Cambridge University Network Maintenance

FlyMine will be unavailable from approximately 9am until 5pm GMT on Thursday 29th December 2005 due to network maintenance.

Release 3.0

  • Data – new and updated
    • UPDATE: FlyBase D. melanogaster genome annotation updated to release 4.2.
    • NEW: Microarray gene expression data – currently five experiments run at the FlyChip facility are available.
    • NEW: Protein domain and family information from InterPro.
    • NEW: DrosDel deletion data added.
    • NEW: D. melanogaster genes now have full name and wild type function set.
    • UPDATE: GO annotation changes:
      • D. melanogaster and C. elegans gene associations are now taken from FlyBase and WormBase respectively.
      • Gene now has a collection of GOAnnotations, an object which contains the GO term id, name, evidence code and text from ‘with’ reference if present. If ‘with’ is a Gene or Protein a reference to the object is added.
      • GOTerm entries now have a description, namespace (‘biological_process’, ‘cellular_component’ or ‘molecular_function’) and a collection of synonyms.

    NOTE – this list does not include all updates to the versions of existing data sources – for a full list of versions see the Datasources section on the FlyMine home page.

  • Data – fixes
    • FIX: is now Gene.symbol, added which has a longer text name.
    • FIX: Transcript.exonCount is now set for all Transcripts.
    • FIX: Only RepeatRegions predicted by TRF are retrieved for A. gambiae from Ensembl.
    • FIX: There are no longer links to UniProt with BDGP identifiers.
    • FIX: Incorrect start and end fields removed from RepeatRegion.
    • FIX: Removed duplicate synonyms for some Proteins.
  • Data – known issues
    • Five genes are annotated incorrectly in the FlyBase release 4.2 annotation. These are eys, Dimp, cp309, Nev3 and kay. It is a known problem with FlyBase and a fix is progress. In FlyMine the symbols(names) are modified so that they are unique and indicate that there is a problem. Examples are: Dimp-duplicate-symbol-1, Dimp-duplicate-symbol-2 instead of Dimp.
    • The latest version of InterPro (11.0) is not yet available as a mysql dump so we still have version 10.0.
    • INDAC microarray oligos were designed to FlyBase version 4.0 transcripts. This means a number now map to old transcripts. These oligos can be queried in FlyMine, however the transcript they are designed to will not have merged with a Gene.
    • A number of proteins from Uniprot have not merged with FlyBase genes. This means that for certain genes there are two objects – one from Uniprot with no other information.
    • Orthologues for A. gambiae did not load.
  • Interface – new features
    • NEW: The start page of FlyMine now has links to a series of ‘aspects’ which are convenient starting points for the different types of data in FlyMine – such as genomics, protein interactions and gene expression. Each aspect lists relevant data sets in FlyMine, template queries and suggested starting points for queries.
    • NEW: Template search box added to the front page.
    • NEW: User templates are now listed on the user’s History page.
    • NEW: Saved bags and saved queries can be renamed from the History page.
    • NEW: Executed queries are now automatically saved to a ‘session history’. The user can permanently save a query from the session history from the History page.
    • NEW: Saved queries and queries in the session history are now displayed with the date and time at which they were created.
    • NEW: Saved queries and queries in the session history are now displayed with their starting point and a summary of the fields selected for output.
    • NEW: You can now edit an existing constraint in the query builder by clicking the blue edit icon next to the constraint.
  • Interface – fixes
    • FIX: History page is now viewable to anonymous users.
    • FIX: Characters from the Greek alphabet within identifier names should now display correctly.
    • FIX: Users can now run separate queries in separate browser windows and view results simultaneously.
    • FIX: Exported results on Windows Internet Explorer now download with the correct file name.

Release 3.1

Data – fixes

  • FIX: D. melanogaster genes from FlyBase and UniProt are now merged correctly.
  • FIX: Missing orthologues from D. melanogaster to A. gambiae are now loaded.

Release 2.1

  • Data – new sources
    • Added D. melanogaster whole genome amplimer tiling path (Genetics Department, Cambridge, UK)
  • Data – fixes
    • Fixed an off by one error with chromosome locations of FlyReg binding sites
    • GBrowse images now appear on Transcript details page
    • Removed duplicate GO (Gene Ontology) Ontology object
    • Sequences are no longer a mix of upper and lower case – now all lower case
    • Added CDS and Translation objects for each A. gambiae Transcript
    • INDAC oligos – Transcripts now correctly merged with other D. melanogaster annotation
    • All genome annotation features now have a chromosomeLocation field
  • Data – known issues
    • Information from FlyBase missing for some D. melanogaster genes due to problems reading FlyBase gff3 (fixed in FlyBase release 4.1)
    • INDAC, FlyReg and Genetics Dept (Cambridge) InfoSource objects are duplicated
  • Interface – new features
    • Template queries now work with bags – an attribute can be constrained to be in/not-in a bag
    • Template search facility added. Users can search public and private templates
    • All string matches in FlyMine queries are now case insensitive
    • Performance improvements while paging through results/collection tables
    • Collection/bag table pages are now bookmarkable
    • Keywords can be attached to template queries
  • Interface – fixes
    • Users with javascript disabled can now run queries
    • Fixed bug that stopped the user from creating certain loop-queries