FAST TRACK TO GENE ANNOTATION AND GENOME ANALYSIS
Sunsetting DNA Subway 1.0

DNA Subway Transition FAQ

  1. Why is DNA Subway being sunsetted?

    2. The current DNA Subway platform is built on outdated software and services that are no longer supported. This creates security vulnerabilities and risks of system failure. Transitioning to DNA Subway 2.0 ensures a modern, secure, and reliable platform for users.

  2. Will I need to create a new account on DNA Subway 2.0?

    3. Yes, all users will need to create new accounts on DNA Subway 2.0. This allows us to ensure the best possible user experience and compatibility with the updated platform.

  3. What will happen to my existing project data on DNA Subway?

    4. Most project data from the current DNA Subway will not transition to DNA Subway 2.0. Users must download or document their project outputs and data before the platform is sunsetted on June 30, 2025.

  4. Will DNA sequence data from Genewiz/Azenta be supported in DNA Subway 2.0?

    5. Yes, DNA Subway 2.0 will continue to support DNA sequence data from Genewiz/Azenta, ensuring seamless integration for Sanger sequencing projects.

  5. What about next-generation sequencing data uploaded to CyVerse?

    6. Next-generation sequencing data that you have uploaded to CyVerse will still be available through your CyVerse account. These data are stored independently of the DNA Subway platform. You can learn about exporting or managing your CyVerse data at https://learning.cyverse.org/ds/.

  6. How do I export or save my data from the current DNA Subway?

    7. Projects cannot be exported from DNA Subway 1.0. Users must use existing download features to export individual results such as trimmed sequences, phylogenetic trees, or other outputs.

  7. What are the existing download features for the DNA Subway blue line?

    • Trace files: Open the "Sequence Viewer" popup and download them with the download icon. Keep in mind trace files uploaded by Genewiz/Azenta will remain available as an upload source in DNA Subway 2.0.
    • FASTA files, including edited data: To download any subset of the sequences in your project as a multi-sequence FASTA file, you can open the "Select Data" popup, choose any number of sequences to include in the download, and click the "Download" button that appears on the right.
    • MUSCLE: Open the "MUSCLE" popup and click the button at the bottom that says "Download this alignment" to download this as a FASTA file. There is no built-in way to download the MUSCLE alignment viewer, so you may wish to use your computer's built-in screenshot options to capture it.
    • Phylogenetic Trees: Open the "PHYLIP NJ" or "PHYLIP ML" popup and click one of the buttons at the bottom to download the tree as an svg, an image, or a newick file.

  8. How can I download green and purple line output files?

    9. You can find the location of the output files for each task by clicking "View Job Info" (or, for FastX Toolkit, clicking the task under the file name) and looking for the archivePath or archiveSystemDir. You can navigate to that path on the CyVerse Data Store. Additionally, the URL for the Green Line Shiny app may remain available, so you can make a note of it.

  9. Can I still access and use the current DNA Subway?

    10. Yes, the current DNA Subway will remain operational until June 30, 2025. However, we encourage users to begin transitioning their projects and data as soon as possible.

  10. What is the timeline for the DNA Subway 2.0 transition?

    • Through June 30, 2025: The current site will remain operational to support ongoing projects through the Spring 2025 semester. Availability is contingent, and new security or operational concerns could alter this availability.
    • June 30, 2025: Full retirement of the Red Line and Yellow Line components.

  11. How do I participate in alpha or beta testing for DNA Subway 2.0?

    12. Users can sign up for alpha and beta testing opportunities on the transition website: https://dnasubway.cyverse.org/sunset/. Testing feedback will help us improve the platform for all users.

  12. Who can I contact if I have more questions about the transition?

    13. For additional support, do not contact CyVerse. Please visit the transition page or contact the DNA Subway team directly at dnalcadmin@cshl.edu.

 

Contact Us Resources Credits About Sunsetting