Dear Drosophila PIs-
As President of FlyBoard, I am writing to call your attention to a critical issue that has arisen for our community. The NIH institute (NHGRI) that supports Flybase and other Model Organism Databases (MODs) is changing their funding approach. These changes are reported today in Nature (http://www.nature.com/news/1.20134) as well as previously in Science (http://science.sciencemag.org/content/351/6268/14.long). NIH has put forth a plan where FlyBase and its equivalents for C. elegans, yeast, zebrafish, mouse and rat would combine into a single ‘uberMOD’, with an upcoming 30% cut in funding. While integration will increase accessibility of the functional data that each community has collected over decades, the current plan with its reduced funding will have a severe impact on Flybase's ability to maintain Drosophila-specific datasets that many of us rely on daily.
Because of the concern about this plan and its broad impact on many thousands of researchers, leaders of model organism communities have come together to write a letter to NIH leadership that strongly supports the MODs and advocates for maintaining species-specific datasets with requisite funding. A bevy of prominent signatories, including Nobel laureates, heads of scientific societies, and National Academy members have already endorsed this initiative. We hope to gather thousands of additional signatures and present the letter to NIH Director Francis Collins at the TAGC meeting in Orlando. The letter can be easily signed on a website, created by our partners at the Genetics Society of America (GSA), with your name and just two simple questions about your location and any NIH funding. These questions simply allow us to collate signatory numbers should NIH request a breakdown along these lines.
The link is http://www.genetics-gsa.org/MODsupport.
We urge you to add your name to the Statement of Support. We also urge you to forward this email to the trainees in your lab, as we aim to collect signatures from all MOD users who concur (for the question about NIH support, we can consider those who work in an NIH-funded lab to be NIH-supported). Finally, we encourage you to spread the word through your colleagues and via social media. We have every hope that a strong show of support, via an outpouring of signatures, will help shape the NHGRI plan to preserve the MOD features that are most important to our research enterprise.
President, Fly Board
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.