FlyBase 102 - Advanced Approaches to Interrogating FlyBase ... Dec 2013
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 Consortium
- FlyBase 102 – Advanced Approaches to Interrogating FlyBase.
- Nucleic Acids Research (2013) doi: 10.1093/nar/gkr1092
Drosophila Species Stock Center user survey ... Jun 2013
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:
Roote & Prokop Mating Scheme Training Package ... Mar 2013
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:
GenBank Release corresponding to FlyBase release 5.48 ... Jan 2013
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:
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
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
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 ... Nov 2012
The following are the tentative dates of FlyBase releases in 2013. There will be 6 releases this year.
FB2013_01 - January 18th FB2013_02 - March 8th FB2013_03 - May 3rd FB2013_04 - July 12th FB2013_05 - September 13th FB2013_06 - November 1st
Please feel free to Contact us with any questions or comments.
Drosophila Board White Paper 2012 ... Jun 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 - the basics of navigating FlyBase ... Dec 2011
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