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Proposal Guidance for EMSL-JGI FICUS Program

Updated December 2023 

This guidance is for authors who have been invited to submit a full proposal for FICUS research with EMSL and JGI, and program partners (APS, CSMB, NEON), following review of their Letter of Intent. Proposals must be submitted electronically through  the EMSL User Portal. The deadline for the EMSL-JGI FICUS full proposal submission is 5 p.m. Pacific Standard Time on May 2, 2024.  

Submitters whose Letter of Intent has been accepted for full proposal submission should: 

  1. Navigate to the portal and click on “LOI XXXXX invited to start full proposal” 

  2. Click on “Start full proposal”. 

  3. Fill in an online form and upload a research document in the portal as part of the submission process. Please save your changes before moving to next submission field. Submissions can be edited in the online form till the full proposal deadline. The uploaded research document can be updated but the most recent version is saved. For more information on these sections, see below.  

  4. The online form will be pre-populated with information you provided in your LOI. Most of the previous information from the LOI can be modified if needed before submitting your proposal.  You can save your work and log-in later to submit your proposal. However, the system saves the most recent pdf file uploaded. If you have multiple versions of your proposed research document, please make sure that the most recent upload is the final version. 

  5. The online form will contain a new 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.  

Information required for Online Form 

The list below summarizes the information required for a proposal submission, to be entered into the online form in the User Portal

  • Pre-populated fields from LOI that should not be edited: Proposal Type, Science Area, Requested Start Date, Estimated End Date, Primary Research Category  

  • Title and Abstract. An abstract (~ 500 words) needs to be submitted through the online portal. It is not required in the project description document below. Titles and abstracts of successful non-proprietary projects will appear on the EMSL website and be shared with the Department of Energy’s Office of Science.  

  • Proposed research description (uploaded PDF document; see instructions below).  The system saves the most recent pdf file uploaded. If you have multiple versions of your document, please make sure that the most recent upload is the final version.  

  • Need of EMSL staff assistance in obtaining and interpreting results 

  • Whether proposal has been discussed with any EMSL staff member (Type name to select from drop-down menu) 

  • Participant details (name, institution, ORCID ID, etc.)  

  • Funding sources  

  • EMSL Resources. This section will request details about resources needed. If you know specific resources needed for the project, select them from the drop-down list and provide the requested sample details for each. If you do not know all the specific resources you will need, describe the type of measurements and analyses desired. The details you provide will help our staff determine which instruments will best serve your research goals.  

  • EMSL Samples/Equipment: The section will request safety-related details about any samples and equipment that you plan to bring to EMSL. This section will also request Proposed Sample Groups being planned to be sent to EMSL.  

  • Terms 

Proposed Research Description  

A detailed description of the proposed research and the appendices need to be uploaded to the online portal as a single PDF file. Please use the Full Proposal Research template to view the instructions for formatting guidelines and draft the proposed research description document. These guidelines are updated annually, and requirements may change from year to year. The formatting guidelines and full proposal research document template description are also provided below.  

Document Formatting   

  • Pagination is required. There is a 10-page limit to the Project Description. 1-inch margins necessary. 

  • Additional 10 pages of supporting materials allowed, such as charts, graphs, and figures. 

  • 11-point fonts (or larger for headings). Captions, symbols, special characters, can have a font 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) 

Describe your research plan for using resources at the requested facilities (maximum of 10 pages). Suggested word counts are given for each section.    

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.  

  1. 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. 

  2. 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. 

  3. Mission Relevance (~700 words): Describe the relevance and impact of this project to DOE’s Office of Biological and Environmental Research mission areas, as well as EMSL, JGI, and other partners’ missions (as relevant), and its economic or societal importance. 

  4. 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, exactly what has been accomplished, and demonstrate why the studies need to be continued.   

  5. 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 (include references where relevant and attach the full citations as an appendix). Address the strategy for preparing and delivering samples to relevant facilities, providing approximate shipping dates to each facility. Refer to the JGI sample preparation requirements for details on quantity and quality of material required for each product type.   

  6. For JGI (if proposed) requests: 

  1. 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, 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.  

  2. For proposals requesting metabolomics, please specify metabolic hypotheses that motivate the analyses, including target classes of metabolites, ideally specific target metabolites, and total number and types of samples (including replicates). 

  3. All proposals including a synthetic biology component must describe the biosecurity, biosafety, biocontainment, and environmental aspects of the proposed research in Appendix 2 (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 the JGI's Synthetic Biology Internal Review process, and missing or incomplete information will jeopardize consideration of the proposal.  

B. Appendices (Not counted under page limit. Appendices 1-3 are compulsory; Appendices 4-6 as relevant to resources requested in proposal. Appendix 7 is optional) 

As part of the Proposal Description PDF file, include the following appendices in the order listed below.  

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 title, 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 in providing citations for source materials relied upon when preparing any section of the proposal. While there is no established page limitation for the references, this section must include bibliographic citations only and must not be used to provide parenthetical information outside of the 10-page Project Description.   

Appendix 2: CVs (required)   

Attach abbreviated CVs (2-page maximum each) for the PI and each of the co-PIs to support the review of the team's qualifications for the research proposed.   

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. Use the template provided

Appendix 4: JGI Resources (if proposed)  

Complete table of resource requests and sample information (see Full Proposal Research template). 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 5: Computing Resources (if proposed)  

Complete the two sections (see Full Proposal Research Template) that include (i) a 1-page description of computing resource description and, (ii) Computing Resource template detailing the proposed computational method or approach, the software or code to be used, and details about the requested computing resources, file storage, and staff support needed.  

Appendix 6: Bio-SANS Resources (if proposed) 

Complete the template if requesting HFIR Bio-SANS through CSMB, describe the groups of samples that share the same characteristics. 

Appendix 7: Letters of Support (optional) 

Note: If you are unsure how to fill out the resource requests, reach out the contacts listed below at least two weeks prior to the 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. 


For general questions: EMSL User Services,, 509-371-6003  

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