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CryoSPARC

About

CryoSPARC is a state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines.

CryoSPARC at The Wistar Institute is installed on a per-lab basis. If you wish to use CryoSPARC for your lab, please send an email to the IT Helpdesk at helpdesk@wistar.org to begin the process.

CryoSPARC

Getting Started

  1. Request an account by sending an email to helpdesk@wistar.org.
  2. Once your account is created, you will receive a TOKEN from the IT Help Desk.
  3. Login into your lab's cryosparc instance (see Login).
  4. Click New Account and input your @wistar.org email address, token, and new password.
  5. Click Create Account.
  6. You can now login with your email and password (see Password Reset).

Login

Login into your lab's CryoSPARC instance (these URLs are subject to change):

If you do not see your lab listed above and would like to use CryoSPARC for your lab, please send an email to the IT Helpdesk at helpdesk@wistar.org.

Scheduling

CryoSPARC runs on a per-lab basis. For example, if you are working on the Pallesen Lab instance, your jobs will be scheduled under the user cryosparc_pallesen.

Job Monitioring

To monitor the jobs you have submitted, use squeue and sacct commands.

squeue -u cryosparc_labname
sacct -u cryosparc_labname

Time Requirements

By default, all CryoSPARC jobs will be set to 1 hour (same as any other job). If you need longer, please ensure that you are setting the time when queuing your job to the wi-slurm lane.

CryoSPARC Time Requirement

Additional Memory Lane

By default, all CryoSPARC jobs will have a default memory request (depending on the job type). If you need more memory, please use the wi-slurm-high-mem lane when queuing your job. By default, this value will be set to 1GB, so you must make sure to request the memory (and time) that you need.

NOTE: Put only the integer value into this field. E.g., if you need 4GB, input 4.

REMINDER: Requesting high memory may lead to longer wait times for your job to start. Please only request the amount of memory that you need.

CryoSPARC Memory Requirement

Password Reset

  1. Navigate to your lab's CryoSPARC instance login page (see Login).
  2. Click Reset Password.
  3. Click I need a reset token and enter your email address.
  4. Click Request Password Reset.
  5. Contact the IT Help Desk at helpdesk@wistar.org to obtain the reset token.
  6. Back to your lab's CryoSPARC instance login page and click Reset Password.
  7. Click I have a reset token and enter your email, reset token, and new password.
  8. Click Reset Password.