Proposal Submittal and Scheduling Procedures for Macromolecular Crystallography

New Proposals

The U.S. Department of Energy Office of Science (SC), which is the primary sponsor of SSRL, requires that a limited set of information relating to user research proposals be transmitted to SC annually. A subset of this information, including user name, institutional affiliation(s), and proposal title(s), will be publicly disseminated at the conclusion of the fiscal year as part of an SC user facility user experiments database on the SC website.  Additionally, abstracts may be made publicly available on the NIH database as part of our grant reporting requirement.

Beam time for macromolecular crystallography projects is obtained by submitting an SSRL Macromolecular Crystallography Proposal. This proposal is peer reviewed by the Structural Molecular Biology and Biophysics subpanel of the SSRL Proposal Review Panel (PRP) for scientific merit and rating and for criticality of synchrotron radiation use.

Rapid Access Proposal

Rapid Access proposals can be submitted at any time. The Rapid Access Program provides quick access to macromolecular crystallography beamlines at SSRL —usually within a month from the time that the application is submitted.  The Rapid Access proposal form provides more details concerning the use of this mechanism to obtain beam time at SSRL.  See Instructions for submitting a Rapid Access application.

Submit Proposal

Block Allocation Group (BAG) Proposals

Block Allocation Groups (BAGs) are a mode of beam time access intended for groups of researchers that want to combine their short beam time requests into a single proposal in order to permit greater flexibility in beam time allocation and scheduling. BAG proposals may be submitted by groups working at a shared university or with a shared affiliation. Combining the beam time of individual groups permits greater flexibility in the choice of projects and samples during a given allocation period and offers the individuals in the BAGs the benefit of access to more regular allocation of beam time.

BAG proposals are accepted on SSRL BL14-1, BL9-2, BL12-2 and BL12-1. Only measurements based on existing, standard setups available at these beamlines will be considered for the BAG beam time. Proposal submission will be very similar to the standard proposal format.  See Macromolecular Crystallography Block Allocation Group Proposals.

Scheduling

SSRL operates as a dedicated synchrotron radiation source for ~9 months per year (usually November through early August). Spokespersons with active proposals are invited to apply for beam time via email notification three times a year, approximately one month to two months in advance of a scheduling period. Experimenters are directed to our User Portal to log in and submit a Beam Time Request by the stated deadline. When scheduling for a particular segment of the experimental run is completed, spokespersons are instructed to login in again to view and accept or decline their beam time assignment(s).

Users should be aware that additional beam time may become available when shifts previously scheduled to other groups are cancelled. If you would like beam time and missed the last deadline or just simply need more shifts than originally anticipated, please contact Lisa Dunn lisa@slac.stanford.edu to inquire about the possibility of additional beam time.

Shift Assignment

If there is over subscription on macromolecular crystallography lines in a given scheduling period, not all beam time requests can be met. Unmet requests are put on a waiting list to either receive consideration for beam time within that same scheduling period as time becomes available or to be given priority (within the proposal's rating bracket) during the next scheduling period.

Extensions

A one-time extension request may be submitted for review by the SSRL Proposal Review Panel (PRP). If approved, the PRP may extend the proposal up to 2 additional years, change the rating, and/or limit the amount of beam time allocated.

When submitting extension requests, keep in mind that attention will be given to published results from experiments utilizing SSRL's facilities and whether or not the papers appropriately acknowledge SSRL and funding agencies. Papers that do not mention or acknowledge beam time at SSRL cannot be added to SSRL's publications list. 

Proposal extension requests should be submitted to SSRL before the initial two-year beam time eligibility period expires. Extension requests will be accepted and reviewed on the same schedule as new proposals.

Extension requests must summarize the following. 

  1. Proposal Number and Spokesperson's Name
  2. Date of Extension Request
  3. Progress: Provide a progress report describing work accomplished at SSRL on this proposal to date, 2-4 paragraphs.
  4. New elements: If applicable, describe any new elements that may add interest to extending the proposal, 1-2 paragraphs.
  5. Future plans: Describe the next steps or future plans proposed to be pursued under the existing proposal, 1-2 paragraphs.
  6. Update collaborators: If different from the original proposal, list current collaborators, including institution and email address; ask new collaborators to register as new users on the user portal.
  7. Summary of beam time: List beam time used at facilities other than SSRL-this will not affect your SSRL proposal extension request.
  8. Publications: List all publications related to work conducted at SSRL on the proposal and include a link or copy of 1-3 of the key publications.

Based on the extension material, the PRP may extend the proposal for up to two years, change the rating, or terminate the proposal.

Extension requests should be submitted via email attachment to Lisa Dunn.

General Policies

Significant Deviation from Proposed Research in a Rated Proposal

It is recognized that, occasionally, significant deviation from proposed research contained in a proposal will occur during the course of an experiment. Deviation that occurs in order to compete with research covered in another user's proposal or for an idea that has been discussed commonly and is in the public domain is not acceptable. Deviation from the proposed work that follows either from a new idea arising from the research or from new information is acceptable assuming it does not cover material in a rated proposal from another user group.

Information regarding significant deviations should be included on the Beam Time Request Form in advance of performing the work whenever possible. If significant deviation occurs in the course of running an experiment, the information should be recorded on the End-of-Run Summary Form which can also be accessed by logging into our User Research Administration Web Interface.

Instrumentation Development

Although most of the proposals active at SSRL are for experimental work aimed at producing significant new scientific results or technological applications, SSRL also welcomes proposals for testing and developing scientific instrumentation, particularly when the instruments are likely to have impact on synchrotron radiation research.

Reporting Requirements

SSRL submits several annual reports to the Department of Energy and the National Institutes of Health, which require up-to-date publications listings. These publications lists are extremely important in presenting scientific achievements and productivity, and thus funding case to these agencies.  A Reference Submittal Form is available to provide reference information.

Acknowledgement Statements

  • All macromolecular crystallography-related publications related to work fully or partially undertaken at SSRL should contain the following acknowledgement:

    Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (P30GM133894). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH.

  • Publications arising from COVID experiments, which were enabled by the CARES Act funding, should acknowledge the NVBL, in addition to the usual SSRL contract acknowledgement:

    Research was supported by the DOE Office of Science through the National Virtual Biotechnology Laboratory, a consortium of DOE national laboratories focused on response to COVID-19, with funding provided by the Coronavirus CARES Act.

Trading Beam Time

SSRL assigns beam time primarily on the basis of a peer-reviewed rating system. Moreover, onsite users are tracked for safety reasons and computer accounts enabled based on the posted schedule. Thus, the practice of beam time trading or brokering among user groups is not allowed.

User Agreement(s)

Fully executed Use Agreement(s) between Stanford University and the spokesperson's home institution, and all collaborator institutions (if personnel physically coming to SSRL or participating via remote access) must be completed and on file prior to beam time. A single User Agreement covers all experimenters from that institution.  A Proprietary Research User Agreement is required for experimenters wishing to perform proprietary research at SSRL.

Changes to the SPEAR Schedule

Changes to the SPEAR schedule can occur due to unanticipated problems with the storage ring. These changes can occur on very short notice and may result in the cancellation of a scheduled experiment.  Short-term adjustments to the crystallography schedule can frequently be made to compensate for unanticipated poor performance of the storage ring or problems with the equipment but usually depends on a group's willingness to take accept last-minute beam time at possibly odd hours.

Proprietary Research

Proprietary Research is defined as that for which users request confidentiality of proposal, data and results for a certain period of time. This research follows the guidelines for implementation by the Stanford University Faculty Senate and is executed through a User Agreement for Proprietary Research for research proposals submitted to SSRL. Proprietary Research is subject to the Department of Energy's full-cost recovery requirement for facility charges for the use of SSRL facilities and advance payment of those charges. The facility charges are established as a dollar rate for each shift of beam time.

Experimenters interested in conducting Proprietary Research should contact SSRL User Research Administration well in advance of the anticipated need for beam time as the legal procedures involved may take up to several months to finalize.

For beam time to be assigned on general user stations, proposals for Proprietary Research must be reviewed for merit and to assure that all ES&H guidelines are met in accordance with standard SSRL policies and procedures. Sufficient generic information to enable Proposal Review Panel review should be provided in standard proposals. Proposals designated as proprietary research will be maintained in confidence during the review process to the maximum extent possible.

Proprietary Research can be performed on Participating Research Team (PRT) time in cases where the industry is a PRT member. However, the three-year performance review of the PRT must include at least sufficient information on how the proprietary research time was used so that a review can be made by the external group appointed to carry out the review.

General Conditions

  • Stanford faculty, students or research staff will not be directly involved in the research aspects of the proprietary program.
  • No more than 15 percent of the SSRL beam time in a given 12-month running period will be used for proprietary research.
  • The SLAC Associate Director for SSRL, or the Associate Director's designate, and the SSRL Safety Officer will be provided with a description of the experiment and its goals prior to the approval of the experiment. The description will be sufficiently detailed so that the Associate Director can understand and monitor the main components of the experiment and the Safety Officer can assure that all ES&H guidelines are met and that there is no risk to people, the facility or the environment. If possible, these should be written so that the confidential nature of the research is not compromised.
  • Disclosure of intellectually significant results of the experimental work will be made within five years from the time of completion of the data collection at SSRL.
  • A yearly disclosure will be made of the scientific and programmatic accomplishments at least in general terms.
  • Barriers, roped-off areas or other similar measures that would restrict access to the experimental stations will not be used.

Requirements for Establishing a Proprietary Research Account

1)     Establish a proprietary user agreement with Stanford. (see User Agreements)

2)     Register in the user portal and submit a proposal. 

3)     Provide a screenshot of your company's SAM.gov registration and DUNS number.

4)     Submit a W-9 and contact information for your accounting department for invoicing purposes.

5)     Remit payment per the terms of the SLAC invoice before beam time.