A Database of Drosophila Genes & Genomes

 

News and Announcements

FlyBase News
hide BLAST Upgrade and FlyBase Forum ... Dec 2007

FlyBase is pleased to announce changes to our BLAST service and a new FlyBase forum.

BLAST

Our BLAST service has undergone a significant overhaul to improve the user interface and make the results easier to view. Here are a few new features to look for:

  • Improved user interface.
  • Improved documentation.
  • Improved result page layout.
  • Added overview graphic of BLAST results
  • Added ability to download the "Hit" sequence in FASTA format.
  • Added ability to send BLAST hits to other FlyBase tools when searching annotated genes or proteins.
  • Upgraded BLAST engine to NCBI BLAST 2.2.17
We hope you enjoy these enhancements.

FlyBase Forum

We would also like to announce the immediate availability of the new FlyBase forum. The FlyBase forum provides a place for reading news from FlyBase, posting announcements, job postings, asking questions about FlyBase to us and the community. It also provides a general discussion area, a place for posting and discussing experimental protocols, and a place to search or offer stocks and reagents. To post messages you must register.

Many of the BLAST improvements and the request for a forum came directly from you so please continue to let us know what you think through the Contact FlyBase form.

Regards,
FlyBase

hide Fly Genomes in Nature ... Nov 2007

FlyBase is pleased to call your attention to the publication of the main community papers describing the sequence and analysis of the 12 Drosophila genomes in the November 8 issue of Nature.

These papers and more than 40 companion papers that are being published over the next few months in several journals represent the initial results of analyses of an incredibly rich body of information. This is a landmark event in the long and wonderful history of Drosophila genetics and genomics, and marks a new phase in comparative genomics.

We are indebted to our colleagues who participated in this community effort and are confident that both the Drosophila and the greater scientific community will benefit from their efforts. On behalf of these communities, we wish to thank the National Human Genome Research Institute (NHGRI) of NIH for funding the sequencing effort and the participating sequencing centers for producing the sequences and assemblies.

FlyBase is actively working on finalizing the annotation sets for display in FlyBase and for their submission to GenBank on behalf of the Drosophila 12 Genomes Consortium. FlyBase will also provide access to other important data sets from these initial analyses. If you have suggestions/requests for information sets from these analyses that you would like to see displayed or accessible from FlyBase, please use our Contact FlyBase form to send us these suggestions.

The specific references for the main papers are:

Drosophila 12 Genomes Consortium, 2007. Evolution of genes and genomes on the Drosophila phylogeny.
Nature 450, 203-218 (8 November).

and

Stark et al., 2007. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Nature 450, 219-232 (8 November).

hide Textpresso for Fly ... Oct 2007

FlyBase is pleased to announce the addition of a link to "Textpresso for Fly", a full-text search engine for the biological literature of the Drosophilidae. Textpresso for Fly currently contains 20,000 full text articles and 39,000 abstracts from the Drosophila literature.

Searches with keywords yield hits that consist of abstracts and (where available) complete sentences from the full text of the matching papers. In addition, more powerful and refined searches can be done with the use of categories. Categories are collections of conceptually related words whose occurrences have been marked up in the full text. For example, if one is interested in finding papers discussing the regulation of bcd, one would type the keyword "bcd" and specify the category "regulation". The search engine then returns sentences from full texts that contain at least one mention of the gene 'bcd' and at least one word or phrase from the list of terms comprising the "regulation" category. The lists of ~100 category types and their constituent terms are easily accessed from the Textpresso site. Links from the Textpresso reports lead users to the FyBase reference reports, from which the FlyBase-curated data can be accessed.

The link to "Textpresso for Fly" may be found in the "Resources" menu of the navigation bar.

hide The FB2007_02 Release ... Sep 2007

Dear Drosophila Community Colleagues:

The FB2007_02 release of FlyBase is a relatively small update to the database that adds new transposon insertions, stocks, cDNAs, and ESTs. An important change in this release is that natural transposons are now treated as a separate data class and have their own entry in QuickSearch and QueryBuilder. For specific details of the changes introduced with FB2007_02 please see the release notes. A link to the list of known problems is provided at bottom of the page.

We are also introducing the Interactions Browser with this release which allows you to explore the genetic interaction data in FlyBase. You can find this tool under the "Tools" menu or alternatively from the Genetic Interactions sections of a gene or an allele report. The tool accepts a valid gene symbol or an allele symbol in the form "fz[15]".

interaction diagram for fz[15]

You can choose to display the data on enhancers, suppressors or both categories of genetic interactions. Different colored lines on the picture displayed indicate the interaction type, and arrows show the direction of the interactions. A diagram drawn for a gene is based on the data of all alleles of a gene, which may include neomorphic alleles so it should be interpreted with care. In both the gene and allele interaction networks the query is shown in brown, and the genes or alleles that directly interact with the query are shown in dark blue. The genes and alleles that interact with the directly interacting ones are shown in light blue. The complexity of the diagrams can be regulated by altering the scan depth, and the picture can be redrawn at a different angle to improve the layout of the network on the page. Each node of the interaction diagram is a hyperlink which allows you to explore the interaction data. In addition, when you mouse-over a node in an allele diagram the context in which the genetic interactions of the allele were observed is reported in a pop-up window. In gene interaction diagrams mousing-over a node produces a pop-up window with information about the gene. We hope you find this new tool useful and look forward to hearing your comments.

Sincerely,

Your colleagues at FlyBase

Known Bugs

For the latest list see the known problems page

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 Seymour Benzer Obituary ... Dec 2007

Dear Colleagues,

It is with sadness that FlyBase notes the passing of one of the true giants of genetics, Seymour Benzer on Nov. 30. Not only did he establish the basic concept of the complementation unit (cistron) through his groundbreaking work on the rII genes in phage T4 in the early days of molecular biology, but he then switched fields completely and founded the modern era of neurogenetics through his seminal work on neurobiology and behavior in Drosophila. The legacy of this work is immense. Just as importantly, he was a dear friend and mentor to many of us and we shall miss him.

hide The Drosophila Board White Paper 2007 ... Nov 2007

Dear Fly Person,

I am writing to ask for your comments on the Drosophila Board White Paper 2007 draft. The White Paper is extremely important for informing funding agencies including the NIH and NSF of our top research priorities for the next 2-3 years. Past White Papers have helped to justify funding for valuable community resources such as insertion mutations, cDNA collections, FlyBase and fly and molecular stock centers. The Drosophila Board White Paper 2007 draft has been assembled by the Board of Directors based on input from many members of the community. For it to accurately reflect the community's priorities, we need your input now. Please download the draft and send me your comments. Do you agree with the priorities? Is something important to your research missing? Are there things in the document you do not agree with? Please send comments even if it is only to endorse the White Paper. The White Paper is most powerful when backed by everyone in the research community including students, postdocs and PI's. Your opinion matters! Download the Drosophila Board White Paper 2007 draft at:

http://flybase.org/static_pages/news/whitepapers/DrosBoardWP2007_DRAFT_11_06_07.pdf

Send comments to trudy_mackaylinkncsu.edu with "White Paper" on the subject line.

Deadline for comments: November 30, 2007.

Thank you for your help,

Trudy Mackay
For the Drosophila Board of Directors

hide 2008 Drosophila Image Award competition ... Nov 2007

Dear Drosophila Colleagues,

This is the first (and only) call for submissions for the 2008 Drosophila Image Award. The award will be presented at the upcoming Drosophila Research Conference in San Diego on April 3, 2008.

Finalists and winners of the past awards can be viewed at: http://www.drosophila-images.org/

The Image Award program has been initiated in recognition of the important role that compelling images have played in Drosophila research. To encourage and celebrate the continuing creation of such images, finalist images will be displayed on the opening evening of the conference, at which time the winner will be presented with a plaque.

The Award will be given to the most striking image that clearly conveys a point of important biological information in Drosophila research. All images that have been or will be published in a primary research journal in 2007 are eligible. Submissions can be made electronically to imageawardlinklists.berkeley.edu

We encourage you to submit your work for consideration. Submissions are open until Jan. 28, 2008

Please see http://www.drosophila-images.org/ for more details and complete instructions for submission.

Sincerely,
The Drosophila Image Award Committee:
Michelle Arbeitman
David Bilder
Ross Cagan
Brian Calvi
Peter Lawrence

hide Bloomington Drosophila Stock Center - U.S. Drosophila Import Permits ... Oct 2007

The Bloomington Stock Center is now providing new web pages on U.S. Import Permits.

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