Frequently Asked Questions

Basics

    Who can apply?

    What does it cost?

Proposal Submission

    What proposal should I apply to?

    What are the proposal deadlines?

    Should I include preliminary data?

    How many proposal can I have?

    What biosafety levels are accepted?

    How do I edit my proposal?

    When will my proposal be approved?

    How do I see my proposal score and review comments?

    When does my time expire?

    How do I apply for more time?

Scheduling

    How do I schedule microscope or training access once my project is awarded?

    How many people our proposal can we send for an on-site visit?

    Can I have multiple reservations?

    What is the minimum and maximum time to schedule?

    Where do I send pre-frozen grids?

    Can I bring my samples on-site to be vitrified at PNCC?

    Can I send other samples than what is listed in my proposal?

Get Data

    How do I get my data?

    What are my imaging parameters?

    Can we send hard drives?

    Where can I leave feedback?

    What should I do when I publish?

 

 


 

 

 

 

 

 

 

 

Who can apply?

    PNCC resources are open to everyone in the global scientific community who wants to learn CryoEM. Access is given out based on peer reviewed proposals.

 

What does it cost?

    No cost for services and training.

 

What proposal should I apply to?

    This depends on your scientific objectives. Limited access receives 8-24hrs of instrument time, focused for preliminary data. General access receives up to 20 days per year with up to 2 years of access, allocated in 5 day increments. This is for long-term significant impact research and cross-training opportunities. More information can be found on Proposal Templates themselves.

 

What are the proposal deadlines?

    All proposals are sent for review monthly and are due by 11:59pm on the 1st of that month. 

 

Should I include preliminary data?

    Yes, this helps reviewers establish feasibility of the project. If your proposal is missing preliminary data, if approved, it might receive reduced allocated hours. If you don't have preliminary data, apply with our Limited access proposal. We provide screening services at PNCC to get preliminary data.

 

How many proposal can I have?

    There is no limit to the number of General Access proposals a PI may have as long as the science focus is distinct and non-overlapping. A PI may only have 1 active Limited Access proposal at any time. 

 

What biosafety levels are accepted?

   PNCC can only work with samples that are categorized biohazard safety level (BSL) 1 and 2. If the sample is, or is derived from, or contains any agent (or its DNA) that can be infectious or toxic in humans, animals or plants (viruses, bacteria, toxins etc.), or is obtained from sources that could potentially harbor (latently) such agents (eg. serum-derived or obtained from human cell lines), then the risk group (RG) must be established, licenses for shipping obtained, and safe operating procedures defined according to biohazard safety level.  Additional guidance on risk groups can be found in Section II of the CDC BMBL 5th Edition and references therein.  The starting point for our review will be the approval from the Institutional Biosafety Committee (IBC) from the applicant's home institution and the protocols on which the approval is based, so please attach both to this proposal after the biosketches. If your final sample might be considered RG1 but preparative work involved steps at BSL2, then a copy of your home-institution IBC approval indicating a down-grading of BSL during the purification will be needed to support that designation. Generally, center staff will oversee approval of RG1 agents, while acceptance of RG2 agents from US institutions will require involvement of OHSU's biosafety officer / IBC which may impact project award timeframes.  Shipping of agents from outside the US often requires additional approval from the CDC and/or USDA, and will be considered on an individual basis. We cannot receive BSL2 samples in liquid form at this time. Only pre-frozen BSL2 samples with IBC documentation can be handled.

 

How do I edit my proposal?

    Please email our User Coordinator any questions regarding editing proposals, including adding users.

 

When will my proposal be approved?

    It takes approximately 45 days for proposal to be approved at this time. If it has been longer than this, please email our User Coordinator.

 

How do I see my proposal score and review comments?

    In the EMSL User Portal, select proposal, on new page select “Peer Reviews.”

 

When does my time expire?

    Limited Access expires 3 months after approval. General Access can have access for up to 2 years, but each 120 hours allocation expires in 6 months if not used.

 

How do I apply for more time?

    If you applied with a Limited Use (or our previous proposal types: Standard or Rapid), then you will need to apply with a new proposal. If you have a General Access (or our previous proposal type: Programmatic), then you will need to submit an Allocation Renewal.

 

How do I schedule microscope or training access once my project is awarded?

    You must have a PNCC Use and Access Agreement on-file (and Unescorted Visitor Information Form for on-site visits). See the User Access Forms webpage for more details. Once your paperwork is completed, contact your Scientific Point of Contact (SPOC) to schedule the session.

 

How many people our proposal can we send for an on-site visit?

    There is a limit of 2 users visiting on-site. Special arrangements can be made, contact your PNCC SPOC.

 

Can I have multiple reservations?

    Yes, but please be aware of our cancellation policy in our scheduling policies.

 

What is the minimum and maximum time to schedule?

    Each awarded proposals can only book 5 days at a time and a minimum of 4 hours.

 

Where do I send pre-frozen grids?

 

    Ship your grids any day after Monday, but please make sure that we can receive them by Friday. Please include in the dry shipper a FedEx label to return the dewar and a copy of your grid submission form. Once you have the FedEx tracking number for this shipment please forward this by email so we can track it. As soon as we receive the shipment we will let you know. Please send the dry shipper to:

    Att: Claudia López
    Oregon Health & Science University
    LVMS Mail Code: CL-P
    2730 SW Moody Ave
    Portland OR 97201

 

Can I bring my samples on-site to be vitrified at PNCC?

    Yes, only if the samples have been included in the proposal's sample table AND are BSL-1. We currently cannot accept liquid BSL-2 samples.

 

Can I send other samples than what is listed in my proposal?

    This depends. All requested samples MUST be in the same scientific scope to be approved. During the General Access Allocation Renewal, approved users can request additional samples be added to their proposal. If BSL-2 samples are added, we will require a copy of your Institutional IBC for approval. Please contact our Co-Director Claudia Lopez in all other cases.

 

How do I get my data?

    We offer 3 routes for you to access your PNCC data. 

  • The fastest transfer option is using GLOBUS and this is the preferred method since you can get near real-time access to the data as it streams off the microscope and detector. GLOBUS also provides a single point of access for you to see old and new data using a single endpoint rather than needing separate download links for each dataset. However, not all institutions permit GLOBUS transfers inbound. PNCC now requires each proposal to list the GLOBUSID for at least 1 team member at time of proposal submission. Once your project is approved the PNCC Data Transfer Team will reach out to the PI and team to do a test transfer via a shared endpoint to confirm if GLOBUS works for you and to establish expected transfer speeds to your local storage. Setting up GLOBUS access is pretty straightforward and is completely free for academics and non-profits. To get the ID go to https://www.globusid.org/create where you can register for a GLOBUS basic account if your institution doesn’t already have an institutional license. 
  • The second fastest transfer option to download PNCC data is to use the ARIA2 parallel download manager. For every dataset collected an autogenerated email will be sent to members of the team to notify that data is available for download. However, this option is only available after a microscope session is complete and the full dataset has been uploaded to the archive. Installation of ARIA2 is straightforward with options to compile from source or direct download of binaries for OS X and Windows. Once installed, the use of ARIA2 is very easy. At the bottom of each PNCC autogenerated dataset email is a link for specific use with ARIA2 which points to the particular dataset. Simply copy this link and launch it with the ARIA2 command line to initiate the transfer. Similar to GLOBUS, if your local connection is intermittent or the download gets halted, ARIA2 will automatically resume after disruption. ARIA2 parallelized download options are particularly helpful for big files or when data transfer rates are slow between your institution and the PNCC archive.
  • The slowest but most accessible transfer option is via the EMSL User Portal “Get Data” tab. To access the datasets, login to the EMSL User Portal then either migrate to the “Get Data” tab OR click the MyEMSL data download link provided in the autogenerated email mentioned above. Note: The portal login gives you a token needed to see the data and the token times out after awhile. So if you have problems seeing the data try logging in to the portal on another browser page then refreshing the data portal page. 

    If you have any issues or difficulties, please contact Evan Felix or Dave Cowley directly by email.

 

What are my imaging parameters?

    Please contact your PNCC SPOC for this. We are hoping to add this to our downloaded data.

 

Can we send hard drives?

    Yes, this must be approved by your PNCC SPOC before shipping hard drives to our facility.

 

Where can I leave feedback?

    You can submit a Microscope Session survey. At the end of your proposal, we will send an NIH required End of the Project survey for you to fill out. You can also contact us with specific feedback.

 

What should I do when I publish?

    Acknowledgements required for all research publications and presentations supported by use of PNCC:

   Co-Authorship of PNCC staff for publications involving data derived from use of PNCC:

   Data sharing and archival of raw and initial processed datasets:

  • All imaging and other data generated by PNCC must be made public following established accepted practices for data validation and deposition to publicly accessible worldwide repositories (EMDB or PDB) prior to manuscript publication. Additionally, all raw and initial processed datasets acquired by PNCC will be archived using the MyEMSL archive. Users can access their project related archived data anytime and anywhere via the “Get Data” tab within the EMSL User Portal. Data is owned by the user during the awarded proposal period and for 1-year following the end of the respective user proposal. During this window only the proposal PI, their designated team and PNCC staff can access the data. However, 1-year after the end of each individual user proposal, all associated data for that specific proposal is made publicly searchable within MyEMSL and is available to the general scientific community. The archiving of PNCC data is automatic and does not remove the requirement to deposit data related to individual publications in worldwide repositories.  

   Public access to publications for dissemination of information and tracking purposes by NIH and PNCC:

  • NIH requires that all research papers describing research supported by the use of PNCC must be available to the public through PubMed Central. Additionally, NIH requires that PNCC have a copy of all resulting publications and information on all deposited structures/maps. All users of PNCC are therefore required to report all journal articles, conference proceedings, books or book chapters, contributed news articles, et cetera that include data generated by use of PNCC. Authors must upload these documents to the EMSL User Portal and link it to their awarded project within 2-weeks of publication.