Proposal Deadline
September 30, 2018

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Proposal Guide


User Proposal Overview

Access to the Foundry requires an approved user proposal. There are several types of proposal available but Standard is the most common. Proposals are submitted through the User Portal and undgergo peer review.

All proposals specify one of the Foundry’s seven research Facilities as the Lead Facility. Most proposal types (excluding Sample-only) also allow users to request access to additional Support Facilities. Approximately 60% of successful Foundry proposals are multi-facility, and users should include requests for all the facilities they need to execute their proposed project. Users should only request the resources they are likely to use in the course of a given proposal and must provide a clear scope of work for each facility requested.

Accepted proposals must be activated before users start work. Prior to activation, one of the users on the proposal must complete a safety questionnaire, which is then reviewed and must be approved by the Foundry Safety Manager. Activation also requires execution of separate User Agreements between Berkeley Lab and each of the home institutions of users included on the proposal.

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User Proposal Types

The following types of proposal are available.

Proposal Type

Maximum Duration


Submission Period


1 year

Full proposal with access to multiple facilities. May be designated a Follow-on Proposal if it is continuation of previous work.

Two annual calls (March and September)

Rapid Access

4-6 months

Short-term projects for time-sensitive research with high potential impact.  

Outside of Standard Proposal call and review periods

Instrument Only

6 months

Limited to one or two instruments with downtime available

Outside of Standard Proposal call and review periods

Sample Only


Single transfer to user of a previously developed material

Any time

Partner User

2 years+

Special partnership projects with broader scope and/or longer time frames than Standard projects, that include contributions to the User Program.

Any time

Note that extensions to activation deadlines and project duration can be requested to accommodate parental leave, medical leave, and other circumstances. Contact the User Office to request an extension.

Standard Proposals

Standard proposals are the most common type of Foundry proposal. Standard proposals can be submitted during the two calls for proposals each year, with submission deadlines of March 31 and September 30.  The review process for Standard proposals is typically completed 6 weeks after the submission deadline.

Standard proposals must be activated within a year of approval and can remain active for up to one year from the date of activation. Continuation of the work requires a follow-on proposal.

See examples of high-scoring Standard proposals.

Standard proposals are subject to requirements for User Agreements and Safety Review.

Follow-on (Standard) Proposals

If more than one year is required to achieve the scientific goals of a Standard proposal, the user may submit a follow-on proposal. Follow-on proposals are submitted during the call for Standard proposals and use the Standard proposal form. They undergo the same peer-review process as all other Standard proposals.

Follow-on proposals must be submitted and approved before the end of an active proposal in order to avoid interruption in access.

Follow-on proposals are subject to requirements for User Agreements and Safety Review.

Rapid Access Proposals

Rapid Access proposals provide an accelerated pathway to Foundry access, outside of the biannual calls for Standard proposals. A limited number of Rapid Access proposals are accepted in each proposal cycle, and priority is given to time-sensitive research with high potential impact, and with direct relevance to the Foundry’s research themes. The Foundry User Office ( can offer preliminary feedback on whether Rapid Access is appropriate for a given proposal.

Rapid Access proposals can be submitted at any time except during the Standard proposal submission and review periods, and undergo an accelerated review, typically completed in 2-4 weeks. A successful Rapid Access proposal must be activated within a month of approval and may remain active until the end of the following review cycle for Standard proposals. Continuation of the work past that date requires that the users submit a Follow-on proposal during the call for Standard proposals.

Rapid Access proposals are subject to requirements for User Agreements and Safety Review.

Instrument-Only Proposals

Instrument-only proposals are suitable for projects that require limited access to one or two Foundry instruments on which users are already trained.  Not all instruments are available for Instrument-only proposals, and users should check with Facility staff to determine if a given instrument is available.

Instrument-only proposals are accepted and evaluated continuously throughout the year, except during the calls for Standard proposals. Instrument-only proposals receive accelerated review, typically completed in 2-4 weeks.

Instrument-only proposals are subject to requirements for User Agreements and Safety Review.

Sample-Only Proposals

Sample-only proposals are requests for materials already available or regularly synthesized at the Foundry, such as routinely generated peptoids or quantum dots. These projects receive accelerated review for feasibility and merit by the Foundry Directorate. Sample-only proposals may be submitted at any time and are evaluated continuously throughout the year.

An executed Materials Transfer Agreement (MTA) is required prior to project activation and shipment of samples, in place of the usual User Agreement.

Available materials

Materials that may currently be available are listed below. Contact the User Office for more information about these or other materials.

  • Luminescent inorganic nanocrystals: Upconverting nanoparticles (ref 1, ref 2); Semiconductor quantum dots (ref 1)
  • WO3 nanorods (ref 1)
  • LaB6 nanoparticles (ref 1)
  • PEDOT-based hybrid thermoelectric materials (ref 1)
  • Mg/graphene oxide nanocrystalline hydrogen storage materials (ref 1)
  • Inorganic perovskite crystals (ref 1)
  • Quinoidal low band gap conjugated polymers (ref 1) More examples of structures and related references available on request.
  • Small molecule electron donors and acceptors (ref 1, ref 2)
  • Porous organic materials, including covalent organic frameworks, graphitic porous materials (examples of structures and related references available)
  • Polyelectrolyte binders (ref 1)
  • Nanosheet-forming peptoids (ref 1)
  • Peptoid diblock copolymers (ref 1, ref 2)
  • Lipitoid 1 (peptoid transfection reagent) (ref 1)
  • Plasmids and bacterial strains for expression of electron transfer proteins, i.e. multiheme cytochromes (ref 1, ref 2, ref 3, ref 4)
  • Plasmids and bacterial strains for expression of surface layer (S-layer) proteins, i.e. SbpA, SbsB, RsaA (ref)

Partner User Proposals

Partner User Proposals accommodate special partnership projects with broader scope and/or longer time frames than Standard projects, and include resource contributions from the user to the User Program. Partner User proposals should be developed with substantial input from Foundry scientists and require a letter of support from the Lead Facility Director.

This proposal type undergoes extensive review by both the Proposal Review Board and the Foundry’s Scientific Advisory Board, which typically requires several months.

The duration of a Partner User proposal is typically two years.

Partner User proposals are subject to requirements for User Agreements and Safety Review.

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Proposals for Proprietary Work

Users wishing to do proprietary work at the Foundry should notify the User Office of their intent to submit a proposal. Most types of user proposals can be designated as proprietary, enabling the user to withhold research results from publication for up to 5 years. Although the proposed work may be proprietary, sufficient information must be included in the proposal to permit evaluation of its scientific merit, as proprietary proposals undergo the same review process as regular non-proprietary proposals.

Proprietary proposals are subject to requirements for User Agreements and Safety Review. Specifically, proprietary projects require execution of a Proprietary User Agreement and the user must pay for the full costs of use of the facility and staff assistance ($311/hr in 2017). Contact the User Office for the current rate.

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Creating and Modifying User Proposals

User proposals are created and submitted through the Foundry's User Portal. Draft and submitted proposals may be viewed and modified by any user listed on the proposal form by logging in to the User Portal with that individual's user account.

It is possible to request the following modifications to approved proposals, before or after activation.   

  • Add a new user:  Discuss request with Assigned Scientist, then submit request on User Portal.
  • Remove an inactive user: Email request to theUser Office.
  • Add a support facility: Discuss request with Assigned Scientist, then email to the User Office.
  • Request an extension to the activation deadline or expiration date: Discuss request with Assigned Scientist, then email to User Office. In particular, users requiring parental or medical leave are encouraged to request extensions.
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Identifying Users on Proposals

The proposal form provides fields for up to five users: a Principal Investigator, a Primary Researcher, and three Co-Researchers.

The Principal Investigator (PI) is the project leader. Usually, the PI is a faculty member or a senior-level scientist who is head of a scientific organizational unit such as research group, program or laboratory. The PI is expected to make final decisions about the project and supervise scientific work. Students and postdoctoral scholars cannot be PI.

The Primary Researcher (PR) is the individual performing most of the research on the proposal. For proposals in which users are working on-site at the Foundry, the PR is the lead researcher performing hands-on work.

Co-Researchers (CRs) are any additional users who will be performing work on the proposal, either on-site or remotely.

After a proposal is approved, it is possible to request that additional users be added to the project as CRs. These requests should first be discussed with the Assigned Scientist and then submitted through the User Portal, either by the new users themselves or by another user on the proposal. The request is subject to review and approval by the Lead Facility Director, and may require execution of a new User Agreement if the new user has a different affiliation.  

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Proposal Questions and Evaluation Criteria

Scientific Significance and Impact (30 points)

Proposal question: Describe the scientific or technological motivation, long term goals, and significance/impact of this project in the context of the field of study.  (300 – 400 words)

Review criteria: To what extent is the proposed research expected to significantly advance the scientific or technological field? How likely is the proposed work to produce impactful publications?

Project Plan (10 points)

Proposal question: Describe your project plan. Clearly outline the scope of work you intend to do at the Foundry within the project term. Be explicit about which aspects will be done at your home institution. (300 – 400 words)

Review criteria: Is the experimental plan achievable at the Foundry within the proposed project term (not to exceed one year)? How will the results obtained at the Foundry complement and propel further follow-up research at the user’s home institution?

Need for the Molecular Foundry (10 points)

Proposal question: Describe your need for specific advanced capabilities and expertise at the Foundry.  If applicable, highlight any interdisciplinary aspects of the project that may require the unique combinations of capabilities of the Foundry. (300 – 400 words)

Review criteria: How well justified are the Foundry resources requested?  To what extent will the proposed work take advantage of the unique capabilities or combinations of capabilities/expertise either within a single facility, or across the Foundry as a whole?

Relevant Experience (10 points)

Proposal question: Describe the experience and accomplishments of each researcher in relation to the proposed work. (100 words per researcher)

Review criteria: How do the users’ track records of innovative, technically demanding research inform the likelihood of success of the proposed project? Are the users adequately prepared for efficient use of limited Foundry resources? 

Support Facility Justification

Proposal question: If applicable, describe the importance of the requested support facility or facilities toward accomplishing the project goals, highlighting specific points of complementarity. (100 words per facility)

Review criteria: To what extent is use of the proposed support facility expected to benefit the primary goals of the project? How well is this additional facility resource request justified?

No score given. Comments made by support Facility Director.

Molecular Foundry Utilization Timeline

Proposal question: Describe the expected timeline of the project, including an estimate of the number and frequency of facility usage visits. (300 – 400 words)                 

Review criteria: Consider the relative amount of both personnel and instrument resources effectively requested by this proposal.  Will the proposal have a low, medium, or high impact on the typical operation of this facility?

Effort rating of low/med/high and comments made by lead Facility Director.

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Tips for Writing a Strong Proposal

A good proposal…

  • Is likely to advance the scientific or technological field and produce impactful publications.
  • Describes work that can be accomplished in one year and contributes to ongoing research at the user’s home institution.
  • Takes advantage of unique Foundry capabilities and/or expertise, and justifies the resources requested.
  • Provides evidence that the researchers have a productive research record and are sufficiently experienced to make productive use of Foundry resources.

Although it is not required, users may wish to contact facility staff before submitting a proposal. The User Office is available to help direct users to the appropriate scientific staff contact. Staff are available to help:

  • Confirm the feasibility of your project.
  • Estimate and justify the time and resources required to complete your project.
  • Identify opportunities for collaboration.
  • Provide details about the equipment and capabilities available.
  • Provide constructive feedback on your draft proposal.

Include background information on why the proposed experiment is important, and how it will impact the field.

  • Clearly articulate the science case; state the problem and its importance.
  • Place your research plan in the context of what others have done and are doing. Include references to literature where appropriate.

Provide specifics about your project plan and timeline.

  • Include a precisely defined objective. What constitutes success for your project?
  • Describe your project deadlines and key milestones.
  • If you need access to high-demand instruments such as the TEAM microscopes, be specific about the amount of time required.

Address the productivity of your previous Foundry user projects, if applicable.

  • If you are submitting a follow-on proposal, be sure to describe results of the prior user project.
  • Make sure all publications resulting from work you have performed at the Foundry have been entered.
  • Complete final summary reports for all prior Foundry user projects.
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Proposal Examples

For more guidance on how to write a user proposal you may refer to the examples below (PDF downloads).