Release 9.0

In release 9.0 we have updated the D. melanogaster genome to release 5.3 and the A. gambiae genome to release AgamP3.4. We have added mRNA localisation data from Fly-FISH (Krause lab) and updated many other sources of data.

Genome Updates

The D. melanogaster genome has been updated to release 5.3 from FlyBase. The A. gambiae genome has been updated to release AgamP3.4 from Ensembl. Note that with this genome build the identifier scheme has changed – the primary identifiers for A. gambiaefeatures now used in FlyMine are those from VectorBase.

Fly-FISH data

mRNA subcellular localisation data for D. melanogaster from Fly-FISH has been added. There is a new widget on the gene list analysis page to display the numbers of genes in the list that are localised, not localised or not expressed.

Other data changes

Many data sources have been updated to the latest available versions. See the Data tab for more details.

  • NEW – Four more D. melanogaster RNAi screens added from the DRSC.
  • UPDATE – All 14 screens from the DRSC have a standardized results annotation, making it easier to query all of them simultaneously.
  • FIX – first authors of publications are now set correctly.
  • FIX - D. melanogaster Affymetrix probes no longer have genome locations – the locations were previously for an old genome assembly.
  • FIX - A. mellifera genes and proteins are now linked together where possible, GO annotation is now attached to genes.
  • FIX – evidence for proteins from UniProt is correctly set to Swiss-Prot or TrEmbl.

User interface changes

  • NEW – spaces can be used as separators again in the list upload page – gene names with spaces should be quoted – e.g. “even skipped”.
  • NEW – widgets and template sections are now collapsed in list analysis page to improve page navigation.
  • FIX – list upload from a file now works on Safari.
  • FIX – FASTA export for Translation sequence is now fixed.
  • FIX – links to VectorBase now correctly access gene pages.
  • FIX – annoying ‘Found 1 match(es) message removed from results page.
  • FIX – correct template name/description displayed when clicking on ‘Show in table’ in a report page.
  • FIX – some classes weren’t listed in the class chooser in the QueryBuilder tab, now fixed.
  • FIX – text in template form dropdowns should now always be displayed correctly.
  • FIX – fixed bug with setting ascending/descending sort order in QueryBuilder.

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I make software & yarn things. Heart open*, scifi, cycling, running, veggies. 🇳🇿🇮🇱🇬🇧🇪🇺🏳️‍🌈. @yoyehudi on Twitter, but also @codeisscience & @intermineorg. @softwaresaved Fellow 2018.