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Proposal Submittal and Scheduling Procedures for Macromolecular Crystallography Beam Lines at SSRL |
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.
Proposals should be submitted under one of the following classifications.
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Single and program proposals are active for two years. Program proposals can be extended for an additional two-years on the basis of an extension request (see last page of proposal form). A replacement Program proposal may be submitted if the scope of the project has not been completed within four years.
A fully completed proposal consists of properly specified proposal and
experiment types, whether or not it is private sector and/or AIDS related
research, a title, abstract, spokesperson and collaborator contact
information, crystal data, proposal text and specifically requested experiment
and safety information and Federal Agency reporting requirements as per
instructions on the SSRL Macromolecular Crystallography Proposal Form.
EXPERIMENT TYPE
Please indicate whether monochromatic, MAD or ultra-high resolution experiments are planned in the scope of the research. Plan to justify the use of ultra-high resolution time well in the body of the proposal text.
PRIVATE SECTOR RESEARCH
Private sector 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 (see Private Sector Research) and is executed through a Supplementary Use Agreement for Private Sector Research for each individual research proposal submitted to SSRL. Private sector 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. As the Supplementary Use Agreement for Private Sector Research can take some time to complete, needing approval of legal department both at SSRL and at the user organization, users should plan to allow the appropriate amount of extra time. For more information on conducting private sector research at SSRL, see Private Sector Research and contact the User Research Administration Manager at 650-926-3191.
TITLE
Titles should be as short as possible, but uniquely descriptive of your proposed work. Please use Title Case (e.g., Studies of Molecular Structures of XYZ.)
BRIEF ABSTRACT
Provide an abstract (~300 words or 2000 characters) of your proposed experiment(s). The abstract should have a brief introduction stating what this project is about and why it is important. Please explain what one is expected to learn and how that fits into the bigger picture. Specifics on what the approach is and, if applicable, why one specific approach needs to be taken should be included. A statement regarding the availability of crystals, etc., can be included but is not essential. If this project is an adjunct to previous work, more background information may be provided.
CRYSTAL DATA
Information regarding the sample(s), size, molecular weight, space group, cell dimensions, maximum resolution, temperature, wavelength, anomalous scattering element and anomalous sites/molecule are required. For single experiment proposals please be aware that if it appears that you do not actually have crystals in hand, your proposal will be reassigned as Trial Beam Time or will receive a lower rating.
SPOKESPERSON AND COLLABORATORS
Please provide COMPLETE, accurate and up-to-date contact information for the Spokesperson and all collaborators. In particular, provide full names, including middle initials, as SSRL has many users who do not have unique names. Accurate information is crucial to timely communications regarding upcoming events and dead lines at SSRL.
The Spokesperson is responsible for all communication with SSRL staff (e.g., scheduling, equipment needs, characteristics of samples, and safety requirements), and should be the person who will actually be responsible for these matters. In most cases, all communications from SSRL will be sent to the Spokesperson ONLY, who is thus also responsible for transmitting any pertinent information to her/his collaborators.
PROPOSAL BODY
A) Description of Experiment
Provide a detailed description of the proposal's subject matter. Include
a statement of its scientific purpose, the reason synchrotron radiation
is needed, the theoretical and/or scientific background, samples to be
used and procedures to be followed. If a proposal is being submitted as a
replacement for an expiring proposal, it should include the number of shifts
previously used, the experimental station(s) utilized, and references to
publications resulting from this work and any SSRL Activity Reports (see
Extension portion of Proposal form).
B) Detailed Safety Concerns
All experiments performed at SSRL must conform to SLAC and SSRL safety
standards. It is the responsibility of the Spokesperson to implement controls
or develop procedures for addressing potentially hazardous situations.
If your proposal does not have a safety component to it, the following
text should appear in Section B:
"No hazardous substances, equipment, or procedure will be brought to SSRL as part of this proposed experiment."
If your proposal indicates that you intend to bring hazardous materials, substances, equipment or procedures to SSRL, then you must include the following in Section B:
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A hazardous material/substance is anything that is ignitable, corrosive, reactive or toxic, radioactive or is a biohazard or infectious agent. Proposals will not be processed if the above information is not included.
Indicate whether or not your experiment will involve human subjects or laboratory animals. If so, you MUST provide details of materials and procedures to be utilized within the text of your proposal and any safety concerns as well. If any proposed research involves the use of human subjects or laboratory animals, a research protocol must be submitted to Stanford University's Panel on Human Subjects in Medical Research or the Panel on Laboratory Animal Care for review and approval prior to acceptance of the proposal. Investigations must comply with University regulations established by the Panels, federal legal standards, and the terms of the University's Assurance filed with the Department of Health and Human Services. Contact Matt Padilla, SSRL Safety Officer, for details.
All proposals are reviewed for safety concerns by SSRL. The Spokesperson is notified if the proposal raises any safety questions. Proposals with unresolved safety concerns are not eligible to be scheduled for beam time. Please remember that experiments at SSRL are performed in an often crowded experimental area in close proximity to other experiments. Thus, procedures that may be reasonable in a small laboratory occupied by a few people all familiar with the possible hazards may not be acceptable at SSRL.
DOE/NIH REPORTING CATEGORIES
The Department of Energy and the National Institutes of Health require that we report annually on research areas and funding agencies for all proposals submitted to SSRL. Please check all that apply to your proposal and provide detailed information where indicated "specify below." Please do not use acronyms for Foreign or Other funding agencies.
Although proposals for experimental work at SSRL are accepted at any time, the
PRP normally reviews Macromolecular Crystallography proposals three times
per year corresponding with the December 1, April 1 and July 1 proposal
submittal deadlines (see also Rapid
Access Application). Users are invited to submit new proposals for
Macromolecular Crystallography before December 1, 2003 for beam time
eligibility beginning in March 2004. For more information on deadlines
related to proposals and beam time requests visit:
http://www-ssrl.slac.stanford.edu/users/user_admin/deadlines.html
We expect that beam will be available for regular user scheduling on most beam lines in March 2004. Users with existing proposals who wish to request beam during this time frame (including the possibility of some commissioning time in February), can submit a beam time request by January 21, 2004 for Macromolecular Crystallography beam lines. Please note that these projections are dependent upon completion of upgrade activities and radiation shielding, and that beam stability early in the run will be difficult to predict.
Proposals should
be submitted as follows:
One electronic copy, sent as e-mail attachment(s) to: lisa@slac.stanford.edu
or 1 hard copy to: Lisa Dunn, SSRL, MS 99, 2575 Sand Hill Road, Menlo
Park, CA 94025
Once a complete proposal is received, it is sent to the Structural Molecular Biology and Biophysics subpanel of the Proposal Review Panel for review and rating.
| Structural Molecular Biology and Biophysics | |
| Ron Stenkamp | University of Washington |
| Robert Scott | University of Georgia |
| Michel Koch | European Molecular Biology Laboratory |
| Chris Hill | University of Utah |
The PRP also advises SSRL management on policy concerning scheduling and the proposal process as well as more general matters affecting the user community.
Ratings Scale
Proposals are rated in a range between 1 (highest) and 5 (lowest). The Panel attempts to maintain the absolute quality scale used during previous PRP meetings so that ratings from all meetings can be used consistently to schedule proposals.
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Appeals to Ratings
Spokespersons may submit proposals for re-review under the following circumstances:
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Normally, proposals will only be re-reviewed within the time-frame of the next
scheduled meeting of the PRP.
SSRL operates as a dedicated synchrotron radiation source for ~9 months per year (usually November through July). Spokespersons with active proposals are invited to apply for beam time via email notification three times a year, approximately two months in advance of a scheduling period. Experimenters are directed to a web page at: http://smb.slac.stanford.edu/public/admin/form_bio_btrf.html to fill out these forms by a stated deadline. When scheduling for a particular segment of the experimental run is completed, spokespersons are notified of assigned beam time in writing. Beam time acceptance is confirmed by using the form at: http://smb.slac.stanford.edu/public/admin/form_bio_btacc.cgi.
Shift Assignment
Due to the oversubscription on macromolecular crystallography lines, not all beam time requests can be met in a given scheduling period. Unmet requests are put on a waiting list to either receive consideration for beam time within that same scheduling period as time becomes available due to cancellations or to be given priority (within the proposal's rating bracket) during the next scheduling period.
Use 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) must be completed and on file prior to beam time. A single Use Agreement covers all experimenters from that institution. Collaborators who are not coming to SSRL do not require a Use Agreement. A supplemental Use Agreement is required for experimenters wishing to perform private sector research at SSRL.
Use Agreement forms for both standard and proprietary research are available
for downloading at:
http://www-ssrl.slac.stanford.edu/users/user_admin/useagreementmenu.html
Required Safety Review
If your proposal has received a safety star or if you indicate on your Beam Time Request Form that you are bringing hazardous materials, you will be required to complete an SSRL Hazardous Substances Form. This form must be returned with two copies of the appropriate MSDSs for each substance you are bringing to SSRL. It is used by the SSRL Safety Office to develop a SSRL Safety Review Summary Form that must be signed by the Spokesperson, and its accuracy attested to, two weeks prior to each experimental run. If these forms are not returned with the Spokesperson's signature, the scheduled time may be withdrawn or significantly delayed.
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. In most cases, short-term adjustments to the SSRL schedule cannot be made to compensate for unanticipated poor performance of the storage ring or problems with the equipment.
Private Sector 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 Supplementary Use Agreement for Private Sector Research for each individual research proposal submitted to SSRL. Private Sector 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 Private Sector Research should contact the User Research Administration Manager well in advance of the anticipated need for beam time as the legal procedures involved may take up to several months to finalize. The Supplemental Use Agreement for Private Sector Research is in addition to the standard Use Agreement, which is required for all user institutions.
For beam time to be assigned on general user stations, proposals for Private Sector 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 external peer and Proposal Review Panel review should be provided in standard and program proposals. Proposals designated as private sector research will be maintained in confidence during the review process to the maximum extent possible.
Private Sector 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 private sector research time was used so that a review can be made by the external group appointed to carry out the review.
- Stanford faculty, students or research staff will not be directly involved in the research aspects of the Private Sector Research program.
- No more than 15 percent of the SSRL beam time in a given 12-month running period will be used for Private Sector 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 (such as a contribution to the SSRL activity report).
- Barriers, roped-off areas or other similar measures that would restrict access to the experimental stations will not be used.
Duplication of effort is not bad per se, and is, in fact, desirable in important experiments. Past experience has shown that a single experimental program often fails to provide solutions that stand the test of time. A new proposal to work in an area where other studies at SSRL are ongoing will be weighed against these proposals. However, no implicit penalty will be applied simply because of the choice of area.
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.
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.
All publications related to work fully or partially undertaken at SSRL should contain the following acknowledgement.
"Portions of this research were carried out at the Stanford Synchrotron Radiation Laboratory, a national user facility operated by Stanford University on behalf of the U.S. Department of Energy, Office of Basic Energy Sciences. The SSRL Structural Molecular Biology Program is supported by the Department of Energy, Office of Biological and Environmental Research, and by the National Institutes of Health, National Center for Research Resources, Biomedical Technology Program, and the National Institute of General Medical Sciences."
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.
Users are requested to submit two copies of each publication or thesis based, fully or partially, on work at SSRL to the attention of Lisa Dunn. A Reference Submittal Form is available to provide reference information in advance of the actual preprint distribution.
SSRL Policy on 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.
SSRL is funded by the Department of Energy, Office of Basic Energy Sciences under contract DE-AC03-76SF00515. The SSRL Structural Molecular Biology Program is supported by the Department of Energy, Office of Biological and Environmental Research, the National Institutes of Health, National Center for Research Resources, Biomedical Technology Program, and the National Institute of General Medical Sciences.
| Last Updated: | 01 NOV 2007 |
| Content Owner: | Lisa Dunn |
| Page Editor: | Lisa Dunn |