Release 10.0

Release 10.0 of FlyMine includes an update of data from FlyBase, a new A. gambiae gene expression data set and some user interface changes.

Data

The D. melanogaster genome has been updated to release 5.4 from FlyBase. We have added a new microarray-based gene expression data set for the life cycle of A. gambiae. ‘Life cycle transcriptome of the malaria mosquito Anopheles gambiae and comparison with the fruitfly Drosophila melanogaster.’ (Koutsos et al 2007 - PubMed).

Other data changes:

  • FIX – duplicate introns have been removed for D. melanogaster and D. pseudoobscura, FlyMine used to infer introns but they are now imported from FlyBase.
  • FIX – introns are now created on the correct strand for A. gambiae and A. mellifera.
  • FIX – orthologues for A. gambiae, A. mellifera and A. aegypti now reference genes as well as translations, they will now appear in results of more template queries.
  • FIX - D. pseudoobscura ‘Unknown’ assembly groups are no longer created as chromosomes.
  • FIX – the ‘localised’ category has been removed for fly-FISH expression data, the data now just shows whether a gene is expressed or not at a particular stage.

List Conversion

The List analysis page has a new ‘Convert’ section for instant conversion between common types (genes, proteins, transcripts and exons). Counts of each type are displayed for a list – e.g. the numbers of proteins, transcripts and exons found for a list of genes. Clicking on the type will bring up a results table from which you can export identifiers, sequence or create a new list.

External links

We have added links to more external databases from report pages – e.g. to model organism databases and REDfly. We now have a simple configuration system for links so if you have suggestions of other databases it would by useful to link to please let us know – support[at]flymine.org.

Tutorial and FAQ

We have added a tutorial on creating and using lists in FlyMine, see the help page. There is also a list of Frequently Asked Questionslinked to from the header.

User interface changes

  • NEW – the queries run when clicking on graphs or tables in list analysis widgets now include more information.
  • NEW – number of rows shown in results tables is remembered.
  • FIX – performance improvement for uploading lists with more than 1000 elements.
  • FIX – fixed problem where user was logged out or history was lost when returning to the home page.
  • FIX – uploading a list from a file is fixed on Safari.
  • FIX – it is now more obvious when long text entries have been truncated in results tables.
  • FIX – fixed ‘div has no properties’ error in templates tab if user created two templates with the same title.
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