Introduction to CryoSPARC for Cryo-EM data using HCC

This workshop will give participants a hands-on experience on running CryoSPARC and processing Cryo-EM data on HCC resources. Participants will learn how to access and launch CryoSPARC on HCC Swan, and how to configure CryoSPARC database and project directories. Participants will also learn how to use CPU and GPU resources for the various CryoSPARC jobs. Part of this training will utilize HCC's new National Science Foundation-funded GPU resource named PLUMAGE (Promoting Learning Using Mixed Advanced GPU Environments). During the workshop, we will process the EMPIAR-10059 dataset, which contains TRPV1 in complex with DkTx and RTX in lipid nanodiscs.

When: Tuesday, March 17th, 9:30am to 5pm CT

Where: Hybrid: In-person at UNL City Campus, Brace Lab 105 and via Zoom

NOTE: This workshop may switch to fully remote if there is not enough pre-registration for in-person attendance.

Cost:

  • $50 - University of Nebraska - UNL , UNO, UNK, UNMC
  • $100 - All other educational institutions
  • $150 - Commercial / Industry

NOTE: Registration is binding!

Workshop Level: Intermediate.

Required Prerequisites:



Learning Objectives:

  • Introduction to HCC resources
  • Access CryoSPARC on HCC Swan
  • Navigate CryoSPARC database and project directories
  • Launch CryoSPARC on HCC Swan
  • Complete hands-on tutorial of Cryo-EM data processing


Registration:

Pre-Register Now!



Schedule:

(please note schedule is still being finalized and subject to change)

9:30am - 10am

Setup and Support

Time available for setting up accounts or troubleshooting issues prior to the day's events.

10am - 10:30am

Introduction to HCC

General introduction to HCC and its resources.

10:30am - 10:45am

Break

10:45am - 11:30am

Introduction to CryoSPARC

Pre-processing, Motion Correction, and CTF Correction.

11:30am - 12:30pm

Lunch Break

12:30pm - 2pm

Introduction to CryoSPARC (cont.)

Particle Picking, Particle Curation, and 2D Classification.

2pm - 2:15pm

Break

2:15pm - 4:15pm

Introduction to CryoSPARC (cont.)

Ab-Initio Reconstruction, 3D Refinement, and Local Refinement.

4:15pm - 4:30pm

Open Questions

Time available for questions about today's events.


Dataset

During the workshop, we will process the EMPIAR-10059 dataset, which contains TRPV1 in complex with DkTx and RTX in lipid nanodiscs. The dataset will be provided for all workshop participants.

Setup for Hands-On

Setup Instructions for OOD.



Useful links and commands:


Logistics Page/

Workshop Feedback

HCC info sheet

HCC SLURM scheduler cheat sheet

Please contact us at hcc-support@unl.edu if you have questions or concerns and we will be happy to help!