FlyBase: News and Announcements

New to flies and need to learn how to design a genetic mating scheme? Thanks to John Roote and Andreas Prokop, there is now a four-part training package available. Explained in their recent G3 paper, this package is designed to ensure that basic knowledge on all key areas is covered in a concise and informative manner. First, a manual introduces the trainee to key topics including fly history, rationale for mating schemes, fly handling, markers and balancers, and transgenic technologies. This self-study section is followed by a practical training session on gender and marker selection, introducing real flies under the dissecting microscope. Next, through self-study of a PowerPoint presentation, trainees are guided step-by-step through a mating scheme. Finally, to consolidate knowledge, trainees are asked to design similar mating schemes reflecting routine tasks in a fly laboratory.

More info about the resource can be found here:

• http://www.g3journal.org/content/3/2/353.full
• http://www.manchester.ac.uk/aboutus/news/display/?id=9524
• http://www.cam.ac.uk/research/news/world-first-for-fly-research/
• http://www.scienceomega.com/article/819/struggling-with-your-fly-why-not-try-reading-the-manual
• http://shar.es/Yis4C

An update to the Drosophila melanogaster annotations was published by NCBI in January 2013. This update is reflected in GenBank (Jan 3), RefSeq (Jan 16), and Entrez Gene (Jan 17) records. This GenBank release corresponds to release 5.48 of the D. melanogaster genome annotation except for the changes noted below. We plan to continue to submit D. melanogaster annotation updates to NCBI approximately once a year. Exceptions to this timetable will occur when the assembly of the reference D. melanogaster genome is updated and annotations are migrated onto the new assembly.

Differences between the January 2013 GenBank annotations and those in release 5.48 of FlyBase:

1. The following transcript isoforms are not present in the GenBank submission and were subsequently deleted in annotation release 5.49 of Dmel in FlyBase as genbank validation and curator evaluation determined they were not valid models:
   • CG17273-RB
   • CG6044-RF
   • su(f)-RH
2. The following protein isoforms (and their transcripts) were deleted from the Genbank submission and a new isoform (listed) was created due to inadvertently introduced annotation errors that were subsequently corrected and are also reflected in release 5.49 of Dmel in FlyBase:
   • CG14869-PD deleted - CG14869-PE created
   • CG43248-PB deleted - CG43248-PC created
   • CG8564-PB deleted - CG8564-PC created
   • RhoGAP18B-PG deleted - RhoGAP18B-PH created
3. The following protein isoforms (and their transcripts) were renamed respectively in the GenBank submission and subsequent FlyBase releases as the listed suffix had been previously used for a different isoform in a previous GenBank submission:
   • CG8290-PC renamed to CG8290-PD
   • CG9314-PB renamed CG9314-PC
   • CG9855-PB renamed to CG9855-PC
   • Pcmt-PB renamed Pcmt-PC
   • cas-PB renamed cas-PC
   • alien-PC renamed alien-PD
   • numb-PC renamed numb-PD
   • CG30020-PB renamed CG30020-PC
   • Su(dx)-PD renamed Su(dx)-PF
   • Fbp1-PC renamed Fbp1-PD
   • Qtzl-PB renamed Qtzl-PC
   • (CG32758-PB) renamed CG32758-PC
   • CG8908-PC renamed CG8908-PE
   • grp-PE renamed grp-PF
   • CG31710-PB renamed CG31710-PD
   • Sur-8-PC renamed Sur-8-PE
   • Sur-8-PD renamed Sur-8-PF
   • CG13135-PB renamed CG13135-PC
   • CG31139-PB renamed CG31139-PC
   • CG1340-PB renamed CG1340-PC
   • Syt14-PB renamed Syt14-PD
   • toy-PB renamed toy-PC
   • Tm2-PD renamed Tm2-PF
   • Uba1-PB renamed Uba1-PC
   • bun-PI renamed bun-PO
   • CG2614-PB renamed CG2614-PC
   • dik-PB renamed dik-PC
   • CG17724-PC renamed CG17724-PE
   • CG11714-PB renamed CG11714-PC
   • CG12788-PB renamed CG12788-PD

FlyBase 2013 Release Schedule

The following are the tentative dates of FlyBase releases in 2013. There will be 6 releases this year.

• FB2013_01 - January 18^th
• FB2013_02 - March 8^th
• FB2013_03 - May 3^rd
• FB2013_04 - July 12^th
• FB2013_05 - September 13^th
• FB2013_06 - November 1^st

Please feel free to Contact us with any questions or comments.

A new version of the Drosophila White Paper is now available for public comment. The first Drosophila White Paper was written in 1999. Revisions were made in 2001, 2003, 2005, 2007 and 2009. The 2009 version is available at:
http://flybase.org/static_pages/news/whitepapers/DrosBoardWP2009.pdf

Here the Drosophila Board of Directors presents an updated White Paper identifying and prioritizing current and future needs of the Drosophila research community. This draft was prepared by the Board and will be modified according to feedback received from community.
http://flybase.org/static_pages/news/whitepapers/DrosBoardWP2012.5.pdf

We invite your participation in identifying and prioritizing resources that benefit our entire community. Please post comments on this topic on the FlyBase forum, http://flybase.org/forums/viewtopic.php?f=12&t=270 , by July 7, 2012.

Would you like to learn how to efficiently use FlyBase for your daily research needs? If so, please click over to the 2012 NAR Database Issue and read our article "FlyBase 101 - the basics of navigating FlyBase".

Peter McQuilton, Susan E. St. Pierre, Jim Thurmond, and the FlyBase Consortium
FlyBase 101 – the basics of navigating FlyBase.
Nucleic Acids Research (2011) 39:21; doi: 10.1093/nar/gkr1030

From this point forward FlyBase will be providing Apollo viewable annotation data in chado-xml format only. The latest version of Apollo has been modified to retrieve annotation data via the web in this format. Therefore, we recommend that you upgrade to the latest available version of Apollo

We will no longer provide annotation data in GAME-XML format and while Apollo is still able to load and view existing GAME-XML data the data files must be available on the local machine as web retrieval of GAME files is no longer supported.

Please be aware that when Apollo is retrieving annotation data from the web it is obtaining precomputed chunks of xml. While the pieces have been generated to not span any gene models retrieval by sequence range may not result in the exact sequence requested being loaded into Apollo.

Please use the contact FlyBase form to send questions and requests for help to FlyBase.

FlyBase offers direct "linkouts" from our gene report pages to other web-based Drosophila data services. The FlyBase Consortium wishes to thank the organizers and developers of these data sets for helping us provide a great deal of valuable information on Drosophila genes and genomes.

• BDGP in situ Gene Expression Database (http://toy.lbl.gov:8888/cgi-bin/ex/insitu.pl)
• Drosophila melanogaster Exon Database (http://proline.bic.nus.edu.sg/dedb/index.html)
• Drosophila RNAi Screening Center (http://www.flyrnai.org/)
• FLIGHT - Integrating Genomic and High-Throughput data (http://flight.licr.org/)
• Fly GRID Interaction Data (http://biodata.mshri.on.ca:80/fly_grid/servlet/SearchPage)
• FlyMine - integrated genomics and proteomics (http://www.flymine.org/)
• NCBI Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/projects/geo/)
• Heidelberg Database for RNAi Phenotypes (http://www.dkfz-heidelberg.de/signaling/ernai/ernai.html)
• Hybrigenics Drosophila PIMRider (http://pim.hybrigenics.com/pimriderext/droso/index.html)
• Yale Developmental Gene Expression (http://genome.med.yale.edu/Lifecycle/)
• InParanoid computed orthology calls (http://inparanoid.cgb.ki.se/index.html)
• PANTHER ClassificationSystem (http://www.pantherdb.org/)

In addition to these links FlyBase also provide direct links to the Drosophila records in the major international nucleotide, protein and bibliographic databases.