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There are numerous ways to access your data. Each have their pro's and con's pros and cons which will be discussed. All data in is kept on SLAC's global file system and is available from all centrally managed hosts.
All experimental data is stored under /sdf/group/cryoem/exp/YYYYMM/YYYYMMDD-AA## where _<instrument> where Y is year, M is month, D is day, and AA## is the 4-character alphanumeric proposal number. Example: if your experiment name is 20180520-CS01CS01 and you collected data on TEMALPHA, then your data will be held under located at /sdf/group/cryoem/exp/201805/20180520-CS01_TEMALPHA.
Permissions to access the data can be controlled via the elogbook https://cryoem-logbook.slac.stanford.edu/lgbk/experiments. One should add the SLAC unix ID whomever should have access to the data to the list of 'collaborators' for the experiment.
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Rsync can be used over ssh to bulk transfer/synchronise data across different locations. Please use dtn02 The data transfer nodes (dtn01.slac.stanford.edu and dtn02.slac.stanford.edu have been deprecated as of January 2024. Please use centos7.slac.stanford.edu for for this purpose until further notice.
Globus
| Anchor | ||||
|---|---|---|---|---|
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One can create a free globus Globus account at at https://globusonline.org. From there, one can download a local client (Globus Connect Personal) so that files may be copied to say your laptop, or staged to another Globus Endpoint that your institution may run.
The Endpoint for SLAC CryoEM's data is Globus 4 endpoint at slac#cryoem is no longer supported.(Globus shut down all version 4 endpoints worldwide on December 18th 2023).
There is a new Globus v5 instance running but is currently (as of Feb 2024) only available to S3DF users. Email your microscope support contact for an invitation to join S3DF (the new cluster), once you accept and complete your registration at coact.slac.stanford.edu, you should be able to access the slac#s3df_globus5 endpoint from globus.org. You should use your SLAC Unix Account as credentials to log into slac#cryoem endpoint (once you have a globus id)will be asked to choose an idP (identity provider), you should be able to log in using your SLAC unix credentials to either option. The Cryo-EM data is mounted on that endpoint at:
/fs/ddn/sdf/group/cryoem/exp/
SAMBA
If you are onsite at SLAC, you can access the data via samba/cifs. You should connect to zslaccfs in order to browse the global directory. From there you can access the cryo-EM disks under cryoem.
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BBCP provides multi-stream parallel transfers of data that allows transfers speeds to be significantly higher than that of scp. Details TBD.
Summary
| Globus | SAMBA | SSHFS | RSYNC/SCP | BBCP | ||
|---|---|---|---|---|---|---|
| Software Install | Clients available, Servers should already have it installed | Implementation already baked into MAC OS and Windows. Simple install for Linux. | Requires FUSE library. Not available for Windows ( |
| I think) | Command line tools usually already installed in most Linux and MAC OSes. GUI's available for SCP. | Command line tools only | ||||
| Graphical Interface | Yes (Web) | Yes (OS) | Yes (OS) | Potentially | No | |
| Command line interface | Yes | Yes (standard OS) | Yes (standard OS) | Yes (standard OS) | Yes (standard OS) | |
| Performance | Fast | Fast | Slow | Slow | Fast | |
| Access | Anywhere | At SLAC Only | Anywhere | Anywhere | Anywhere | |
| Credentials | Globus ID + SLAC Unix | SLAC Windows | SLAC Unix | SLAC Unix | SLAC Unix | |
| Ease of Use | Easy | Easy | Medium | Difficult | Difficult |