Questions and answers

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  • Access is awarded based on peer reviewed proposals.
  • There is no cost for services and training.
  • Proposals are due by 11:59 p.m. on the first day of each month.

Proposal submission

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.
Which proposal type should I apply to?

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

When I apply, 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 one active Limited Access proposal at a time.

What biosafety levels are accepted?

PNCC can only work with samples that are categorized 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, PNCC staff will oversee approval of RG1 agents, while acceptance of RG2 agents from U.S. institutions will require involvement of OHSU’s biosafety officer or the IBC which may impact project award timeframes. Shipping of agents from outside the U.S. 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 submitted 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, then 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-hour 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.

Scheduling

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, but special arrangements can be made — contact your PNCC SPOC.

Get Data

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 Globus ID 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, 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 ofAria2 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 withAria2 which points to the particular dataset. Simply copy this link and launch it with theAria2 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.

Learn more

What are my imaging parameters?

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