Background

The web application that has been responsible for much of sequencing data delivery, SLIMS, will be retired on May 30, 2025.  The DNA Technologies Core will be moving to a single data delivery tool, Bioshare, for all types of sequencing data.  Old or existing sequencing data will still be available through the new application, but should best be downloaded at the earliest opportunity.  This page explains what the transition will entail for clients.

Accessing New Sequencing Data

New sequencing data will be delivered to clients using Bioshare, much the way it is currently done for PacBio and Nanopore data.  Each sample submission that clients create will have data delivered in a new "share".

When the sequencing data is ready for delivery, a share (a "bucket" of data) will be created for that submission, and access will be granted to the submitter, the PI, and any contacts that were added for that submission.  Bioshare uses the emails from the submission to control access, so please be sure to enter the correct emails when submitting your samples.  Bioshare should automatically email you (from no-reply@bioshare.genomecenter.ucdavis.edu) when you have been granted access to a new share.  If you are a first time Bioshare user, an account creation email will also be sent with a temporary password.

Data can be browsed and downloaded using the web application, but when downloading large datasets, it is recommended that you use SFTP or rsync.  Please see the documentation for Bioshare for details.

Accessing Old Sequencing Data

We know clients may still need to access their past sequencing data from SLIMS for a few months, which is why we have created an application that will permit access to older data as we transition.  The application, which will go into production mode on Wednesday, May 21, is available at:

https://slims.coreomics.com

Please note, that the same login that you were using for the old SLIMS application should work.  If you are unable to remember the password or would like to change it, you may do so using the password reset link (password resets made before May 21 will have to be redone):

https://slims.coreomics.com/accounts/password_reset/

Once logged in, you should be directed to your user profile, which contains a list of runs and associated data.  You may also export the full list of runs as a CSV, which includes the URL for accessing the data.  The associated data is still hosted on the same server, and the new system will simply link to it (e.g. http://slimsdata.genomecenter.ucdavis.edu/Data/RANDOM_DIR/).  Instructions for archiving SLIMS data from this source will remain the same for old data.  Please archive your old data as soon as possible, as this access is only temporary.