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Proposal Guidance for EMSL-JGI FICUS Program

Updated January 2025

This guidance applies to the FICUS EMSL-JGI call.

This guidance is for authors submitting a full proposal in response to the FICUS EMSL-JGI call. Full proposals for these calls may only be submitted by invitation following a successful letter of intent (LOI). Applicants should read the following guidance carefully. Failure to comply with the requirements will result in proposals being returned without review. Not following current FY 2026 guidance or uploading prior templates is considered failing to comply.

Proposals must be submitted electronically through the EMSL User Portal. The online form for full proposal submission will require the same information as the LOI (see LOI Guidance), and these fields will be prepopulated with the information provided in your LOI. All previously entered information from the LOI can be modified as needed.

The online form for full proposal submission will contain a new “Resources” section for detailed information about requested EMSL resources. Researchers preparing proposals are encouraged to contact or continue discussions with scientific staff at the facilities regarding their research goals and resource needs. For help identifying the appropriate contacts, see the contacts identified in the proposal call announcement or contact User Program Services.

1. Enter the required information in the EMSL User Portal

The following information must be entered into the online form in the EMSL User Portal (NEXUS):

  • Proposal Type (Open Calls > Call Name)
  • EMSL Science Area that best fits your proposed research. Please do not select “Other.”
  • Primary Research Category (drop-down options provided)
  • Title
  • Abstract (~400 words)
  • Proposed Research (uploaded PDF document; use only the Full Proposal Template below)
  • EMSL staff member(s) included in proposal discussions
  • Participant Details (name, profession, email, institution, ORCID iD, etc.)
  • Funding for Each Participant
  • EMSL Resources. This section will request details about resources needed. Select the EMSL-specific resources needed for the project from the drop-down list and provide the requested details for each. If you do not know all the specific resources needed, contact User Program Services for assistance.
  • Samples/Equipment

2. Prepare and upload the Proposed Research document

Please use the FY 2026 FICUS EMSL-JGI Full Proposal template to view the instructions for formatting guidelines and draft the proposed research document. These guidelines are updated annually, and requirements may change from year to year.

A detailed description of the proposed research and the appendices need to be uploaded to the online portal as a single PDF file and should contain the required and requesting parts described below:

  • Project Description (required). The Project Description should provide details about the proposed research including the title, scientific questions and specific objectives, mission relevance, background, and approach or work plan. Detailed guidance is provided below and in the Full Proposal template. This section is a maximum of 10 pages.
  • Supporting Materials (optional). Up to an additional 10 pages for figures, charts, and graphs to support the proposed research above. Ensure that your materials are oriented in portrait (vertical) compared to landscape (horizontal) to assist in the review of your submitted proposal.
  • Appendix 1: List of References (required). Each reference must include the names of all authors (in the same sequence in which they appear in the publication), the article and journal titles, book title, volume number, page numbers, and year of publication. If the document is available electronically, the website address also should be identified. Proposers must be especially careful to follow accepted scholarly practices when providing citations for source materials when preparing any section of the proposal. This section does not have a page limit but must not be used to provide parenthetical information outside the 10-page Project Description.
  • Appendix 2: CVs (required). Provide abbreviated CVs for the PI and each co-PI (2-page maximum per person). CVs are not required for participants identified as “Team Members.”
  • Appendix 3: Active Collaborators List (required). Provide a list of active collaborators and individuals who may represent a conflict of interest for the PI and co-PI(s) from the past 2 years.
  • Appendix 4: Resources for eBERlight Advanced Photo Source (if proposed). Complete the template if requesting APS resources with the requested number of samples.
  • Appendix 5: Resources for Bio-SANS (if proposed). Complete the template if requesting HFIR Bio-SANS through CSMB; describe the groups of samples that share the same characteristics.
  • Appendix 6: Resources for EMSL (if proposed). Fill out the table with details about your samples, including the specific resources or instruments being requested at EMSL. For EMSL’s purposes, a sample is any material intended to be analyzed or used with EMSL resources.
  • Appendix 7: EMSL Computing Approach (if proposed). Provide a written description of the proposed computational method or approach and the software to be used (1-page maximum). Then, complete the subsequent Computing Resource Request form including utilization guidance provided at the end of the form.
  • Appendix 8: Resources for Joint Genome Institute (if proposed). Complete the table of resource requests and sample information. The table will include the total number of samples to be sent, as well as product type and details for each organism or environmental sample being submitted.
  • Appendix 9: Resources for National Ecological Observatory Network (if proposed). If you are proposing to use soils from the NEON Biorepository, you must also include a letter of support from NEON for the specific samples.
  • Appendix 10: Letter of Support (optional).

Note: If you are unsure about how to fill out the resource requests, reach out to the specific resource contacts in the proposal call announcement  at least two weeks prior to the submission deadline. They will work with you regarding the specific needs for your research aims. Failure to complete the table correctly will affect your proposal’s resource score, and insufficient details justifying your request can impact the review panel discussions.

Document Formatting Requirements

  • Pagination is required for full upload. There is a 10-page limit to the Project Description with the advised word limits. 1-inch margins are necessary.
  • An additional 10 pages of supporting materials are allowed, such as charts, graphs, and figures.
  • 10 appendices (2 required, 6 if proposed, and 2 optional). Word limits apply for certain parts.
  • 11-point fonts (or larger for headings). Captions, symbols, and special characters can have a font size of less than 11 points.
  • No more than 5 lines of text within a vertical space of one inch and single-column format for text.

Project Description (limit to 10 pages, excluding charts, graphs, and figures)

The Project Description should be written at a level appropriate for someone familiar with your general area of research who is not necessarily an expert on the specific topic. Refer to the review criteria on the proposal call announcement to assist in targeting your research description. The abstract submitted in the web-based proposal form does not count against the 10-page limit and should not be repeated in your Project Description.

  • Title. The project title must be brief, scientifically or technically valid, intelligible to a scientifically or technically literate reader, and suitable for use in the public press.
  • Scientific Questions and Specific Objectives (~700 words). Describe the scientific question(s) being addressed. State the specific objectives of the research proposed (e.g., to test a stated hypothesis, create a novel design, solve a specific problem, challenge an existing paradigm, address a critical barrier to progress in the field, or develop new technology), providing concise and unambiguous details.
  • Mission Relevance (~700 words). Clearly explain how your research addresses this call’s relevance to the listed call topics and describe the value/impact of its economic or societal importance.
  • Background (~400 words). Provide a concise discussion of previous work to make clear what the research problem is, why you want to do this study, and exactly what has been accomplished and to demonstrate why the studies need to be continued.
  • Approach or Work Plan (~1200 to 1500 words). Describe the work to be conducted, along with any preliminary data, background measurements, or tests completed that validate the approach. Address the strategy for preparing and delivering samples to relevant facilities, providing approximate shipping dates to each facility. For EMSL resources, provide a short description of planned data analyses relevant for the proposed work, indicating which aspects would require EMSL assistance. If your research includes computation, describe what EMSL capabilities and expertise you will need and how those capabilities complement your own. Refer to the JGI sample preparation requirements for details on quantity and quality of material required for each product type. If JGI requests are proposed, additionally include the following information depending on what is requested:
    • For proposals including a sequencing component, specific technical details describing how the sequencing should be carried out are not necessary. If your proposal is accepted, JGI staff will work with you to define the sequencing scope in detail based on current capabilities and technologies, which are constantly changing. Include expectations from JGI beyond generating the raw sequencing reads and output from JGI’s standard analysis pipelines, along with justifications for the additional support.
    • For proposals requesting metabolomics, please specify metabolic hypotheses that motivate the analyses, including target classes of metabolites, ideally specific target metabolites, and total numbers and types of samples (including replicates).
    • All proposals including a synthetic biology component must describe the biosecurity, biosafety, biocontainment, and environmental aspects of the proposed research in Appendix 8 (resource request), including both the current aspects and the long-term implications of the work (desirable or otherwise). This information will be critically assessed during JGI’s Synthetic Biology Internal Review process, and missing or incomplete information will jeopardize consideration of the proposal.

Contacts

For questions about the proposal submission process, please contact User Program Services.

For technical help with NEXUS, please contact NEXUS Support.

For technical and scientific questions: Refer to the proposal call announcement for scientific contacts at each partnering facility.