Walter Jakob Gehring
March 20, 1939 – May 29, 2014
It is with extreme sadness, FlyBase announces that Walter Gehring, one of the major figures of Drosophila genetics tragically passed away on May 29th as a result of injuries from an auto accident. Walter‘s fundamental contributions to the molecular genetics and developmental biology of Drosophila are too numerous to list here. As important as his research contributions are, he also leaves behind the legacy of an exceptional list of former students and postdoctoral fellows. For most of his career, he was a Professor at the Biozentrum and we refer you to their obituary of Walter. We extend our deepest sympathies to his wife Elsbeth, his family, friends and colleagues.
Insect Genetic Technologies
Research Coordination Network
Insect genome sequence data provide enormous insights into insect biology. Genetic technologies that enable genomes to be manipulated are critical for gaining a deep understanding of how genomes function.
On April 1, 2014 a five-year National Science Foundation Research Coordination Network focusing on Insect Genetic Technologies was begun. The public face and organizational node of the Insect Genetic Technology Research Coordination Network (IGTRCN) is the network's recently launched website – www.igtrcn.org.
The IGTRCN's goal is to connect research communities working on insects that have an abundance of genetic technologies and technical knowledge with others who have fewer technologies and less experience.
The IGTRCN will leverage the abundance of knowledge and technology already available against the needs of researchers working on insect systems with genome sequence data but few functional genomic technologies.
The IGTRCN will organize symposia, offer laboratory-based technical workshops, and fund peer-to-peer training fellowships, all of which are intended to enhance research capacity and encourage collaboration.
Reed's law asserts that the utility of large networks, particularly social networks, can scale exponentially with the size of the network. This is an exciting project that has the potential to significantly contribute to the study of insects.
This is an open network and students, postdocs, research associates, technicians, researchers and faculty at all career stages are welcome to become affiliated with the IGTRCN.
For more information visit www.igtrcn.org or David O'Brochta, dobrochtumd.edu, 240-314-6343
FlyBase 2014 Release Schedule
The following are the tentative dates of FlyBase releases in 2014. There will be 6 releases this year.
- FB2014_01 - January 17th
- FB2014_02 - March 14th
- FB2014_03 - May 9th
- FB2014_04 - July 11th
- FB2014_05 - September 5th
- FB2014_06 - November 11th
Please feel free to Contact us with any questions or comments.
Already read our FlyBase 101 paper, so you think you know all there is to know about searching FlyBase? What about using TermLink to search using our controlled vocabulary terms, or using QueryBuilder to search across multiple report pages? What's that, want to query our database directly but don't know how? Sounds like you need our FlyBase 102 - Advanced Approaches to Interrogating FlyBase paper:
Susan E. St. Pierre,
Laura Ponting, Raymund Stefancsik, Peter McQuilton, and the FlyBase
FlyBase 102 – Advanced Approaches to Interrogating FlyBase.
Nucleic Acids Research (2013) doi: 10.1093/nar/gkr1092
The UCSD Stock Center has created a survey to assess the use of its services. Please take this 5-minute survey to help the Drosophila Species Stock Center align its mission with the needs of the Drosophila community:
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:
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:
transcript isoforms are not present in the GenBank submission
subsequently deleted in annotation release 5.49 of Dmel in FlyBase
validation and curator evaluation determined they were not valid models:
protein isoforms (and their transcripts) were deleted
from the Genbank
submission and a new isoform (listed) was created due to
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
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
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.