FlyBase News
Support Statement: D. Bilder

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.


Sincerely,

David Bilder

President, Fly Board

Professor, UC-Berkeley

Video tutorials survey results

FlyBase Community Advisory Group (FCAG) survey: Video Tutorial

Thank you for all of you who participated in our latest survey, it has been very helpful. The results of the survey are available here.

If you wish to contribute to future surveys, please join FCAG.

GenBank Release

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

White Paper 2012

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.

FlyBase 101

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

Drosophila Network News (bionet.drosophila)

  • Search and read Drosophila network news at www.bio.net
  • Post a new article to dros/bionet.drosophila via the BIOSCI mail-Usenet gateway: droslinknet.bio.net