New Release: FB2014_04, released July 21st, 2014
FB2014_04, released July 21st, 2014
 
 

A Database of Drosophila Genes & Genomes

News and Announcements

FLYBASE NEWS
hide The FB2007_01 release ... Aug 2007

Dear Drosophila Community Colleagues:

FlyBase is pleased to release FB2007_01, which provides an updated set of gene annotations, new data curated from the literature, new images and new and updated stock lists, and resolves many of the problems present in FB2006_01. Of special note, thanks to a collaboration with the BDGP and DHGP, FB2007_01 includes Drosophila melanogaster genome Release_5.2, which is the first nonredundant release of the D. melanogaster euchromatin and heterochromatin assemblies and annotations. For specific details of the changes introduced with FB2007_01 please see the release notes. We are aware that some problems still exist, and we welcome your feedback if you find a mistake on the web pages. A link to the list of known problems is provided at bottom of the page.

With this release we are introducing new versions of QueryBuilder and the "Field Data" option of the Batch Download By ID tool. Both of these programs now list a set of options closely corresponding to the fields present on the report pages, and we hope this will make them much easier to use. We have also revised the QueryBuilder interface so that common operations can be performed within a single window. In addition, the list of results produced by QuickSearch now offers you the chance to analyse your search results for the frequency of common data. For example, you can list the results of a gene search by the frequency of shared GO molecular function terms. The "HitList Conversion Tools" button, found above a list of search results, has also been updated to allow you to export your list of results to QueryBuilder and refine your query by adding additional search criteria.

There have also been a few small changes to the web pages. In the polypeptide reports we have added values for the molecular weight and pI, and in the transcript reports we have added a measure of confidence for each transcript. The criteria used to generate these confidence scores are described in detail in the reference manual.

We hope you enjoy working with FB2007_01 and look forward to your input.

Sincerely,

Your colleagues at FlyBase

Known Bugs

For the latest list see the known problems page

hide New GBrowse feature ... May 2007

Gene summaries and information on transgenic insertions

We have introduced pop-ups into GBrowse to provide you with a gene summary when you place your mouse over a gene span, and information on an insertion when you hover over the transgene insertion site.

These features are available for the D. melanogaster genome and the "Insertions in Stock Collections" data.

In the GBrowse view of the D. pseudoobscura genome mousing over a gene span also produces a pop-up with information on the gene. However, we do not provide information about the GLEANR high confidence prediction sets in the other genomes, but you can obtain information about the putative D. melanogaster ortholog by hovering over the ortholog track if an orthology call has been made.

We hope you find the pop-ups useful and welcome your feedback.

hide Summaries and in situ images ... May 2007

FlyBase is introducing two major changes to the the gene report pages.

In situ images

In a collaboration with FlyExpress we are including in situ images in the FlyBase gene reports. These images, which originate from the BDGP gene expression project, are located under the "EXPRESSION DATA" section of the "GENE PRODUCTS & EXPRESSION" part of the report page. If you click on one of the images you are taken to a FlyExpress page showing in situ images of the gene for that particular stage of embryonic development. If you would like to see all the FlyExpress in situ images of the gene, or search for similar patterns, you can click on the link at the bottom of the section.

Gene summaries return

Many respondents to the FlyBase User Survey requested the return of gene summaries. Summaries that provide an overview of selected classes of gene information have now been incorporated into FlyBase gene reports. Like the previous gene summaries, the new summaries are automatically generated, but using a different algorithm that better represents the range of information in a selected class. The included categories are: gene identifiers, map location, molecular function, biological process, number of alleles and their phenotypes, and numbers of transcripts and proteins. A file of the summaries can be downloaded from the Precomputed Files page. We hope you find these summaries useful and welcome your feedback.

hide Profile Manager released ... Feb 2007

FlyBase has released a new feature for our collapsible reports called Profile Manager. The Profile Manager lets you configure the open and closed state of sections on a report page and save the configuration to a named profile. Here is a list of things you can do with the Profile Manager:

  • Save multiple configurations of a report page to named profiles of your choice.
  • Create profiles that span more than one data class (e.g. Gene -> Alleles).
  • Backup your profiles in case your browser cookies are deleted.
  • Transfer profiles to other computers.
For a full list of functionality and instructions on how to use it please see the Profile Manager help.

FLYBASE ANNOUNCEMENTS
hide Apollo Support ... Sep 2006

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.

hide Linkouts in FlyBase ... Mar 2006

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.

COMMUNITY NEWS & ANNOUNCEMENTS
hide AAA Nature Submission Announcement ... Aug 2007

Dear Colleagues,

The AAA 12 Fly Genomes Coordinating Committee is pleased to announce that the two main papers on the analysis of these genomes were submitted to Nature on July 19 and 23, and are currently in review. Mike Eisen and Andy Clark are the lead authors on the comparative evolution paper and Manolis Kellis on the comparative approaches to the annotation of D. melanogaster manuscript.

We want to again state our appreciation to the National Human Genome Research Institute (NHGRI) for their support of the sequencing and analysis of these genomes. We especially want to thank you all for your patience in working with us on contributions to and coordination with these manuscripts.

If the reviews on the Nature papers are positive, and factoring in some time for revisions, we and Nature are targetting early November 2007 for publication. Nature will be coordinating with the companion paper journals on publication and associated announcements.

We want to be sure that we know of all companion papers that are in the queue, either from the journals listed above or from other journals. This will help us and Nature do the necessary coordination. Just to be sure that we know of all the companion papers, even if you've notified us previously, please forward the following information to Bill Gelbart (gelbartlinkmorgan.harvard.edu):

  • Title
  • Authors
  • Journal
  • A .pdf file of your paper

You should also check that your companion paper journal editor is communicating with the lead editor at Nature (Chris Gunter: c.gunterlinknaturedc.com) on coordination.

Again, thank you for your support and understanding, and we look forward to the celebration of this special event in print in the near future.

Sincerely,

The AAA 12 Fly Genomes Coordinating Committee

hide modENCODE Request ... Aug 2007

The groups within the modENCODE project would like community input in deciding on a list of transcription factors to test for genome-wide binding sites using ChIP-chip and ChIP-Seq methods. The availability of suitable antibodies as well as community priorities are important factors in deciding which transcription factors will be mapped first.

Please visit the modENCODE project wiki pages to nominate and vote on the transcription factors that you believe should have high priority. (You will need to create an account, but it should only take a minute or two.)

hide Degree in Genetics and Molecular Biology honoris causa Awarded to Dan L. Lindsley ... Jun 2007

On behalf of our Drosophila colleagues at the University of Rome, FlyBase is delighted to announce that on July 2nd 2007 the University of Rome "La Sapienza" will confer on Dan L. Lindsley a degree in Genetics and Molecular Biology honoris causa. The ceremony will take place in the Aula Magna of "La Sapienza" at 10:30 am.

As many of you know Dan's tireless efforts in the production of the Red Books laid the ground-work for what you now see on the www as FlyBase. However Dan's contributions go well beyond this community effort and include seminal contributions to the field of chromosome mechanics and our understanding of the genetic regulation of meiosis and male fertility to name but three.

We at FlyBase offer Dan our heartfelt congratulations on this very well deserved honor.

hide Tucson Drosophila Stock Center - new international rates ... May 2007

The Tucson Stock center has announced a change in its rates for International customers.

hide 12 genomes - update ... Mar 2007

Dear Drosophila Genome Colleagues,

This is an update on the status of the submissions of the main manuscripts on the initial analyses of the 12 Drosophila genomes. Though there has been unavoidable slippage due to the complexities of handling all of this genomic data at once, the manuscript preparation is in its final phase and the manuscripts are targeted for submission by mid-March.

If you have a companion paper that you have submitted, the lead authors of the two papers (Manolis Kellis, conservation paper; Michael Eisen and Andy Clark, evolution paper) request that you send them the Author, Title and Journal information for cross-referencing for our submissions and, if possible, a pdf of the submitted manuscript.

Their email address are:

  • Manolis Kellis: manolilinkmit.edu
  • Michael Eisen: MBEisenlinklbl.gov
  • Andy Clark: ac347linkcornell.edu

Thank you for continuing input in bringing this challenging project to a successful conclusion.

Sincerely,

The 12 Genomes Coordinating Committee

hide 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