nsf95159.txt (complete) ascii

mdilwort at NSF.GOV mdilwort at NSF.GOV
Thu Oct 19 12:33:10 EST 1995


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Title  : NSF 95-159--ARABIDOPSIS GENOME SEQUENCING PROJECT
Type   : Program Guideline
NSF Org: BIO
Date   : October 17, 1995
File   : nsf95159





ARABIDOPSIS THALIANA
GENOME SEQUENCING PROJECT
Interagency Program Announcement
NSF/DOE/USDA Joint Program

DEPARTMENT OF ENERGY
NATIONAL SCIENCE FOUNDATION
U.S. DEPARTMENT OF AGRICULTURE

Program Announcement
NSF/ DOE /USDA Joint Program
Arabidopsis thaliana Genome Sequencing Project

Purpose

The purpose of this program announcement is to solicit proposals
to initiate systematic sequencing of the genome of Arabidopsis
thaliana. The ultimate goal of this project is to sequence the
entire Arabidopsis genome within a reasonable time frame and at
the maximum, by the year 2004. Initially, it is anticipated that
up to 3 three-year awards will be made in FY 1996, contingent
upon the quality of proposals received and the availability of
funds.

Introduction

The Multinational Coordinated Arabidopsis thaliana Genome
Research Project was established in 1990 to develop Arabidopsis
thaliana as an experimental model system for studies of
flowering plants. Given rapid scientific advances in Arabidopsis
research, coupled with progress in large scale genome sequencing
of several genomes from other model organisms, it is now
estimated that sequencing of the entire Arabidopsis genome could
be completed by the year 2004 (ref. North American Arabidopsis
Steering Committee Workshop Report - pages 35-39, NSF95-43).
This time frame is based on the current genome sequencing
technology and the available resources. It is expected that the
time frame may be reduced substantially as the relevant
technologies are further developed.

Recognizing the potential of an Arabidopsis genome sequencing
effort to contribute to their missions, the Departments of
Energy (DOE), and Agriculture (USDA) have joined with the
National Science Foundation to initiate a U.S. Arabidopsis
thaliana Genome Sequencing Project. This project will be
coordinated with other ongoing U.S. genome projects including
the National Institutes of Health's human genome research
project and the USDA plant genome project in order to minimize
duplication of effort and to maximize efficient use of available
resources. U.S. efforts will be coordinated on an international
level with other national and transnational programs.

Who may submit

Proposals are solicited from a broad community of scientists at
U.S. institutions.  Consortia of eligible individuals or
organizations may apply, but a single organization must accept
overall management responsibility. Federally Funded Research and
Development Centers, Federal laboratories and private
organizations with relevant expertise are eligible to apply in
partnership with academic institutions. Involvement of
international collaborators is encouraged although primary
support for foreign participants/activities must be secured
through their own national programs.

 Principal Investigator and Other Senior Staff

The principal investigator (PI) and other senior staff
responsible for the project are expected to have expertise and
experience in large scale genomic DNA sequencing. If the
application is submitted by a consortium of several research
groups from one or more institutions, the consortium must make
a convincing case that it can function in an effective and
timely manner.

Award

The program anticipates supporting up to 3 three-year awards,
through cooperative agreements or grants. The exact amount of
the award will depend on the advice of reviewers and on the
availability of funds. The cost of the awards will be shared by
the participating Federal agencies.  It is anticipated that
approximately $3 million per year will be made available for
this program beginning in FY 1996.

Proposal Submission

All participating agencies have agreed to use the NSF forms and
general guidelines as described in  Grant Proposal Guide  (GPG,
NSF95-27).

Proposals should be prepared following the GPG guidelines and
the instructions below. Where the guidelines conflict between
the GPG and this program announcement, the latter supersedes the
GPG. The proposals must use standard letter size pages and be
printed single-spaced on a single side of the page using 2.54 cm
(one inch) margins on all sides. The type size must be clear and
readily legible, in standard size which is 10 to 12 point. (No
smaller than 10 point font size may be used.) If constant
spacing is used, there should be no more than 12 characters per
inch, while proportional spacing should provide no more than an
average of 15 characters per inch.

Each proposal must contain the following elements in the order
indicated:

      1. NSF Cover Page (NSF Form 1207).  Clearly indicate that
      the proposal is submitted for consideration by the BIR
      Special Projects Program in response to this program
      announcement in the appropriate boxes.

      2. Project Summary (NSF Form 1358).

      3. Table of Contents (NSF Form 1359).

      4. Project Description. A description of the project must
      not exceed 25 pages inclusive of tables, diagrams and
      other visual material. The following points must be
      addressed in this section and integrated into the general
      format described in GPG.

A. Sequencing Strategies - The proposal should include
descriptions of:

      -     DNA substrates to be sequenced: Should include
            source of the DNA (clones), map of the chromosomal
            region involved, the method of preparation and all
            other pertinent information. The selection
            strategies proposed must be applicable to future
            efforts to sequence the entire Arabidopsis genome,
            and be justified on that basis.

      -     Sequence quality and quantity: The level of accuracy
            to be sought and the expected amount to be sequenced
            should be discussed. The quantity of DNA to be
            sequenced in this initial project will depend on the
            approach selected.  However, if production of
            completely finished sequences with no gaps is
            proposed, it is expected that at least 10 Mb of DNA
            should be sequenced by the end of the three year
            period with the support provided by this Program.

      -     Genome sequencing technologies and strategies:
            Technologies/strategies that will be initially used
            should be described as well as plans for keeping
            aware of and incorporating into the ongoing work new
            developments and /or improvements in sequencing
            protocols, strategies and technologies as they
            become available.

      -     Costs of production sequencing in relation to the
            product proposed: The cost-effectiveness of the
            sequences generated will be a very important issue.
            If investigators are proposing a strategy that will
            yield less than the complete genome sequence as an
            initial product, investigators must provide an
            overall vision of how this strategy will contribute
            to the cost-effective completion of the entire
            Arabidopsis genome by the year 2004 or earlier.

B. Project management - The proposal should include descriptions
of:

      -     Plans for establishing coordination with other
            existing or planned Arabidopsis sequencing projects,
            both nationally and internationally.

      -     Plans for establishing a close linkage to the plant
            biology research community at large in order to
            ensure a close collaboration between the sequencing
            project and the ultimate user community of the
            sequence information.

      -     Ways to assess progress of the project, including
            establishing milestones and measuring progress
            toward them.  It is recommended that the applicants
            appoint an advisory committee to help them evaluate
            progress.

      -     Available facilities including a statement of
            institutional commitment for the successful
            completion of the project.

C. Information Management - The proposal should include:

      -     Data management plan, including: (1) quality of data
            to be prepared in terms of accuracy and degree of
            annotation provided; (2) mechanisms to deposit data
            into public databases; (3) community access to data
              mechanisms of data distribution; and (4)
            interactions with other community databases.


      -     Data release policies including how rapidly sequence
            data will be publicly released after production.
            The sponsoring agencies encourage an immediate
            release of raw as well as finished genome sequence
            data.  All data must be made available to the public
            within 3 months of their production.

      -     A clearly described institutional policy on sharing
            information and materials resulting from this work
            with other researchers.

      5. Bibliography. Citations must be complete, and arranged
      in alphabetical order by author.

      6. Budget (NSF Form 1030).  Provide a budget for each year
      of support requested as well as a summary budget for all
      three years.  If there are subcontracts, signed separate
      budget(s) must be included for each subcontractor.  Funds
      for facility construction or renovation may not be
      requested.

      7. Budget Justification. A brief explanation for funds in
      each budget category should be provided.  For major
      equipment or software materials, a particular model or
      source and the current or expected price should be
      specified whenever possible. A brief explanation of the
      need for each item whose costs exceeds $10,000 should be
      provided.  This section should also include a summary of
      institutional cost sharing, if any, and other sources of
      support for the project, such as government, industry, or
      private foundations.  Appropriate documentation of any
      such commitments should be provided in the appendix.
      Although cost-sharing is not required, any such commitment
      specified in the proposal will be made a condition of an
      award.

      8. Existing Facilities and Equipment. Include a brief
      description of available facilities, including space and
      relevant equipment available for the project. Where
      requested equipment or materials duplicate existing items,
      explain the need for duplication. This section is limited
      to 2 pages.

      9. Biographical Sketches. For each of the key personnel,
      provide a curriculum vitae or short biographical sketch.
      Briefly describe relevant experience, list up to 10
      publications (to include the individual's 5 most important
      and up to 5 other, relevant publications). The section is
      limited to 2 pages for each individual.

      10. Current and Pending Support.  Provide a complete list
      of current and pending research support for each of the
      key personnel. Use NSF Form 1239.

      11. Appendices. Those individuals, institutions, or
      programs that are participating in the project in a
      significant way, but have not endorsed the cover page as
      official co-PIs, must submit letters describing the nature
      of their collaboration and commitment to the proposed
      project. They can be included as appendices. General
      letters of endorsement may not be included.

      12. Additional Information. The following items must be
      provided:

      -     One complete copy of NSF Form 1225.

      -     A list of current and past collaborators of senior
            personnel whose CVs are included and of other staff
            mentioned by name in the proposal.  This should
            include names of their graduate and postdoctoral
            mentors, all graduate students and postdoctoral
            fellows who have trained with them, all co-authors
            of papers within the last 4 years, and individuals
            who have served as paid consultants to the
            investigators named in the proposal.

Attach these items to the copy of the proposal that bears the
original signatures, with the Form 1225 and the lists of
collaborators on top.  These items are for the agency's internal
use only and will not be available to reviewers. Do not provide
additional copies of these items with the other proposal copies.

When and Where to Submit

Proposals, original plus 18 copies, submitted in response to
this program announcement must be received by NSF on or before
January 16, 1996.

Complete application should be sent to:

            Arabidopsis thaliana Genome Sequencing Project
            Division of Biological Instrumentation and Resources
            Room 615, National Science Foundation
            4201 Wilson Boulevard, Arlington, VA  22230

Evaluation of Proposals

Selection of awards will be based on merit review by experts
using established peer review systems. A special emphasis panel
will be formed to review the applications and site visits may be
used as needed. All participating agencies use similar general
criteria in the evaluation of proposals submitted to their
respective competitive research grants programs. These criteria
will be interpreted in light of the objective of this
solicitation as follows:

       1. Performance competence:  This criterion addresses the
      technical soundness of the proposed approach, the
      capabilities of the proposed personnel, including those of
      the PI and other senior staff as discussed above, the
      adequacy of the resources available or proposed, and a
      likelihood that this project will lead to a successful,
      timely, cost-effective completion of Arabidopsis genome
      sequencing by the year 2004 at the latest.

      2. Project management:  This criterion addresses the
      overall quality of the technical and managerial aspects of
      the proposal, including plans for sharing the information
      and resources resulting from the project, and for
      management oversight and long-range planning.

      3. Utility or relevance of the proposed activity:  This
      criterion will be used to assess the likelihood that the
      proposed activities will serve as the basis for new or
      improved technology and/or scientific concepts in meeting
      the needs in agriculture, environment, energy and general
      societal well-being.

      4. Effect of the activity on the scientific
      infrastructure: This criterion addresses the potential of
      the proposed activity to contribute to better
      understanding or improvement of the quality and
      effectiveness of the Nation's scientific research,
      education, and human resources capabilities. An important
      issue is a likelihood of national impact and widespread,
      appropriate dissemination and use of results in
      strengthening the scientific infrastructure of this
      nation.

      5. Scientific collaboration and information sharing:
      Sequencing of the genome of a model organism is a
      community activity.  As such, a close collaboration among
      the scientists and organizations involved in sequencing
      activities and effective dissemination to the users of the
      information (the scientific community) are important
      components of this criterion.

Award Administration

The Arabidopsis thaliana Genome Sequencing Project will be
administered and managed as an interagency program involving all
participating agencies throughout the entire process from the
development of the program announcement to the review, selection
and administration of the awards.

Other Information

Potential applicants are strongly encouraged to contact project
officers and discuss their plans. Inquiries regarding the
announcement can be directed to any one of the following agency
representatives:

Machi F. Dilworth
Special Projects / BIR
Rm 615, National Science Foundation
4201 Wilson Blvd, Arlington, VA  22230
Phone: 703/306-1422
Fax: 703/306-0356
E-mail: mdilwort at nsf.gov

Edward K. Kaleikau
Plant Genome Program
NRI Competitive Grants Program
CSREES, U.S. Department of Agriculture
AGBox 2241, Washington, DC  20250-2241
Phone: 202/401-1901
Fax: 202/401-6488
E-mail: ekaleikau at reeusda.gov

Gregory L. Dilworth
Division of Energy Biosciences
Office of Basic Energy Sciences
U.S. Department of Energy
ER - 17, GTN, Washington, DC  20585
Phone: 301/903-2873
Fax: 301/903-1003
E-mail: greg.dilworth at mailgw.er.doe.gov

The Foundation provides awards for research in the sciences and
engineering. The awardee is wholly responsible for the conduct
of such research and preparation of the results for publication.
The Foundation, therefore, does not assume responsibility for
such findings or their interpretation.

The Foundation welcomes proposals on behalf of all qualified
scientists and engineers, and strongly encourages women,
minorities, and persons with disabilities to compete fully in
any of the research and research-related Programs described in
this document.

In accordance with Federal statutes and regulations and NSF
policies, no person on grounds of race, color, age, sex,
national origin, or disability shall be excluded from
participation in, denied the benefits of, or be subject to
discrimination under any program or activity receiving financial
assistance from the National Science Foundation.

Facilitation Awards for Scientists and Engineers with
Disabilities provides funding for special assistance or
equipment to enable persons with disabilities to conduct
research.  See the program announcement or contact the Program
Coordinator in the Directorate for Education and Human Resources
at (703)306-1636.

NSF has TDD (Telephonic Device for the Deaf) capability which
enables individuals with hearing impairments to communicate with
the Division of Personnel Management for information relating to
NSF programs, employment, or general information.  The number is
703/306-0090.

The program described in this publication is in the Catalog of
Federal Domestic Assistance:

      NSF -Number 47.051, Biological Sciences.

      DOE -Number 81.049, Basic Energy Sciences, High Energy and
      Nuclear Physics, Magnetic fusion Energy, Health and
      Environmental Research, Program Analysis, Field Operations
      Management.

      USDA -  Number 10.206, Competitive Research Grants
      Program.

Privacy Act and Public Burden Statements

The information requested on the application materials is
solicited pursuant to the National Science Foundation Act of
1950, as amended.  It will be used in connection with the
selection of qualified proposals and may be disclosed to
qualified reviewers and staff assistants as part of the review
process; to applicant institutions/grantees; to provide or
obtain data regarding the application review process, award
decisions or the administration of awards; to government
contractors, experts, volunteers and researchers as necessary to
complete assigned work; and to other government agencies in
order to coordinate programs.  See Systems of Records, NSF-50,
 principal Investigator/Proposal File and Associated Records, :
and NSF-51, 60 Federal Register 4449 (January 23, 1995),
 Reviewer/Proposal File and Associated Records, , 59 Federal
Register 8031 (February 17, 1994).  Submission of the
information is voluntary.  Failure to provide full and complete
information, however, may reduce the possibility of your
receiving an award. Public reporting burden for this collection
of information is estimated to average 120 hours per response,
including the time for reviewing instructions, searching
existing data sources, gathering and maintaining the data needed
and completing and reviewing the collection of information.
Send comments regarding this burden estimate or any other aspect
of this collection of information, including suggestions for
reducing this burden, to:

            Herman G. Fleming
            Reports Clearance Officer
            Division of Contracts, Policy and Oversight
            National Science Foundation
            4201 Wilson Blvd.
            Arlington, VA  22230

and/or to

            Office of Management and Budget
            OIRM -Paperwork Reduction
            Project (3145-0058
            Washington, D.C. 20503)

PT 34
KW 1002037
NSF 95-159
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