CryoSPARC
CryoSPARC (Cryo-EM Single Particle Ab-Initio Reconstruction and Classification) is a state-of-the-art scientific software platform for processing cryo-electron microscopy (cryo-EM) single particle analysis data used in research and drug discovery activities by solving 3D structures of biological specimens, such as soluble and membrane proteins and their complexes, viruses, nucleic acids, and more. It can also process negative stain electron microscopy data.
Available
The software can be installed on Puhti and Mahti. CSC recommends using Mahti for CryoSPARC usage due to its large needs of scratch disk space.
License
CryoSPARC has non-profit and commercial licensing options. The software is free-of-charge for non-profit academic use, but users must request a licence key from the CryoSPARC home page. Please consult Structura Biotechnology Inc. (sales@structura.bio) for commercial usage.
Installation
Note that every user needs to install their own instance of cryoSPARC. Shared installations are not recommended. Request port numbers for your CryoSPARC usage by sending an e-mail to CSC Service Desk. The port number and login node will be reserved to you on Puhti and/or Mahti.
The CryoSPARC installation tar file contains over 160k files, which exceeds the
default file quota (100k) for /projappl disk space. Thus, users need to apply
for an extension to the default quota when installing CryoSPARC.
CSC maintains a centralised installation of cryoSPARC worker. If you follow CSC internal instructions and use the correct lane templates, you do not need to install worker at all. The internal installation instructions on Puhti or Mahti are available at path:
Setting up SSH keys and adding your public key to MyCSC are required to be able to log in to Puhti and Mahti with SSH. SSH keys enable passwordless login, which is also helpful for CryoSPARC usage.
Please consult our documentation on:
CryoSPARC cannot be used from HPC web interfaces
CryoSPARC users may not use web interfaces for logging in to Puhti/Mahti as login nodes are randomly assigned. Please note that each user is assigned to a specific login node with a specific port range for CryoSPARC usage.
References
Please consult all publications including the one mentioned below:
Punjani, A., Rubinstein, J.L., Fleet, D.J. & Brubaker, M.A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nature Methods 14, 290-296 (2017).