FAQs

Table of Contents

1. Who does CEMC serve?
2. Is CEMC a part of S2C2/SLAC?
3. How can I begin a project with CEMC?
4. What is iLabs and how do I set it up?
5. How do I access SLAC for TEM1 and TEM4?
6. How can I access data processing resources?
7. How do I retrieve my data?
8. What are the prices for CEMC services?
9. Can I purchase grids and other consumables?
10. How can I talk to staff/manager?

Who does CEMC serve?

CEMC serves Stanford University, external academic institutions, external industries/for-profits, or anyone looking for cryo-EM services. Internal personnel need to submit a training request on iLabs. External personnel need to submit a request to begin using resources. See “How can I begin a project with CEMC?” to learn more.

Is CEMC a part of S2C2/SLAC?

While TEM1 and TEM4 are housed on SLAC property, CEMC is a separate entity from S2C2 and SLAC. We are NOT an NIH-funded national center. This means that our turnaround is usually quick and we are able to service non-academic insitutions (industry), but our revenue comes from usage fees. See “How can I begin a project with CEMC?” below for more information.

How can I begin a project with CEMC?

CEMC does not require a written proposal prior to using our facilities or requesting service. Therefore, turnaround is quick depending on staff ability.

Training for Stanford personnel begins with a training request on iLabs. See our training policy for more information.

All other inquiries (e.g. full service) begin with a request for service. We will then set up a virtual meeting to discuss the scope of the project, feasibility, and any further steps. Please provide information such as type of material to be imaged and whether it is for single-particle analysis, tomography, or FIB-Milling. You may provide any further information for the project you deem useful.

For external applicants (outside Stanford), a service contract will need to be drafted after the initial virtual meeting.

What is iLabs and how do I set it up?

iLabs is our booking and billing platform. iLabs handles all training requests, booking instruments, and billing for CEMC.

All new users need to create an account and register on iLabs. To begin, go to the iLabs website and log-in with your Stanford information (SUID) or request to obtain a new account if external.

• Stanford Personnel: Ask your lab’s financial manager for help setting up an account if needed, or reach out to staff. You will need to add your PTA info for billing.

How do I access SLAC for TEM1 and TEM4?

Follow our Work Control Plan to gain access to SLAC.

How can I access data processing resources?

Stanford Researchers doing sponsored research can request access to Sherlock, Stanford’s high performance computing cluster. To access the compute resources, you will need a valid SUNetID and PI who is willing to add you to their Sherlock group. Any member of the faculty is eligible for their own Sherlock group. All Sherlock users have access to the public partions, which include CPU nodes, GPU nodes, and large memory nodes. Users who are a member of a PI group that has purchased their own nodes will have access to those resources, as well as the entire Owner’s partition. For more information on Sherlock and all it is capable of, please visit the Sherlock documentation website. Sherlock provides a lot of pre-installed software through its module system. The Cryo-EM Center also maintains its own suite of cryo-EM software for shared use through Sherlock’s module system. To load the cryoem category, use the following command while logged into Sherlock:

module load contribs cryoem.

To see what software is available in the cryoem category, run the following command and scroll to the top of the output:

module avail

For more information on the software module system, please see the Sherlock Modules page and the Contributed Software subpage. The Cryo-EM Center cannot provide computational resources to external personnel. We can, however, process data for users (both internal and external). This is defined as a “collaboration” project.

How do I retrieve my data?

We will provide instructions for retrieving data during training. For TEM1 and TEM4, review the SLAC WCP. Globus is used for SLAC and the Aquilos data transfers. We will be converting all of our data transfers to a Globus system in the future.

For external users, a staff member will assist you in transfering data as needed.

What are the prices for CEMC services?

Stanford personnel can view our prices for Stanford via this link. You will need to be logged in to your Stanford Google account to access.

All others, please contact us.

Can I purchase grids and other consumables?

Yes! We sell grids, c-clips, rings, and grid boxes. Available and price are subject to change, and we only charge for what we bought the consumables for. We recommend that users only use us a backup. DO NOT rely on availability. Labs are encouraged to buy their own consumables.

Contact staff to purchase consumables. A table of the available consumables and prices are available here.

How can I talk to staff/manager?

Visit our communications policies for more info.