General Lab Information

Laboratory for Biomolecular Structure

Get Started as a LBMS User

All Laboratory for BioMolecular Structure (LBMS) microscope time is allocated based on a peer-reviewed proposal process. LBMS operates in two 6-month cycles: January – June (proposal deadline Sept 15) and July – December (proposal deadline March 15). All microscope time is requested each cycle through the web-based Proposal Allocation, Safety, and Scheduling System (PASS) system. In this system, a proposal describes the scientific experiments to be performed and identifies the experimental team. Proposals have different durations depending upon the type of proposal submitted. For any proposal that has a duration of more than one cycle, an experiment time request (ETR) must be submitted for every cycle that a user needs microscope time. Every proposal also requires a Safety Approval Form (SAF), which is also submitted through the PASS system once microscope time is allocated.

To start, you need to know three things:

  1. What type of proposal fits your needs? See the description of proposal types below for more details.
  2. Do you need a screening microscope, high-end microscope, or both? Here are the instruments available at the LBMS.
  3. Do you want to perform single-particle cryo-electron microscopy (cryo-EM) or cryo-electron tomography (cryo-ET)?

Questions: Please contact the User Services Office.

1. Determine the proposal type and download your template

Proposal types

There are three types of proposals for microscope time at LBMS, which are described below. They all follow a common life cycle that involves the following steps: proposal submission, feasibility evaluation, peer-review, allocation of microscope time, scheduling, carrying out the work, and reporting the results. They all require the submission and approval of screening data prior to the allocation of microscope time.

General User

General User (GU) proposals are for individual principal investigators that have preliminary (screening) data and require routine access to the microscope(s). More »

GU proposals are valid for two year (four cycles). Each proposal requests a lifetime number of 8-hour shifts to complete the work for each microscope requested. For each cycle that a user requests microscope time, an experiment time request (ETR) must be submitted against the GU proposal. Proposals are peer-reviewed by the LBMS Proposal Review Panel (PRP). All GU proposals are considered active until either: (a) all microscope time allocated to the proposal for its lifetime has been used, (b) the proposal is withdrawn, or (c) two years have elapsed. All users submitting a GU proposal are encouraged to contact the LBMS staff prior to submission.

At this time, GU proposals cannot be combined for NSLS-II and LBMS; a separate GU proposal must be submitted for each facility. All GU proposals should be submitted through the web-based Proposal Allocation, Safety, and Scheduling (PASS) system.

Users may find the GU Proposal template(.docx) handy for writing the proposal and then copying/pasting the information into PASS.

Rapid Access

Rapid Access (RA) proposals (available January 2021) are specifically for rapid access to microscope time for “hot topics” or straightforward experiments with a fast turnaround time where preliminary (screening) data are available. More »

RA proposals are valid for one cycle and typically request a very small amount of microscope time. These proposals are peer-reviewed and allocated by the LBMS PRP with a 2 – 3 week turnaround time prior to running the experiments. Any user submitting a RA proposal must contact the LBMS staff prior to submission to ensure that microscope time is available, and that the proposal complies with the RA criteria.

All RA proposals should be submitted through the web-based Proposal Allocation, Safety, and Scheduling (PASS) system.

Users may find the RA Proposal template (.docx) handy for writing their proposal and then copying/pasting the information into PASS.

Block Allocation Groups

Block Allocation Groups (BAGs) are a mode of microscope time access intended for groups of researchers that want to combine their short microscope time requests into a single proposal in order to permit greater flexibility in time allocation and scheduling. More »

BAG proposals may be motivated by shared scientific interest, geographical location, affiliation, or other synergistic reasons. Combining the microscope 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 microscope time. The term of a BAG proposal is two years (four cycles). New BAG proposals are rigorously reviewed by the LBMS Proposal Review Panel (PRP). If a BAG proposal scores well, this results in an initial microscope time allocation. For time requests in future cycles, BAGs will be required to submit a progress report reviewing their past work and a shift estimate for the next cycle. The reports are reviewed at the PRP meeting and an allocation for the next cycle will be considered. All users submitting a BAG proposal are required to contact the LBMS staff prior to submission.

At this time, BAG proposals cannot be combined for NSLS-II and LBMS; a separate BAG proposal must be submitted for each facility. All BAG proposals should be submitted through the web-based Proposal Allocation, Safety, and Scheduling (PASS) system.

Users may find the BAG Proposal template (.docx) handy for writing their proposal and then copying/pasting the information into PASS.

2. Determine the microscope(s) you need for your experiments.

The LBMS offers access to state-of-the-art cryo-electron microscopes and laboratory equipment for sample preparation. Currently, the facility has one high-end Krios G3i microscope ("Empire microscope") with a cryo-sample autoloader designed for automated applications such as single particle analysis (SPA) and cryo-electron tomography (Cryo-ET) and a K3 Direct Electron Detector with a BioQuantum energy filter for increased signal-to-noise ratio of recorded images.

LBMS also has two screening microscopes – a Talos L120C ("Powell microscope") and a Jeol 2100F ("Stonewall microscope").

For more details, see the LBMS instruments and laboratory equipment webpages.

3. Submit your proposal into the PASS system

Authentication to the Proposal Allocation, Safety, and Scheduling (PASS) system requires either a Brookhaven Lab domain account, an InCommon Federation account, or a Google account. For users that do not have a Brookhaven Lab domain account, we recommend logging in through the InCommon Federation. Many institutions participate in InCommon; see the list. If not, use an existing Google account to log into PASS or sign up for a free Google account before continuing.

If you already use your Google account to log into PASS and would like to transfer to an InCommon login through your home institution, then follow these instructions.

Transferring Your Gmail Login in PASS to an InCommon Login Through Your Home Institution

A new log-in option called InCommon is now available in the PASS system. InCommon is a federated identity management system, and if your home institution is part of the InCommon Federation, you may be able to use your home institution credentials to log into PASS instead of using a Gmail account.

If you currently use Gmail to log into PASS, below you will find the process to transfer your current PASS login account from Gmail to your home institution credentials using InCommon.

***IMPORTANT: DO NOT try to sign into PASS using InCommon until you have followed all of these steps carefully. ***

  1. Verify that your home institution is part of the InCommon Federation. You can view the list of institutions that are currently available here.
  2. Once you have verified that your home institution is part of InCommon, sign into PASS using your existing Gmail account as you usually do.
  3. Go to the “My Account” tab.
  4. If your home institution account is not already listed as an alias in the “My Email Addresses” section, you must add it there first by following the on-screen instructions to add (and verify) that email address.
  5. Once you see the home institution email address in the “My Email Addresses” section, click the “Transfer My Account” link. You will be automatically logged out of PASS.
  6. Sign in to PASS again using your existing Gmail account.
  7. You will be brought to the transfer page where you will see the email addresses available for transfer. Click the radio button next to your home institution account and click the “Transfer” button. Again you will be automatically logged out of PASS.
  8. You can now sign in to PASS with your home institution account using InCommon.

For questions please contact Nancye Wright at 631-344-USER or wright@bnl.gov.

Once you log in with your authenticated account, you will be able to view a list of your proposals and submit new proposals using the information from your proposal template. Login to PASS.