Helix/bwVisu/CryoSPARC

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

CryoSPARC License

For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to CryoSPARC and fill out the form. The license ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.

CryoSPARC in bwVisu

The application

The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute resources. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs.

The database

The CryoSPARC application creates a database in the .cryosparc directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.

Downloads

When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.

CryoSPARC and Topaz

CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: /opt/bwhpc/common/bio/topaz/0.25/bin/topaz

CryoSPARC Documentation

You can find usage information and tutorials for CryoSPARC at CryoSPARC Docs.

Known Issues

• For the default lane 'localhost', the total installed memory of a compute node is displayed. Note that you can only use the memory that you requested for the CryoSPARC application.