling would be harder than future additions, but it seems
> > >like this is a reasonable number of new journals to support. I hope we can
> > >get them all in. I will wait until Friday to see if there are any
> > >more feedback from others to send the list to NCBI.
> > >
> > >Cheers,
> > >Sue
> > >
> > >
> > >On Mon, 29 Jul 2002, Ed Coe wrote:
> > >
> > >>  Updated list attached, ...29jul02.
> > >>  The tallies for MaizeDB sometimes extend back as far as 1900.
> > >>  If most or all of these journals can be covered in PubMed, we will be
> > >>  greatly aided!!!
> > >>  Ed
> > >>
> > >

-----------------------------------------------------------------------------
Sue Rhee                         	rhee at acoma.stanford.edu
The Arabidopsis Information Resource	URL: www.arabidopsis.org
Carnegie Institution of Washington	FAX: +1-650-325-6857
Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
260 Panama St.
Stanford, CA 94305
U.S.A.
-----------------------------------------------------------------------------



From pj37 at cornell.edu  Wed Jul 31 11:16:12 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 31 Jul 2002 11:16:12 -0400
Subject: Important Plant Journals into PubMed--Attached
References: <Pine.GSO.4.44.0207291850590.15272-100000@acoma.Stanford.EDU> <p05100305b96c345206d8@[128.253.184.76]>
Message-ID: <3D47FF3C.ABAC46CE@cornell.edu>

Dear Sue,

We have gone through the list of journals you provided. Based on it and one from
PubMed, we have added a few more to the list (marked in red) and updated the
numbers from Gramene. I hope this will help in mobolizing the PubMed to cover a
variety of plant journals.

The updated list is attached both in excel and tab delimited file format

Best
Pankaj

Susan McCouch wrote:
> 
> Sue,
> 
> We will look at the list you sent and get back to you shortly with
> any additional journals of interest to Gramene.  It's a great idea to
> go forward together on this and it sure would make our jobs easier.
> 
> Best,
> Susan
> 
> >Thanks Ed!
> >
> >I think backfilling would be harder than future additions, but it seems
> >like this is a reasonable number of new journals to support. I hope we can
> >get them all in. I will wait until Friday to see if there are any
> >more feedback from others to send the list to NCBI.
> >
> >Cheers,
> >Sue
> >
> >
> >On Mon, 29 Jul 2002, Ed Coe wrote:
> >
> >>  Updated list attached, ...29jul02.
> >>  The tallies for MaizeDB sometimes extend back as far as 1900.
> >>  If most or all of these journals can be covered in PubMed, we will be
> >>  greatly aided!!!
> >>  Ed
> >>
> >
-------------- next part --------------
JOURNAL TITLE	TAIR	PubMed	MaizeDB	Gramene
ACTA BOTANICA NEERLANDICA	5	0	20	1
ACTA BOTANICA SINICA	15	0	55	111
AMERICAN JOURNAL OF BOTANY	37	11		14
ANNALS OF BOTANY	47	8		12
ANNUAL REVIEW OF PLANT PHYSIOLOGY AND PLANT MOLECULAR BIOLOGY	17	0		0
AUSTRALIAN JOURNAL OF PLANT PHYSIOLOGY	85	1		24
BIOCHEMICAL SOCIETY TRANSACTIONS	56	0		6
BIOLOGIA PLANTARUM	24	0	59	15
BIOLOGY OF THE CELL	22	1		4
BOTANICA ACTA	13	0		3
BOTANICAL BULLETIN OF ACADEMIA SINICA	10	0		54
BOTANICHESKII ZHURNAL	13	0	0	0
CANADIAN JOURNAL OF BOTANY	22	1		7
CEREAL CHEMISTRY	0	0	231	49
CROP SCIENCE				174
CURRENT PLANT SCIENCE AND BIOTECHNOLOGY IN AGRICULTURE	18	0	0	0
CURRENT TOPICS IN PLANT BIOCHEMISTRY AND PHYSIOLOGY	90	0	25	0
CURRENT TOPICS IN PLANT PHYSIOLOGY	11	0	7	
CYTOL GENET (ENGL TRANSL OF TSITOLOGIA I GENETIKA)			21	1
DAI	69	0		
DOKLADY : BIOLOGICAL SCIENCES - AKADEMIIA NAUK SSSR	16	0		13
EXPERIENTIA	12	0		7
FIZIOLOGIYA RASTENII	16	0	94	19
INTERNATIONAL JOURNAL OF PLANT SCIENCES	18	2		2
INTERNATIONALE ZEITSCHRIFT FUER THEORETISCHE UND ANGEWANDTE GENETIK	21	0		0
JOURNAL OF PLANT BIOLOGY	16	0	5	14
JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE	64			15
JOURNAL OF PLANT PHYSIOLOGY	55	1		93
JOURNAL OF PLANT RESEARCH	41	5		4
MOLECULAR BREEDING	16	0		45
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON. SERIES B: BIOLOGICAL SCIENCES	33	0		1
PHOTOCHEMISTRY AND PHOTOBIOLOGY	16	0		7
PHOTOSYNTHESIS RESEARCH	19	0		6
PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY	15	0	17	15
"PHYSIOLOGY, BIOCHEMISTRY, AND MOLECULAR BIOLOGY OF PLANT LIPIDS"	14	0	0	0
PHYTOPATHOLOGY	24	0		103
PLANT AND CELL PHYSIOLOGY	191	0		204
PLANT AND SOIL	16	0		22
PLANT BIOLOGY	11	0	5	23
PLANT CELL AND ENVIRONMENT	78	0		5
PLANT CELL REPORTS	59	1		59
PLANT GROWTH REGULATION	18	2		16
PLANT MOLECULAR BIOLOGY REPORTER	33	0		3
PLANT PHYSIOLOGY AND BIOCHEMISTRY	45	0		17
PLANT SCIENCE	92	29	0	113
PLANT SCIENCE LETTERS	13	0	62	3
PROTOPLASMA	53	19		7
RADIATION BOTANY	12	0	12	3	
RUSSIAN JOURNAL OF GENETICS	0	0	10	0	
RUSSIAN JOURNAL OF PLANT PHYSIOLOGY (ENGL TRANSL OF FIZIOLIYA RASTENII)	0	0	62	0	
SEED SCIENCE TECHNOLOGY	0	0	35	0	
SEXUAL PLANT REPRODUCTION	33	0	51	5	
SOVIET GENETICS	15	15		0	
THE NEW PHYTOLOGIST	24	0		1	
THEORETICAL AND APPLIED GENETICS	66	0	481	394	
WEED SCIENCE	11	0		1	
TSITOLOGIYA I GENETIKA	7	0	68	0	
ZEITSCHRIFT FUER PFLANZENPHYSIOLOGIE	23	10		4	
rice genetics newsletter				269	
japanese journal of breeding				248	
breeding science				374	
plant breeding				57	
International Rice Research Notes				51	
Photosynthetica				4			
Journal of Plant Nutrition				15			
Plant Pathology				42			
Euphytica				91			
Journal of Bioscience and Bioengineering				10			
"Memoirs of the Faculty of Agriculture, Hokkaido University"				82			
Genes and Genetic Systems				23			
Zeitschrift fuer Naturforschung				5			
Japanese Journal of Crop Science				57			
Chinese Journal of Rice Science				44			
Biochemical Genetics				13			
Biologia Plantarum Prague				12			
"Bioscience, Biotechnology and Biochemistry"				73			
"CRRN, Chinese Rice Research Newsletter"				25			
Hereditas Landskrona				5			
Hereditas				13			
Indian Journal of Agricultural Sciences				28
Indian Journal of Biochemistry and Biophysics				31
Indian Journal of Experimental Biology				33
Indian Journal of Genetics and Plant Breeding				36
Indian Journal of Plant Physiology				10
International Rice Research Newsletter				25
Japanese Journal of Genetics				78
"JARQ, Japan Agricultural Research Quarterly"				18
Molecular plant-microbe interactions :  MPMI				33
Oryza				27
Pakistan Journal of Agricultural Research				4
Science in China Series C Life Sciences				21
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