FlyMine 33.0


New Expression Data

Genome-wide RNA_seq expression data for D. melanogaster have been added.  This data was produced by the modENCODE project ( and analysed by FlyBase, who calculated a single value for the expression level of each gene at each developmental stage or tissue (see for more details).  This data is available on report pages for each gene and can searched through template queries (for example: and

Improved RNAi Data

RNAi data for D. melanogaster is now loaded from  This data provides a number of new RNAi experiments and improved phenotype descriptions for both new and existing RNAi experiments.  See the RNAi templates to learn more about this data (for example: and

Yeast Interactions are back

Due to popular demand, we have put the yeast interaction data back into FlyMine.


List Analysis

  • Your list is automatically mapped to other organisms via orthologs loaded from Ensembl and TreeFam
  • Orthologue and Interactions widgets have been restored (after a user request)

Region Search

  • Extend regions at both sides by entering a value in the new input box
  • Download links are icons
  • Added the option to download chromosome sequence


  • GFF3 export correctly storing parents’ relationship
  • “Hidden” export menu now direct links on results tables
  • FIX – Export works correctly when all columns of an outer join are removed
  • FIX – Missing attributes restored in fasta format

List Upload

  • Specific object types can have a different example list on Bag Upload page, eg. protein accessions displayed if a user selected proteins, gene identifiers displayed if a user selected gene.
  • Go back in history to the filled in form, preserves the input values.
  • “Match on case” – checkbox added to list upload form to toggle case sensitivity

Report page

  • Delay fixed – caching intelligently now
  • Templates displayed in summary also displayed in “Other” category
  • Displayers show nice “No Results” message if data fails to load
  • Displayers by default loaded through AJAX to speed up page loading. Can be set to display immediately without waiting for the DOM to render.
  • Left aligned displayers to make more readable
  • FIX – counts in overlapping features displayer are now correct
  • Protein sequence – added a new displayer
  • Protein Structure ATM: turned into a popup window
  • FIX – links to Reactome correct now


  • Add toggle to show/hide empty fields in the QueryBuilder tree
  • Added a button to save/update then run template
  • FIX – if a user clicks [SHOW] in the query builder twice really fast, the field only gets added once
  • FIX – displaying messages too late when the constaint logic is edited
  • FIX – can now build templates with Chrome
  • FIX – deleting a query from query history doesn’t forward user to my mine
  • FIX – prevented name of last saved query becoming the default name in the text box

Query results

  • The values the user selected on the template form are displayed on the results page
  • Updated results table with an exact count of results when available

Template form

  • Show OR logic when appropriate
  • Fixed hyphen breaking on auto-complete in template search on template list page


  • Timestamps are now client specific and handle timezones correctly
  • Prompt users if they want to delete a list that’s being used by a query
  • Login/create account page improvements
  • Cookie saved remembering the list order preference(s).
  • Show the new size of a list after upgrade.
  • MyMine table sorting correctly
  • Renaming lists now works as expected


  • FIX – Importing templates with ONE OF constraints works correctly
  • FIX – 4 year old bug which prevented LOOKUP constraints for non-bioentities from working correctly with wildcards
  • FIX – If you remove columns when exporting number of rows returned is not changed

Published by


I make software & yarn things. Heart open*, scifi, cycling, running, veggies. 🇳🇿🇮🇱🇬🇧🇪🇺🏳️‍🌈. @yoyehudi on Twitter, but also @codeisscience & @intermineorg. @softwaresaved Fellow.