January 21, 2005

2010 Project
To determine the function of all genes in Arabidopsis thaliana by the year 2010

The Directorate for Biological Sciences (BIO) of the National Science Foundation (NSF) announces its intention to continue support of research to determine the function of all genes in the model plant Arabidopsis thaliana by the year 2010. Individual investigators or groups of investigators will be supported to conduct creative and innovative research designed to determine, using all available means, the function of a suite of genes of the investigator's interest and choice. This year, the Program continues to solicit proposals that will use high throughput methods to understand the gene circuitry underlying plant processes and proposals to determine the function of genes of unknown function. Also supported will be development of Arabidopsis functional genomics tools that will enable a broad community of scientists to participate in the 2010 Project.

The Directorate for Biological Sciences (BIO) of the National Science Foundation (NSF) announces its intention to continue support of research to determine the function of all genes in the model plant Arabidopsis thaliana by the year 2010. This represents a continuation of the Arabidopsis genome research initiative BIO has supported since 1990 and of the 2010 Project begun in FY 2001.

The entire DNA sequence of Arabidopsis thaliana was completed at the end of 2000. For the first time, we know the sequence of all genes necessary for a flowering plant to function.   Based on the continued genome annotation efforts, the number of protein-encoding genes in the Arabidopsis genome currently exceeds 28,000. As a follow-up to the Arabidopsis genome sequencing efforts, and to take full advantage of the opportunities created by them, the community of plant biologists has proposed an important and revolutionary new initiative to determine the function of all genes of a reference species within their cellular, organismal and evolutionary contexts by the year 2010 (the 2010 Project). Details can be found at https://www.nsf.gov/cgi-bin/getpub?bio011 and http://www.arabidopsis.org/info/workshop2010.jsp. In response, the Directorate for Biological Sciences has established the 2010 Project as a Directorate-wide activity.

As with the original Multinational Coordinated Arabidopsis thaliana Genome Research Project, research on functional genomics in Arabidopsis is an international effort. The Multinational Arabidopsis Steering Committee has issued a long-range plan in a report, "The Multinational Coordinated Arabidopsis thaliana Functional Genomics Project: Beyond the Whole Genome Sequence". The report is posted at https://www.nsf.gov/pubsys/ods/getpub.cfm?bio0202. This was followed by annual reports updating the progress and goals of this international effort (see https://www.nsf.gov/bio/pubs/reports/masc_annual_june03.pdf and http://www.arabidopsis.org/info/2010_projects/MascReport2ndEdition.pdf for the 2003 and 2004 reports).  These reports identify several areas of research and resources that are needed urgently for sustaining rapid progress in Arabidopsis functional genomics.

One of the factors that contributed to the success of the Multinational Coordinated Arabidopsis thaliana Genome Research Project was worldwide collaboration among the researchers involved. The Arabidopsis research community has become a model for international research collaboration. It is expected that continued efforts by the international community of scientists would be essential for the success of the 2010 Project. NSF will continue to foster activities to advance international collaboration and coordination of the 2010 Project.

The 2010 Project is distinct from the Plant Genome Research Program. The Plant Genome Research Program will not consider proposals in which Arabidopsis is the primary research focus. The 2010 Project is also distinct from existing disciplinary programs in the Directorate for Biological Sciences and is not meant to be an alternative source of funding for all proposals involving Arabidopsis. Proposals investigating the function of individual genes or small families of genes and proposals addressing specific biological questions using Arabidopsis as a model system should be submitted to the appropriate disciplinary program (See https://www.nsf.gov/bio/ for description of various BIO programs.)

Projects that are not responsive to this program solicitation or are inappropriate for funding under the 2010 Project may be transferred to an appropriate disciplinary program, or returned without review if such transfer is deemed inappropriate.

In FY 2005, the 2010 Project will focus on the following two activities:

1. Determination of gene function of a network or a large group of genes with special emphasis given to gene networks underlying biological functions as well as to the genes of unknown function, and

2. Development of research tools and resources.

In both types of projects high throughput and cost-effective approaches will be encouraged.  Although these two areas are the focus of the FY 2005 competition, all imaginative and/or innovative proposals will be considered as long as they are justified on the basis of the goal of the 2010 Project.

While keeping in mind the emphasis as described above, proposers are strongly encouraged to consult the scope of the awards in the previous years of the 2010 Project Program (see the lists of previous awards at https://www.nsf.gov/bio/pubs/awards/2010awards.htm), as well as the projects funded elsewhere in the world including the German Arabidopsis Functional Genomics Network Program (http://www.uni-frankfurt.de/fb15/botanik/mcb/AFGN/AFGNHome.html) and GARNET (the genomic Arabidopsis Resource Network in the U.K. (http://www.york.ac.uk/res/garnet/garnet.htm). Proposers are further encouraged to coordinate proposed activities with funded projects prior to submission of new proposals. If activities similar to an already funded project are to be proposed, the proposal must describe clearly a mechanism to coordinate with ongoing activities as well as a rationale based on benefits to the overall goal of the 2010 Project. NSF encourages participation of investigators and institutions that have not been involved in the previously funded 2010 activities.

In addition to research, this Program will support workshops, summer courses and other outreach/training activities designed to educate and train a broad community of scientists and students in unique scientific opportunities and approaches afforded by the 2010 Project.

Determination of gene function:

Individual investigators, or groups of investigators, will be supported to conduct creative and innovative research designed to determine, using all available means, the function of a specific set or network of genes in Arabidopsis thaliana of the investigator's interest and choice. The number of investigators involved in a single proposal should be determined by the scope and approach used in the proposal. The NSF expects that both large and small laboratories should be able to participate in the 2010 Project by taking advantage of various publicly available genomic tools and resources, such as knockout mutants and cDNA clones.

During FY 2005, emphasis will be placed on: 

• Identification and analysis of function of networks of genes that underlie plant processes. Special consideration will be given to proposals describing innovative approaches to dissect nodes in network(s) and for integration of computational modeling with experimentation.
• Understanding roles of the genes with currently unknown functions: Many Arabidopsis genes encode many plant-specific proteins with no known function. Imaginative projects using high throughput methods for identifying functions of these genes will be given higher priority for funding than the projects that experimentally demonstrate functions of genes with fairly certain putative functions (based on homology).

Investigators are expected to have selected a set of genes as the subject of their research prior to the submission of a proposal. These genes must be identified in the proposal by GenBank accession number or by other identifiers from a publicly accessible database. The size of the selected gene set will depend on a number of factors, such as how the particular set was selected (e.g., based on a specific sequence motif or a set of genes expressed under a specific condition), and the interest and throughput capacity of the proposer. During FY 2005, higher priority will be given for the proposals that include large gene sets and use high throughput methods in functional analyses than is used in traditional research projects. Projects that focus on small numbers of genes, those that depend on existing low throughput methods, or proposals addressing specific biological questions using Arabidopsis as a model system are more appropriate for the disciplinary programs at NSF. During the FY 2005 competition of the 2010 Project, priority will be given to proposals to study genes unique to plants and to study genes not being studied in other currently funded Arabidopsis functional genomics projects. Genes being investigated by the previous 2010 Project awardees are publicly posted on an individual 2010 project's website, addresses of which can be found in the award abstracts available through the award lists (https://www.nsf.gov/bio/pubs/awards/2010awards.htm). 

For required items to be included in the proposal please see "Project Description" section below.

Development of research tools and resources:

While the genome sequence and annotation information in public databases, microarray expression data at public websites, and a variety of biological resources at the Arabidopsis Biological Resource Center provide a good start for the community to begin the 2010 Project, NSF recognizes that additional tools and community biological resources are needed to enable individuals or groups of individuals in the scientific community to participate in the 2010 Project. As in previous years, proposals to build necessary and critical tools and resources will be supported in FY 2005. Special consideration will be given to:

• New informatics tools that allow individual investigators to access, analyze, and utilize the vast amounts of rapidly accumulating data on Arabidopsis. Proposals are especially encouraged that enable individual researchers to query available resources to determine the function of genes.
• Also encouraged are proposals to design and provide bioinformatics and experimental tools to facilitate the study of genes of unknown function.
• New technologies that allow high throughput analyses of large sets of gene products and/or mutants, including projects that include innovative informatics, engineering developments and biological tools and approaches. 

Proposals for developing community resources must have a clear focus on service, and should not include research on the materials or information to be produced. No selected group including the Principal Investigator (PI's) should have priority access to the resources/tools to be produced for general community use.

For required items to be included in the proposal please see "Project Description" section below.

Additional considerations:

Broadening participation: As in all other NSF programs, investigators are expected to integrate research and education in proposals submitted to the 2010 Project. Activities that promote participation of under-represented and under-served groups, including investigators at small institutions, minority serving institutions, and community colleges are especially encouraged.

Coordination among projects: If research on the chosen set of genes is already funded in another NSF 2010 award or in similar functional genomics programs in other countries (http://www.arabidopsis.org/info/2010_projects/index.jsp), the PI should provide a plan for coordinating activities with the funded project. If two or more proposals with substantially overlapping goals and scope remain in consideration for funding after initial merit review, the PIs of those proposals may be asked to collaborate, and to submit a coordination plan prior to the final funding decision.

International opportunity: The 2010 Project encourages laboratory-to-laboratory interactions between US and foreign laboratories whenever such opportunities exit. NSF 2010 Project funds may be requested to support foreign investigators and students to work in US laboratories and for US investigators and students to work in international laboratories. However, foreign counterparts should secure support for their projects from their own national programs. A list of Arabidopsis functional genomics projects in other countries can be found at http://www.arabidopsis.org/info/2010_projects/index.jsp.

Intellectual property: When the project involves the use of proprietary data or materials, any data or materials resulting from NSF-funded research must be made promptly available, without any restrictions, to the users of such data or materials. It should be noted that prospective awardee institutions may be requested, prior to an award decision, to submit copies of any intellectual property agreements or material transfer agreements that any of the key project personnel have signed, or are planning to sign, that would impact the unrestricted and timely distribution of the outcomes of the NSF-funded research. Only NSF officials will review this material. In the case of a multi-institutional proposal, the lead institution will be responsible for coordinating and managing the intellectual property resulting from the 2010 Project award.

Industrial interactions: NSF recognizes that some of the resources and technologies needed to address the next set of challenges in Arabidopsis functional genomics exist in industry and encourages the use of their services if it would result in cost-savings and more rapid progress of the project. Such arrangements are likely to involve purchase of resources or services from industry, and must be without any restrictions on the distribution of the resources to other researchers or on depositing information and physical resources in The Arabidopsis Information Resources (http://www.arabidopsis.org/) and The Arabidopsis Biological Resources Center (http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/abrchome.htm), respectively. In these cases, the usual procurement procedures and rules of the grantee institution will be followed. Another mode of industrial interactions may involve sharing of knowledge, services and resources without any transfer of NSF funds to the industrial partner. The key to successful public-private collaboration is participation of both sides as equal partners by bringing their own resources to the project and sharing the results openly and quickly with the rest of the community. In such interactions, all details should be clearly stated in the supplementary materials, including the credit and advantages for the private sector investigators.

Proposals are invited from US academic institutions, US non-profit research organizations including museums, research laboratories, professional societies and similar organizations in the US that are directly associated with educational or research activities, and consortia of such organizations with appropriate research and educational facilities. The eligibility criteria apply to both the main and sub-awardees.

PI Eligibility Limit: None Specified.

Limit on Number of Proposals: None Specified.

It is anticipated that approximately $13 million will be made available for an estimated 15 awards in FY 2005, contingent upon the quality of proposals received and the availability of funds.

The award size for proposals to determine gene function will range widely and may be up to $1 million per year for up to 4 years. Proposal budgets should be based on the realistic assessment of resources necessary to accomplish the stated proposal goals. Proposals with large budgets are expected to determine the function of a large number of genes.

The award size for proposals to build community resources may be up to a total of $3 million for 2 years. Budget requests must be justified in relation to the proposed activities. Budget requests larger than the above guidelines will be considered if justified well.

Funding decisions are anticipated by the end of July 2005, with awards expected to start in September 2005. Awards will be made either as grants or cooperative agreements.

Proposals must be submitted by FastLane (see "FastLane Submission" section below) and must follow guidelines described in the GPG. The following additions or modifications apply to proposals submitted to this Program:

Proposal Cover Sheet:
In the NSF FastLane system, follow instructions on proposal preparation. When completing the Cover Sheet, click on the GO button at "Program Announcement / Solicitation / Program Description No." Highlight 2010 Project, and click on the Select button. Your proposal will automatically be assigned to BIO - 2010 Project. You must then "Go Back" to the Cover Sheet Components Form and complete the remainder of the cover sheet.

BIO Proposal Classification Form (PCF):
Complete the BIO PCF, available on the NSF FastLane system. The PCF is an on-line coding system that allows the Principal Investigator to characterize his/her project when submitting proposals to the Directorate for Biological Sciences. Once a PI begins preparation of his/her proposal in the NSF FastLane system, selects any cluster within the Directorate for Biological Sciences as the first (or only) organizational unit to review the proposal, and saves the cover sheet, the PCF will be generated and available through the Form Preparation screen. Additional information about the BIO PCF is available in FastLane at http://www.fastlane.nsf.gov/a1/BioInstr.htm .

Project Summary (1 page):
The project summary should consist of three parts in the following order: 

1. A list of senior personnel (PI, Co-PIs, and Key Collaborators) along with their home institutions; 
2. A summary of the proposed project in 200 words or less.  Principal Investigators must state in the very first sentence of the Summary whether the proposed work pertains to: 

(1)  Determination of gene function for a network or group of genes 

OR

(2)  Development of research tools or resources for the community. 

3. Broader Impacts of the proposed research project in 200 words or less. 

Please note that a project summary that does not include both scientific goals and the expected broader impacts will be returned without review.  Detailed explanation can be found at https://www.nsf.gov/pubsys/ods/getpub.cfm?iin127

Project Description (maximum 15 pages including figures and tables):
In addition to the standard description in GPG, the following guidelines must be followed: 

• Results from Prior NSF Support (up to 5 pages): Only the most relevant prior awards should be included in this section for any of the PIs and Co-PIs listed in "Project Summary".
• Justification: Briefly explain how the proposed activities meet the goals of the 2010 Project. 
• For proposals aimed at determining the function of a network of genes, the following information must be included in the project description: (1) a list of genes to be studied identified by their accession numbers in GenBank or other identifiers in a publicly accessible database. If the list is long, this can be attached as an appendix outside of the 15 page limit [See Special Information and Supplementary Documentation A-1 below]; (2) why and how those genes were selected; (3) experimental plans to determine their function, including the level at which the functions are determined, e.g., the molecular/protein, biochemical, cellular, or higher levels; (4) how the investigators plan to add their results to the community-wide effort to update and add value to the primary sequence information in GenBank; and (5) a projected timetable for accomplishing the stated proposal goals. If research tools and resources such as mutants and global expression data are produced during the course of the proposed project, the proposal should describe a plan for their public release and coordination with the existing distribution mechanisms. 
• For proposals aimed at building research tools and resources for the Arabidopsis functional genomics community, the following information must be included: (1) a list of deliverables including necessary informatics tools; (2) experimental plans to develop the resources/tools including mechanisms of quality assessment; (3) project timetable; (4) detailed plan for public release of the resources/tools; (5) any conditions to be placed on users, e.g. material transfer agreement; (6) if applicable, list related, ongoing activities in the US as well as elsewhere in the world so as to maximize the efficiency and the usefulness to the research community. Coordination mechanisms can be provided as an appendix outside of the 15 page limit. [See Special Information and Supplementary Documentation A-3 below]); and (7) a plan to maintain and distribute the resource after NSF support has ended. It should be noted that resources (biological materials, software, etc.) produced with the support of NSF must be made available as soon as their quality is checked to satisfy the specifications described in the proposal and approved by reviewers. Further, they must be made available to all segments of the scientific community. Budgeting for short-term and long-term distribution of the project outcomes needs to be described in the proposal. A reasonable user charge is permissible, but the fee structure must be clearly outlined in the proposal. If accessibility differs between industry and the academic community, the differences must be clearly spelled out. It will be permissible to use a qualified commercial operation for long-term maintenance and distribution of the project outcome, if appropriate; however, such an arrangement should be made clear in the proposal. 
• The broader impacts of the proposed activities should be described [See "NSF Review Process" below for examples of "broader impacts"] Plans for integration of research and education must be described within the context of the proposed activity.  

Proposal Budget:
Provide a summary budget and a yearly budget for the duration of the proposed project. When subawards are involved, summary and yearly budgets are required for each subaward. A Budget Justification should be provided for both the proposer and any subawardees. Institutions that do not meet the eligibility criteria described above may not participate as subawardees. The 2010 Project program is fully committed to provide sufficient funds to complete any project it supports. A careful and realistic budget will add to the overall strength of a proposal. Funds for facility construction or renovation may NOT be requested. It is expected that foreign collaborators’ projects will be supported by their national sources. NSF funds may be used for US investigators, postdoctoral fellows and students on exchange visits to their foreign collaborator's laboratory or to cover expenses associated with hosting foreign collaborators in the US investigators laboratory.

Special Information and Supplementary Documentation:
Include the following materials, if applicable, in addition to the 15 page Project Description. Additional materials should be clearly labeled and included in the Supplementary Documents section of FastLane.

(A-1) List of genes to be studied (no page limit):
If the proposal is to determine the function of a network of genes, a list of genes to be studied must be included. Each gene must be identified by its accession number in GenBank or other identifiers in a publicly accessible database. Provide this information in a tabular form, using a font size no smaller than 10 point. Inclusion of the list is needed to ensure avoidance of unnecessary overlap and to facilitate interactions among Arabidopsis researchers. Consequently, if the proposal is funded, the PI will be required to have a website specific to the 2010 project and make the list available on the site. NSF recognizes that functions and interactions of additional genes will be discovered during the progress of the research and the PI is expected to update the list of genes on the project web site. 

(A-2) Management Plan (maximum 3 pages):
Each proposal involving 4 or more PIs (1 PI and 3 Co-PIs) OR with PIs/Co-PIs from 3 or more different institutions, OR proposing to develop community research tools and resources must provide an additional description of the management plan for coordinating activities of the group or the management of the service aspect. This description should include plans for internal means of communication, coordinating data and information management, evaluating and assessing progress, allocating funds and personnel, interacting with users in a service project, and other relevant issues specific to the proposed activities. The overall project leader (normally the PI) must be identified and his/her role should be described. Change of project leader will require prior NSF approval. For complex projects, appointment of a project manager/administrator in addition to the PI(s) is strongly encouraged. The exact time commitment of each key member to the project should be indicated in the management plan, regardless of whether any of his/her salary has been requested from NSF. A project timetable with yearly goals should be included for all projects, regardless of the number of personnel involved.

(A-3) Coordination with Outside Groups (maximum 3 pages): If the proposed activity is part of a national or international collaborative project including public-private partnerships, describe the relationship of the proposed activity to the overall collaborative project and how the components will be coordinated. If a project similar to the proposed project (e.g., either addressing the same set of genes or producing the same kind of community resources) is already supported elsewhere, a coordination plan is mandatory.

(A-4) Color Images: Be advised that NSF cannot accommodate the printing of color images as part of proposal submission through the FastLane system, and submitted proposals that require the use of color or of very high resolution photographic images will necessitate additional steps.

Provide only the allowable and applicable items as noted in the GPG. Include the materials in the FastLane submission by transferring them as PDF files through the "Supplementary Docs" module of the FastLane system.

Single-Copy Document(s):

A "conflict of interest" list must be included as an "additional single-copy document" at the time of FastLane proposal submission. This document must be in the form of a single alphabetized table  that includes full names of all conflicts of interest for all senior personnel (PI and Co-PIs) as well as for any named personnel whose salary is requested in the project budget. Conflicts to be identified are (1) PhD thesis advisors or advisees, (2) postdoctoral advisors or advisees, (3) collaborators or co-authors for the past 48 months, and (4) any other individuals or institutions with which the investigator has financial ties (please specify type).

An alphabetized list of suggested reviewers can be submitted through the single-copy document module of FastLane.  

Proposals that are not compliant with the guidelines may be returned without review.

Proposal Checklist:

NSF again stresses the importance of reading the program solicitation and GPG, and following the guidelines and requirements before the SPO submits the proposal through FastLane. Below is a checklist of items that, if not compliant, will most likely result in proposals being returned without review. This is not meant to be an exhaustive checklist. It is the submitting organization's responsibility to ensure that the proposal is totally compliant with the applicable guidelines.

• Project summary is one page and consists of the three required parts.
• Project description is no more than 15 pages including tables and figures, using the correct font size and margin as required by GPG. (It might be useful to print the submitted proposal from within the FastLane module to check for font size and margins because Acrobat-pdf conversions may cause changes in the NSF-viewable version of your proposal.)
• Biographical sketches for all personnel listed on the project summary page are included, and each is no longer than 2 pages and follows the format in the GPG.
• Current and pending support information is provided for all personnel listed on the project summary page.
• Budget and budget justifications – yearly and summary budgets with a budget justification of no more than 3 pages: the same applies to any subaward budget.
• Supplemental documents – All applicable and/or required items included. No unallowable items (e.g., letters of general endorsement or reprints) should be included.
• Conflict of interest list conforms to the required format and is submitted through the single-copy document module of FastLane.
• No extraneous materials are included.

January 21, 2005