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September 26, 2019

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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 and most proposal types also allow users to request access to additional Support Facilities.

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

Scope

Submission Period

Standard

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 (foundry-useroffice@lbl.gov) 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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Proposal Form Content Guide

The Proposal Form Content Guide is available as a PDF download below. This document presents the content requested in the form for a Standard Proposal to the Molecular Foundry. Most of the prompts and guidance are taken verbatim from the form, but some modifications and omissions have been made for clarity.

Note that this document is provided only as a guide and that proposals must be submitted through the User Portal using the interactive form, not as a compiled document.

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Lead and Support Facility Requests

When requesting Foundry resources on your user proposal, it is important to correctly identify which Foundry Facilities you will need to access in order to accomplish your proposed project. We encourage proposals that use more than one Facility, if needed, but you should only request the resources you are likely to use in the course of a given proposal and must provide a clear scope of work for each Facility requested.

Lead Facility: The most important step is to identify the appropriate Lead Facility, which is the Foundry Facility in which the majority of your work will take place in the specified project timeframe (12 months for a Standard Proposal). Your proposal will be peer-reviewed by a group of external subject-matter experts for the Lead Facility, and resources will be allocated based on the Lead Facility’s current capacity to accommodate and support users.

Multiple Lead Facilities: Some projects require significant resources from more than one Facility, beyond what would be appropriate for a Support Facility request (see below). These projects can be accommodated by submitting a separate proposal to each of the heavily used Facilities as Lead. Each scientifically related but independent proposal will undergo peer review by the Proposal Review Board of the specified Lead Facility and may be accepted or rejected independent of any associated proposals. These related proposals can have identical scientific narratives or may be customized to the different Lead Facilities.

Support Facilities: About half of all Foundry proposals also request access to one or more Support Facilities. These requests must be more modestly scoped than Lead Facility requests as they are not taken into account during resource allocation. As described in the Facility-specific examples below, Support Facility requests can include access to routine tools on which users are already trained or on which minimal training is required, or other activities that pose a similarly low burden on staff time and limited resources. If additional Support Facilities are deemed necessary after a project is accepted, it is possible to add them later.

Determining Lead versus Support Requests: Below you can find Facility-specific examples of the type of work that is typically considered appropriate for Lead versus Support requests. Users are also encouraged to consult with Foundry staff before submitting proposals in order to determine appropriate resource requests. For guidance on which staff member to contact, contact the User Office (foundry-useroffice@lbl.gov, 510-486-7423).

Imaging Facility

Imaging Capabilities & Tools

Examples of activities suitable for Lead Facility requests to the Imaging Facility:

  • Setting up new optical microscopy measurements
  • Building microscope environmental cells
  • Using a new material for STM/AFM experiments
  • Cryo electron tomography
  • Training users in laser spectroscopy, or probe or electron microscopy
  • Developing new measurement techniques, software and analysis routines

Examples of activities suitable for Support Facility requests to the Imaging Facility:

  • Routine use of instruments like XPS, SEM, and AFM by previously trained users (specific qualified users, not research groups)
  • Staff support in figuring out approaches to experimental problems
  • Where appropriate, access to an instrument session to determine the feasibility of future Lead Facility projects in Imaging

Nanofabrication Facility

Nanofabrication Capabilities & Tools

Examples of activities suitable for Lead Facility requests to the Nanofabrication Facility:

  • Development of new complex fabrication processes
  • Modification of existing setups to suit user processes
  • Extensive use of complex tools, such as atomic layer deposition, focussed ion beam, and electron-beam lithography
  • Use of ultrafast laser system

Examples of activities suitable for Support Facility requests to the Nanofabrication Facility:

  • Routine use of routine tools, such as deposition of standard materials, reactive ion etcher, and ellipsometry
  • Staff support in figuring out approaches to experimental problems
  • Standard processing that will not require heavy development

Theory Facility

Theory Capabilities & Tools

Examples of activities suitable for Lead Facility requests to the Theory Facility:

  • Training a user (experienced or novice) to use or modify an existing piece of code
  • Training a user to build a theory or piece of simulation code in order to tackle a problem outside of the scope of existing theories or codes

Examples of activities suitable for Support Facility requests to the Theory Facility:

  • Discussion and consultation to help guide a users’ work
  • Helping an experienced simulator run an existing piece of code

Inorganic Nanostructures Facility

Inorganic Nanostructures Capabilities & Tools

Examples of activities suitable for Lead Facility requests to the Inorganic Facility:

  • Performing a high-throughput synthesis screen on WANDA or HERMAN
  • Requests for staff to program new robotic or data analysis routines
  • Developing or synthesizing a new material on a Schlenk line
  • Use of metal-organic chemical vapor deposition for materials development
  • Frequent use of any chemical hood, glovebox or instrument
  • Glovebox use for anything other than sample preparation and/or temporary storage
  • Transport measurements involving thermal, gas, electrical, or optical measurements

Examples of activities suitable for Support Facility requests to the Inorganic Facility:

  • Routine use of instruments like XRD, confocal Raman microscopy, TGA, DSC, DLS, FTIR, table-top SEM, and fluorescence spectroscopy
  • Glovebox use for sample preparation and temporary storage
  • Infrequent use of a fume hood to run standard reactions or prepare samples.
  • Infrequent use of tube furnaces for annealing samples
  • Staff support in figuring out approaches to experimental problems
  • Routine liquid handling on the Nimbus robot
  • Where appropriate, access to an instrument session to determine the feasibility of future Lead Facility projects in the Inorganic Facility

Biological Nanostructures Facility

Biological Nanostructures Capabilities & Tools

Examples of activities suitable for Lead Facility requests to the Biological Nanostructures Facility:

  • Design, synthesis, purification and characterization of peptoid polymers
  • Synthesis and functionalization of nanoparticle probes for bioimaging applications
  • Expression, purification, modification or self-assembly of proteins
  • Fluorescence imaging of material interactions
  • Bioelectrochemical characterization of bacteria

Examples of activities suitable for Support Facility requests to the Biological Nanostructures Facility:

  • Preparation of samples for analysis
  • Routine/infrequent use of bioanalytical instrumentation

Organic Facility

Organic Capabilities & Tools

Examples of activities suitable for Lead Facility requests to the Organic Facility:

  • Porosity measurement training
  • Access to the single crystal X-ray diffractometer
  • Routine use of fume hood or glove box, beyond sample preparation or storage
  • Synthesis of new materials
  • Comprehensive OPV or OFET device fabrication and characterization

Examples of activities suitable for Support Facility requests to the Organic Facility:

  • Staff consultation in figuring out approaches to new experimental problems.
  • Temporary access to fume hoods or glove boxes for sample handling
  • Routine use of instruments listed in the previous section by trained users (specific qualified users, not research groups)
  • Routine use of instruments like NMR, MALDI, chromatographic systems, DSC, FTIR, and fluorescence spectroscopy
  • Where appropriate, access to an instrument session to determine the feasibility of future Organic Facility projects

NCEM Facility

NCEM Capabilities & Tools

Examples of activities suitable for Lead Facility requests to the NCEM Facility:

  • Training new users (experienced or novice) to become independent microscope operators
  • Access to the Helios G4, TitanX, ThemIS, TEAM 0.5 or TEAM I microscopes
  • 4D-STEM (scanning nanobeam diffraction), exit wave reconstruction, or other processing-intensive analysis
  • Developing new measurement techniques, software, and analysis routines

Examples of activities suitable for Support Facility requests to the NCEM Facility:

  • Limited use of routine instruments such as CM200, JEOL 3010, Libra 200, and Tecnai by previously trained, independent users (specific qualified users, not research groups)
  • Routine sample preparation such as mechanical polishing, microtomy, and argon ion beam milling
  • Staff consultation in figuring out approaches to new experimental problems
  • Where appropriate, limited access to an instrument session with staff support to determine the feasibility of future Lead Facility projects in NCEM
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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

Project Goals and Significance (20 points)

Proposal question: Describe the scientific or technological motivation, long-term goals, and significance of your project in the context of your field of study. Describe your immediate goal in the context of a one-year Molecular Foundry User Project.

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 high-quality publications?

Resource Request (15 points)

Proposal question: Describe how Foundry capabilities and expertise are needed to realize the immediate goal identified in “Project Goals and Significance”. Identify the lead facility and any support facilities requested, and give a short description of the intended work at each.

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?

Project Plan and Timeline (15 points)

Proposal question: Describe your project plan, indicating the work to be done at your home institution and in the Foundry Facilities requested in “Resource Request”. Describe how each of these pieces of work contributes to the immediate goal identified in “Project Goals and Significance”. Describe the expected timeline of your project, including an estimate of the time required for each piece of work.

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

Relevant Experience (10 points)

Proposal question: Describe the current level of expertise of each researcher in relation to the proposed work. For researchers expected to do hands-on work at the Foundry, be explicit about their level of training or experience on the requested instruments and capabilities.

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

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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).

IMPORTANT: As of March 2019, the questions on the proposal form have been updated, particularly the guidance given regarding the scope of work suitable for a Support Facility request. Several of the examples below may be expected to submit more than one Lead Facility request proposal under the current guidance.

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