Cryosparc at OSC

CryoSPARC is a scientific software platform for cryo-electron microscopy (cryo-EM) data processing. OSC hosts dedicated CryoSPARC instances for research groups, allowing users to process cryo-EM data using OSC's GPU computing resources through a web browser interface.

Getting Access

CryoSPARC instances at OSC are set up on a per-group basis. Each research group gets a dedicated instance tied to their OSC project allocation.

Requesting a new instance

If your group does not yet have a CryoSPARC instance, submit a request through the OSC Help portal at https://www.osc.edu/contact/client_support_request. Please include the following information:

  • Your OSC project code (e.g. PAS1234)
  • Your CryoSPARC license ID (obtained from https://cryosparc.com)
  • Name and email of the designated PI or administrator for the instance

OSC will set up a dedicated instance and provide you with the URL to access it (e.g. https://cryopas1234.osc.edu).

Requesting access to an existing instance

If your group already has a CryoSPARC instance, your PI or designated administrator can add you as a user directly from the CryoSPARC web interface. Please see instructions below.

Adding Users

Only the instance administrator (usually the PI) can add new users. To add a user to your CryoSPARC instance:

  1. The new user must have an active OSC account. If they do not have one, direct them to https://www.osc.edu/supercomputing/portals/getting_an_account.
  2. The PI or administrator must also add the new user to the OSC project (e.g. PAS1234) through the OSC client portal at https://my.osc.edu.
  3. Log into your CryoSPARC instance as the administrator.
  4. Navigate to the top-right menu and select Admin Panel.
  5. Under the Users tab, click Create New User.
  6. Enter the new user's name, OSC username and email address and click on  Create
  7. Check User Management Tab again where you will find Newly added user with a registration tockem. Share the token with the new user and they should be able to access the instance.

Connecting to Your Instance

Your CryoSPARC instance is accessible through a web browser at the URL provided by OSC. You will need an OSC account to authenticate. If you do not have an OSC account, visit https://www.osc.edu/supercomputing/portals/getting_an_account.

Project Storage

Your CryoSPARC instance is connected to your OSC project storage on the ESS filesystem. Your project data directory will be located at:

/fs/ess/<project_code>/cryosparc/<instance_name>/project

Use this directory to store your cryo-EM datasets and project files. Make sure your project allocation has sufficient storage for your data before starting processing.

Submitting Jobs

CryoSPARC jobs at OSC run via SLURM using Lane templates. When submitting a job from the CryoSPARC interface:

  • Select the appropriate compute lane for your cluster (Pitzer or Ascend)
  • Select your OSC project account to charge the compute time to
  • Select resources based on workflow

Jobs will appear in your SLURM queue and results will be available in the CryoSPARC interface once complete.

 

Getting Help

For questions about your CryoSPARC instance, configuration, or access issues, contact OSC through the client support portal at https://www.osc.edu/contact/client_support_request.

For general CryoSPARC usage questions, refer to the official CryoSPARC documentation at https://guide.cryosparc.com.