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.
- 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)
- 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
- 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
- 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
- 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
- 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