From ksupekar at stanford.edu  Mon Oct  3 17:31:10 2005
From: ksupekar at stanford.edu (Kaustubh Supekar)
Date: Mon, 3 Oct 2005 14:31:10 -0700
Subject: Your ontology is valuable to us.
Message-ID: <19e0e230510031431k71dafa5bxfb176902a6a5ab4b@mail.gmail.com>

(Note, this was sent 3 times, but as moderator I thought it should be passed on at least once. Claire)

Dear Curator,

We would like to invite you to submit your Cereal plant development
Ontology in the Knowledge Zone application
(http://smi-protege.stanford.edu:8080/KnowledgeZone/). Knowledge Zone
is a web-based portal that allows users to submit their ontologies, to
search for existing ontologies, to find out their rankings based on
user reviews, to post their own reviews, and to rate reviews. Our
application is part of a larger effort to build a National Center for
Biomedical Ontology (http://www.ncbo.us) that will provide access to a
diversity of ontologies for knowledge engineers and application users.
 The Knowledge Zone is one of the efforts to provide metadata related
to ontologies to help users find, access, and assess ontologies for
their applications as well as promote dissemination of ontologies and
their re-use.

If you are familiar with or using any of the ontologies that are
already in the repository, we invite you to provide reviews and
ratings for them. If you know anyone who uses your ontology or would
be a good person to provide a review for it, we invite you to send
them the link to the KnowledgeZone and encourage them to review and
rate your ontology.

Your contribution to this effort will be valuable to us and it will
benefit the ontology community.

Thank you in advance for your help,
Kaustubh Supekar
Doctoral Student, Stanford University
http://smi-protege.stanford.edu:8080/KnowledgeZone/



From cer17 at cornell.edu  Fri Oct  7 09:08:41 2005
From: cer17 at cornell.edu (Claire E. Hebbard)
Date: Fri, 07 Oct 2005 09:08:41 -0400
Subject: Nonprofit Academic Permission Request
In-Reply-To: <200509291845.j8TIjknQ013968@night.its.uiowa.edu>
References: <200509291845.j8TIjknQ013968@night.its.uiowa.edu>
Message-ID: <6.2.1.2.2.20051007090521.02c24960@postoffice8.mail.cornell.edu>

Good morning, Jennifer.

I apologize for the delay in getting back to you. We are preparing to 
release a new build of the database next week, and I am still learning the 
process. I assure you, it normally does not take this long to respond.

Upon receiving your email, we reviewed your website and project goals. It 
looks like an excellent project, and fits with our goals of making our 
resources available to the global community. Thank you for contacting 
Gramene about this opportunity. Gramene curates publicly available data and 
puts it into the Gramene database in order to provide agricultural 
researchers and plant breeders with invaluable and compiled  biological and 
genomic information on rice and other grasses. Rice is the first crop 
genome to be fully sequenced and is a model organism for research within 
the grasses. Understanding the rice genome, which is comparatively small, 
can assist in research on agriculturally important features in rice and 
similar genes in maize, wheat and other grasses.

One of our current goals is to examine how to better distribute the 
database, expecially in developing countries. We know that this data is of 
great interest in Africa, for example, but providing our resources on slow 
connections, or to those without internet connections, has been an 
increasing concern for Gramene. Quarterly releases in January, April, July 
and October keep online researchers up-to-date with new information and 
tools, but the database growth also contributes to the large size  which 
can be a problem on slow connections. Some individuals download the 
database to use with their own data on their own machines, so intranet or 
hard-drive access is certainly feasible. But others need to keep abreast of 
the new information and tools in each release, so these sources would 
frequently need to be updated.

Gramene is a curated, free for use, web-accessible data resource for 
comparative genome analysis in the grasses.  It is supported by the 
National Science Foundation (NSF) award #0321685, the USDA Initiative for 
Future Agriculture and Food Systems (IFAFS) (grant no. 00-52100-9622) and 
USDA-Agricultural Research Service specific cooperative agreement (grant 
no. 58-1907-0-041). The database and the curated datasets are freely 
available for local use and installation. We would like to join you in your 
efforts in distributing educational information and resources to the global 
audience.

Please let me know how we can best work with you. For the specific details 
obtaining our digital resources I would be happy to put you in touch with 
our database professionals, as well as for obtaining the quarterly updates.

Sincerely,

Claire Hebbard
Gramene Outreach Coordinator

415 Bradfield Hall
Ithaca, NY 14853

Phone - 607-255-4199 or 607-255-3103
e-mail: cer17 at cornell.edu



At 02:45 PM 9/29/2005, you wrote:

>subject: Nonprofit Academic Permission Request
>
>to: 
><mailto:gramene at gramene.org?subject=Nonprofit%20Academic%20Permission%20Request&body=Dear%20unknown:%0DAfter%20reviewing%20Gramene:%20A%20Comparative%20Mapping%20Resource%20for%20Grains,%20published%20on%20the%20internet%20at%20http://www.gramene.org/,the%20WiderNet%20Project%20would%20like%20to%20ask%20your%20permission%20to%20include%20this%20web%20content%20in%20the%20eGranary%20Digital%20Library.%20Before%20you%20decide,%20please%20let%20us%20tell%20you%20about%20The%20WiderNet%20Project%20and%20the%20eGranary%20Digital%20Library.%0DThe%20WiderNet%20Project,%20a%20non-profit%20organization,%20aims%20to%20improve%20digital%20communication%20and%20access%20to%20information%20for%20students%20and%20scholars%20in%20developing%20countries.%20You%20can%20find%20more%20information%20about%20the%20WiderNet%20Project%20at%C2%A0http://www.widernet.org.%0D%0DMany%20of%20the%20institutions%20we%20work%20with%20do%20not%20have%20Internet%20connections%20or%20have%20slow,%20unreliable%20and% 
>20very%20expensive%20ser>gramene at gramene.org
>
>body:
>Dear unknown:
>
>After reviewing Gramene: A Comparative Mapping Resource for Grains, 
>published on the internet at 
><http://www.gramene.org/>http://www.gramene.org/, the WiderNet Project 
>would like to ask your permission to include this web content in the 
>eGranary Digital Library. Before you decide, please let us tell you about 
>The WiderNet Project and the eGranary Digital Library.
>
>The WiderNet Project, a non-profit organization, aims to improve digital 
>communication and access to information for students and scholars in 
>developing countries. You can find more information about the WiderNet 
>Project at <http://www.widernet.org>http://www.widernet.org.
>
>Many of the institutions we work with do not have Internet connections or 
>have slow, unreliable and very expensive service. Often, professors and 
>students must pay per minute while online and it literally takes days to 
>search a website. The eGranary Digital Library delivers digital 
>information directly to Web servers inside the institution, bypassing the 
>problem. With the eGranary Digital Library, students and scholars access 
>the information over their local area networks quickly and at no cost.
>
>If you consent, your materials will appear in the eGranary Digital Library 
>without modification, retaining all citations, copyright information, 
>author information, and credits ? exactly as they appear on the Internet 
>now. You can find more information about the eGranary Digital Library, 
>including a list of authors and organizations already donating materials, 
>at 
><http://www.widernet.org/digitallibrary>http://www.widernet.org/digitallibrary.
>
>Specifically, we would like permission to:
>
>-- Mirror (copy) the following materials for future versions of the 
>eGranary Digital Library:
>
>--<http://www.gramene.org/>http://www.gramene.org/
>
>--Distribute the Internet content you donate to participating educational 
>institutions via hard drive installation and/or satellite transmission 
>(when that becomes available),
>
>--Allow project participants to make your materials available to their 
>educational community without cost, via their intranets (but not on the 
>Internet,)
>
>--Create an archive copy of your material on our password-protected 
>intranet server (for use in the event that your publicly available link 
>ceases to function.)
>
>
>
>Please reply directly to this email, and tell us if you give:
>
>FULL PERMISSION (Donate requested materials and updates as they become 
>available)
>
>PARTIAL PERMISSION (Donate only materials that you specify, or limit our 
>delivery of your content to only hard drive installation or only satellite 
>transmission.)
>
>NO PERMISSION (Prefer not to help institutions in developing countries at 
>this time.)
>
>
>We hope that you will join our efforts to provide students and scholars 
>around the world with access to educational information and resources.
>
>Sincerely,
>
>Jennifer Mills
>
>jenn at widernet.org
>
>----------------------
>The WiderNet Project
>University of Iowa
>226 International Center
>Iowa City, IA 52242
>
>USA
>tel: (319) 335-2200
>fax: (319) 335-0820
>
>
>
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From archak at www.cdfd.org.in  Fri Oct  7 15:42:40 2005
From: archak at www.cdfd.org.in (Sunil Archak JRF)
Date: Fri, 7 Oct 2005 12:42:40 -0700
Subject: Nonprofit Academic Permission
In-Reply-To: <6.2.1.2.2.20051007090521.02c24960@postoffice8.mail.cornell.edu>
Message-ID: <Pine.SGI.4.44.0510071224120.30894-100000@www.cdfd.org.in>

Congratulations Gramene

Eversince I read the mail from Jennifer Mills of The Widernet Project I
was impressed by their objectives and efforts. I was keenly waiting for
the news about the decision taken by Gramene in this regard.

Today after reading Claire Hebbard's mail, I was extremely happy and
believe many of Gramene's followers felt the same.

Every additional information and tool in the Gramene brought that much
more power to the scietific research, and perhaps no one has imagined the
cumulative power of scietific inquiry an "open to all" system can bring
about. Now, by deciding to join hands with the Widernet Project, Gramene
has exponentially increased that cumulative power. Only time will tell the
value of addition of this humanitarian facet to the Gramene.

I do not know how many in the developed world appreciate the impact of
such a forward looking step; believe me scientific empowerment of a
community can go a long way in realising an equal world.

There are positives for everyone. I am eager to see contributions from the
beneficiaries due to access to the genetic and genomic information
provided by Gramene.

I am sure Gramene's decision will be hailed as a landmark develpoment.

Best wishes,

Sunil Archak
India




From bpenning at purdue.edu  Thu Oct  6 13:38:06 2005
From: bpenning at purdue.edu (bpenning at purdue.edu)
Date: Thu,  6 Oct 2005 12:38:06 -0500
Subject: Site down
Message-ID: <1128620286.434560fe75f14@webmail.purdue.edu>

Hi,

I tried to access gramene.org, but the site has been down since Wednesday 
afternoon. Any ETA as to when the site will be back up?

Thanks,

Bryan Penning
Purdue University Dept. of Botany and Plant Pathology

bpenning at purdue.edu




From liang at cshl.edu  Mon Oct 10 12:35:55 2005
From: liang at cshl.edu (Chengzhi Liang)
Date: Mon, 10 Oct 2005 12:35:55 -0400
Subject: Site down
In-Reply-To: <1128620286.434560fe75f14@webmail.purdue.edu>
References: <1128620286.434560fe75f14@webmail.purdue.edu>
Message-ID: <434A986B.2080607@cshl.edu>

Hi Bryan,

The site is up now (wasn't really down, it just wasn't routed to some 
users by ISP company).
Please let me know if you still have problems.

Chengzhi

bpenning at purdue.edu wrote:

>Hi,
>
>I tried to access gramene.org, but the site has been down since Wednesday 
>afternoon. Any ETA as to when the site will be back up?
>
>Thanks,
>
>Bryan Penning
>Purdue University Dept. of Botany and Plant Pathology
>
>bpenning at purdue.edu
>
>
>  
>



From cer17 at cornell.edu  Mon Oct 10 13:35:55 2005
From: cer17 at cornell.edu (Claire E. Hebbard)
Date: Mon, 10 Oct 2005 13:35:55 -0400
Subject: Site down
In-Reply-To: <1128620286.434560fe75f14@webmail.purdue.edu>
References: <1128620286.434560fe75f14@webmail.purdue.edu>
Message-ID: <6.2.1.2.2.20051010085729.035a3cd0@postoffice8.mail.cornell.edu>

Hi, Bryan,

Thanks for your email.

Unfortunately, due to a dispute between two major ISPs, the Gramene web 
site (www.gramene.org) may not have been accessible to certain Internet 
users. The dispute is resolved temporarily for now, and you should be able 
to access the website. We apologize for the inconvenience.

For more information, please see: 
http://biz.yahoo.com/prnews/051007/laf057.html?.v=17


Sincerely,

Claire Hebbard
Gramene Outreach

At 01:38 PM 10/6/2005, you wrote:
>Hi,
>
>I tried to access gramene.org, but the site has been down since Wednesday
>afternoon. Any ETA as to when the site will be back up?
>
>Thanks,
>
>Bryan Penning
>Purdue University Dept. of Botany and Plant Pathology
>
>bpenning at purdue.edu




From cer17 at cornell.edu  Mon Oct 10 13:51:31 2005
From: cer17 at cornell.edu (Claire E. Hebbard)
Date: Mon, 10 Oct 2005 13:51:31 -0400
Subject: Gramene Website should be available
Message-ID: <6.2.1.2.2.20051010134342.04774cf0@postoffice8.mail.cornell.edu>

To Gramene users and Rice-e-Net:

The Gramene website at www.gramene.org should be accessible to all users 
once again.

Due to a dispute last week between two major ISPs, the Gramene web site may 
not have been accessible to certain Internet users. This may have been true 
for many other sites, as well. The dispute is resolved temporarily for now, 
and you should currently be able to access the database at Gramene. We 
apologize for the inconvenience this may have caused. Thank you for your 
patience and understanding.

For more information, please see: 
http://biz.yahoo.com/prnews/051007/laf057.html?.v=17

Sincerely,



Claire E. Hebbard
Gramene Outreach Coordinator
G15 Bradfield Hall
Ithaca, NY 14853

607-255-4199 or
607-255-3103

www.gramene.org


Cereals are mankind's most important source of calories. Gramene can assist 
in research on agriculturally important features in rice, maize, wheat and 
other grasses.







From archak at www.cdfd.org.in  Sat Oct 15 12:27:59 2005
From: archak at www.cdfd.org.in (Sunil Archak JRF)
Date: Sat, 15 Oct 2005 09:27:59 -0700
Subject: ftp download
Message-ID: <Pine.SGI.4.44.0510150925590.86339-100000@www.cdfd.org.in>

Dear Sir/Madam,

I want to download all gene sequences and mRNA sequences used by gramene
for blast purpose. However, at
ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/blast_databases/
I could see only readme file.

Please advise

Sincerely,

Sunil Archak
CDFD, India



From pj37 at cornell.edu  Wed Oct 26 07:40:02 2005
From: pj37 at cornell.edu (pj37 at cornell.edu)
Date: Wed, 26 Oct 2005 13:40:02 +0200
Subject: here
Message-ID: <200510261140.j9QBeAwR012447@brie4.cshl.org>

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