Time Reservation Info

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Updated EM time reservation information

Here is the UPDATED procedure to schedule EM times at LBMS.

1. Check the online calendar at https://lbmscalendar.bnl.gov Select desired resources and dates. Note: As sessions run from 9am to 9am, please change to week view to see whether a specific date is available. As the screen updates very slow, please be patient (up to a few tens of seconds).

2. Email your reservations to lbms-em@bnl.gov Note: To reserve access to the high-end EM, please attach a figure showing cryo-EM micrograph and class averages to show the sample’s readiness. Note: Please include your proposal number when contact LBMS.

3. You will receive an email after your reservations are confirmed.

4. All PIs and experimenters who have active awarded LBMS proposals, please register at your earliest convenience.

5. The experimenters, who will participate the data collection process (both remote and onsite), please take the required trainings and make sure you finish all the trainings at least one week prior to the start of microscope time.

Rules to reserve the EM time:

• Each GU proposal may have up to two reservations.

• Each BAG proposal may have up to four reservations

• Reservations may be made at most 3 months in advance

• Each reservation can be at most 6 shifts for high-end EM and 2 shifts for screening EMs, and at least 2 shifts for high-end EM.

• For each cycle, up to the allocated time may be reserved.

Recommended holey grids to be used at LBMS:

• Please use either 300 mesh or 200 mesh grids.

• Please use grids with a hole spacing no more than 1.5 microns (edge to edge).

• Gold grids are preferred.

• If grids were clipped already, please use the grid box for AutoGrid rings instead of the normal type.


Requirement for mail-in samples and remote data collection:

• A Safety Approval Form (SAF) must be submitted at least 14 days in advance of your scheduled EM time for remote experiments and 21 days in advance for proposals with onsite users.

• To ensure a timely handling of the shipment, please use the shipping address shown in the “Dry Shipper Information” form (https://www.bnl.gov/cryo-em/forms.php), put a copy of the completed form and a FedEx return label inside the dry shipper, and email “FedEx Incoming” tracking numbers to your LBMS contact.

• Samples must arrive at LBMS at least one week prior to the allocated microscope time. If this is not possible, or for questions, please contact the LBMS local contact for your microscope time. Please always send in duplicate grids as accidents may happen.

• A completed sample form (https://www.bnl.gov/cryo-em/forms.php) must be submitted to lbms-em@bnl.gov before sending samples to LBMS.

• A completed imaging parameters form (https://www.bnl.gov/cryo-em/forms.php) must be submitted to lbms-em@bnl.gov at least one week prior to the allocated microscope time. 

Note: Please see details at https://www.bnl.gov/cryo-em/userguide/next-steps.php.

• Please note that failure to send the samples on time, or provide the dry-shipper form, sample form and imaging parameter form on time, can result in cancellation of your EM time.

At this time, please make sure that every experimenter that will be participating in the cryo-EM time (onsite, remote, or mail-in) has a valid BNL appointment and has completed the required training. To do so, follow the instructions here: https://www.bnl.gov/ps/userguide/beforearrival.php.

Submitting an SAF

To submit your SAF, please logon to the PASS System at: https://pass.bnl.gov. Please note that failure to submit a SAF at least 14 days in advance can result in cancellation of your EM time and reallocation to another user. If all the following questions below can be answered “no”, you may use the envelop SAF instead of the standard SAF.

1. This envelope is for low risk electron microscope experiments with biomolecules. Does your work at LBMS exceed the standard techniques defined in the ESRs for LBMS resources?

2. Does your experiment require significant change to the standard User laboratory or LBMS hardware configuration for sample preparation or data collection?

3. Will your work at LBMS involve viable or infectious agents or systems (BSL-1 or BSL-2)?

4. Will your work at LBMS involve viable or infectious agents with recombinant DNA/RNA or synthetic nucleic acids?

5. Will your work at LBMS involve any of the CDC Select Agents or Toxins?

6. Will you be transporting frozen materials in any container other than a commercial LN2 dry shipping container?

7. Is there any additional safety issue not addressed above that requires analysis and control?

In order to ship samples to LBMS, you must have an approved SAF. Once approved, you can print a shipping label from the "General" tab on your SAF in PASS. For more instructions on shipping your samples to/from LBMS, and other useful information for your beam time, please see the Users’ Guide at https://www.bnl.gov/ps/userguide/beforearrival.php.

If you have any questions, please contact the Proposal Coordinator, Nancye Wright, at (631) 344-5132 or lbms-em@bnl.gov.

Remote Data Collection

1. Request a Brookhaven Lab Account The user must first be registered and have a BNL ID. They can then request a BNL domain account at the following link: BNL | Account Management Office | ITD. Once they have a BNL domain account they will be led to install DUO and VPN.

2. Install DUO: DUO is BNL’s two-factor authentication app, which needs to be installed on your Android or iOS smartphone. Go to the DUO installation page and look for “Get Started” and follow the instructions on the screen.

3. Install VPN: To access BNL’s internal network, you will need to install Brookhaven’s VPN client on your computer. Then start the VPN client and enter vpngateway.bnl.gov in the box and click connect. You will be prompted to enter your username and password then click OK. The DUO app on your smartphone will pop up to approve your login request. Lastly, you will need to accept the logon banner popup in the VPN client.

4. Start Cisco AnyConnect to connect to BNL network

5. Start VNC viewer with the address and password provided to you in the session info email you will receive prior to your reservation.


Data transfer:

1. Setup your globus account following the steps shown in the Globus tutorial at https://www.bnl.gov/cryo-em/forms.php Note: This step can be skipped if you have already set it up.

2. An email will be sent to you from Globus when the files are ready for download. Note: the link will be invalid after a month and the data will be deleted after two months.


End of run:

The session information will be sent to you after the session.

If you have any questions, please contact the Proposal Coordinator, Nancye Wright, at (631) 344-5132 or lbms-em@bnl.gov.