FlyMine is looking for an experineced biologist to join the team on part-time maternity cover.Â More Information.
A joint FlyMine/FlyBase workshop will held on Thursday 23rd November in the Department of Genetics, Cambridge University. For more information and booking please seeÂ workshop information.
The FlyMineÂ tutorials have now been updated. Tutorials on using the QueryBuilder, working with bags and building your own templates have been added.
FlyMine 5.0 adds genome annotation forÂ D. pseudoobscura (release 2.0 from FlyBase) andÂ A. mellifera (release 2.0 from Ensembl) with InParanoid orthologues to the other genomes in FlyMine. Also added are InParanoid orthologues to many other species and GO annotation for some of them. Interface improvements include the ability for users to tag favourite templates and to change their password.
- NEW: Genome annotation forÂ D. pseudoobscura version 2.0 from FlyBase.
- NEW: Genome annotation forÂ A. Mellifera release 2.0 from Ensembl version 37.
- NEW: InParanoid orthologues fromÂ D. melanogaster, D. pseudoobscura, A. gambiae, C. elegans andÂ A. mellifera to many other organisms.
- NEW: GO annotation (accessible via orthologues) forÂ M. musculus, R. ratticus, S. cerevisiae andÂ A. mellifera.
- NEW: Protein interaction and UniProt data for S. cerevisiae.
- NEW: IntergenicRegion class – objects to describe intergenic regions on chromosomes, sequence and overlapping features available. Genes now have references to upstream and downstream intergenic regions.
- UPDATE: Genome annotation forÂ A. gambiae updated to build AgamP3 from Ensembl version 37.
- FIX: INDAC microarray oligos now have sequences.
- FIX: OMIM disease names are no longer duplicated, new templates added to the Disease aspect.
- FIX: mRNA sequences no longer include intron sequences.
- FIX: Protein Interactions – some interactions referenced isoform ids so data didn’t merge correctly with other protein information. Now have correct UniProt accession.
- FIX: Protein interactions are now correctly assigned to Formstecher et al, 2005 – was fixed in IntAct.
- User Interface
- NEW: Favourite templates – logged in users can see a * beside template query names to select then as favourites. They are listed in a new ‘Favourites’ tab on the History page.
- NEW: Change password – users can now choose there own password when creating an account. Passwords can be changed when logged in by clicking on the username in the top menu bar.
- FIX: Missing class descriptions completed.
- NEW: Boolean fields are now constrained by a true/false dropdown.
- FIX: GBrowse images on object details pages are now oriented correctly for features on reverse strand. Also now show absolute coordinates.
- Known Issues
- Due to a change in format of XML from IntAct there are no confidence scores for protein interaction experiments, we will release a fixed version as soon as possible.
- Gene.goAnnotation collection not filled in for A. Gambiae genes, need to use Gene.annotations instead.
FlyBase gene reports now include a link directly to FlyMine gene details pages.
Major changes to layout and content of summary pages. These pages can now display the results of template queries inline to give immediate access to data. The http://www.flymine.org home page now shows aspect icons and query options. Many other interface improvements. Addition of Arbeitman et al, 2002 Drosophila time course microarray data and human disease gene matches from Homophila.
- NEW: microarray data from “Gene Expression During the Life Cycle ofÂ Drosophila melanogaster“, Arbeitman et al 2002.
- NEW: added data human disease gene matches from Homophila (http://superfly.ucsd.edu/homophila/).
- NEW: more protein interaction experiments from IntAct – see Protein Interaction aspect.
- NEW: Gene now has an “allGoAnnotation” collection that contains the term assigned to a gene plus all the parents of the term. Using this collection to find genes with a particular term will find all genes with that term *and* any with a more specific term.
- ENHANCEMENT: MRNA now references threePrimeUTR and fivePrimeUTR.
- ENHANCEMENT:Â D. melanogaster translation symbols now set from FlyBase.
- ENHANCEMENT:Â D. melanogaster chromosome bands now loaded from FlyBase.
- UPDATE:Â D. melanogaster genome annotation updated from 4.2 to 4.2.1.
- UPDATE: GO annotation and UniProt proteins updated.
- FIX:Â D. melanogaster regulatory regions from FlyBase now have chromosome location.
- FIX:Â D. melanogaster insertion sites and point mutations from FlyBase reference genes correctly.
- FIX:Â A. gambiae genes from Ensembl and InParanoid orthologues now merged correctly.
- NEW: a graph of interacting proteins on protein summary pages.
- NEW: graphs ofÂ D. melanogaster time course expression on gene details pages (Arbeitman et al, 2002).
- NEW: FASTA retrieval icon to access sequence of all features with sequence.
- FIX: insertion sites now displayed correctly on GBrowse.
- User Interface
- NEW: Template queries are now viewable inline on object summary pages.
- NEW: bags saved in history can now be subtracted from one another.
- NEW: Query constraint logic can now be manipulated within the query builder – can constrain A AND B/A OR B.
- NEW: Added Run query link to run a query directly from the History page.
- NEW: Template queries can now include a choice of several different output formats.
- ENHANCEMENT: Template search terms are highlighted in results lists.
- ENHANCEMENT: Template building integrated into query builder interface.
- Known issues
- DATA: Protein interactions from Formstecher et al, 2005 (PubMed: 15710747) are incorrectly assigned to Rain et al, 2001 (PubMed: 11196647) which in IntAct is a secondary reference.
- DATA: OMIM disease names contain the same text repeated multiple times.
FlyMine will be unavailable from approximately 9am until 5pm GMT on Thursday 29th December 2005 due to network maintenance.