FlyMine 30.0

We have changed the way the lists are handled between FlyMine releases.

After each FlyBase release, we build a new FlyMine database and release a new version of FlyMine.  It is possible that genes saved in a user’s list have been merged or deleted from the new FlyBase database.  Previously, the FlyMine team upgraded everyone’s lists for them automatically.  This has the drawback of being time-consuming and opaque to the users.

So we have updated our system to require the user to manually resolve any conflicts.  Usually there will be no changes and no action will need to be taken.  However, if a user’s list has changed in FlyBase, users must go to the “My Mine” section of FlyMine and upgrade their lists manually before the list can be used.

You can check the status of your lists by visiting the “Lists” page in the “My Mine” section of FlyMine at http://www.flymine.org/query/mymine.do.  In the last column will be the list’s status:

  1. Current – The list is current, no action is needed
  2. Not current – The list is in the queue to be upgraded, you may have to wait a minute or so.
  3. Upgrade – The list contains genes that have been merged or deleted and needs to be upgraded.  Click on the “Upgrade” link and follow the instructions.

We hope the new system will be an improvement and make it more clear if list contents change over time.

UPDATES AND BUG FIXES

  • NEW – Sequence features can be exported as a file or sent to Galaxy in UCSC BED format
  • NEW – We now use human readable names for data labels and column names; previously we used the database field name
  • NEW – The region search has an additional parameter that allows you to extend your regions at both sides
  • NEW – Expression enrichment widget for Probesets
  • FIX – Some yeast and worm genes had not merged properly, the duplicates have now been removed
  • NEW – Better link outs to more external databases
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