FlyMine 33.0

Data

New Expression Data

Genome-wide RNA_seq expression data for D. melanogaster have been added.  This data was produced by the modENCODE project (www.modencode.org) and analysed by FlyBase, who calculated a single value for the expression level of each gene at each developmental stage or tissue (see http://flybase.org/reports/FBrf0212041.html for more details).  This data is available on report pages for each gene and can searched through template queries (for example: www.flymine.org/query/template.do?name=Gene_RNA_seq and www.flymine.org/query/template.do?name=RNA_seq_Genes).

Improved RNAi Data

RNAi data for D. melanogaster is now loaded from http://www.genomernai.org.  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: http://www.flymine.org/query/template.do?name=Gene_RNAi&scope=all and http://www.flymine.org/query/template.do?name=RNAiScreen_genes&scope=all)

Yeast Interactions are back

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

Website

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

Export

  • 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

QueryBuilder

  • 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

MyMine

  • 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

Other

  • 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
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