News and Announcements

The FB2009_01 release includes an overview of the precomputed files generated by FlyBase, and several new ways to view molecularly localized aberrations, including by entire arm or chromosome.

In GBrowse a new view is available that shows molecularly localized genes and aberrations. To select this view choose "Drosophila aberrations" from the "Data Source" menu in the main GBrowse window. It allows you to view aberrations up to 3Mb in size, and will also display the location of transposon insertion sites when you look at an interval of less than 300Kb.

Aberrations that delete the entire interval displayed are referred to as "Spanning Aberrations" and hovering over the dark red line produces a table listing these aberrations. Hyperlinks within the table allow you to navigate to the report on each aberration.

When you place your mouse over an aberration an alphabetical list of all the genes predicted to be affected by the aberration (deleted or truncated) appears. Clicking on the aberration will take you to the FlyBase report page for the aberration. Similarly, hovering over a gene or transposon insertion site displays information about it, and clicking on it takes you to the corresponding report.

Aberration Maps for Arms and Chromosomes

Images showing all molecularly localized aberrations and genes by arm or chromosome are also availabe from the Aberration Maps page listed in the Tools menu. The links on the page take you to the left end of the arm or chromosome, and the entire extent can be viewed by scrolling to the right. Like the new GBrowse view, information about an aberration or gene can be obtained by hovering over it. A copy of the images of the arms and chromosomes can be downloaded from the aberrations section of the precomputed files page.

Deficiency Maps in Aberration Reports

Each FlyBase report describing one of the Df()ED, Df()Exel, Df()BSC and Df()FDD class of aberrations contains an image showing the genes predicted to be uncovered by the aberration, and overlapping or neighbouring molecularly localized aberrations. Clicking on a gene or aberration will take you to the appropriate report. You can also move to the new GBrowse view of the molecularly localized aberrations by clicking on the "GBrowse" link listed on the left hand side of the picture.

FlyBase has eliminated the e-mail address flybase-helpmorgan.harvard.edu because that address had been hopelessly compromised by spammers. Although the address had been hidden behind our help form in recent years, it was exposed on the site for many years prior and had become the source of a vast and relentlessly growing quantity of spam. If you use the Contact FlyBase help form on the web site you will not be affected by this change. If you prefer to e-mail us directly you will need to use the help form to ask for the new address. This address may change periodically in the future, but you will always be able to reach us via the Contact FlyBase form and we will continue to provide the direct e-mail address to those who request it.

We are introducing chromosome maps for the 12 sequenced Drosophila species with the FB2008_08 release, which are based on the ones publised in Schaeffer et. al., Genetics 179: 1601-1655 2008, and the well characterised physical and genetic maps for Drosophila melanogaster. The maps show the sequence scaffolds aligned to the polytene chromosome maps for the Muller elements of each species. For more information on the syntenic relationships among the 12 sequenced genomes, their standard chromosomal numbering and corresponding Muller element please see the Muller Element Arm Synteny Table. The different Muller elements of the species selected can be viewed by using the controls at the top right hand side of the map.

The aligned sequence scaffolds are indicated on the maps in blue and and moving your cursor over a scaffold will produce a yellow box that corresponds to a window in GBrowse.

The location of the GBrowse window is updated as you move along a sequence scaffold and clicking on the yellow box will take you to the corresponding location in GBrowse. The controls at the top of the page allow you to alter the size of the GBrowse window.

You can move around the chromosome maps by using the arrows at the top left hand corner of the map, or by dragging on the surface of the map. Alternatively, you can change your location by dragging the blue box shown in the overview map at the bottom right hand corner of the map window. The "Center" button allows you to rapidly return to the initial view of the map. You can also zoom in or out of the maps by clicking on the "+" and "-" buttons found under the arrow keys in the top left hand corner of the map in a similar fashion to Google Maps.

We hope you find the maps useful and welcome your comments and suggestions.

Report on the results of the FlyBase survey undertaken November 2007.

We were very pleased that respondents find that FlyBase is proving a valuable resource, with 65% of using FlyBase once a day or more and 80% finding FlyBase invaluable or very helpful in their genetic research activities. We were also pleased that most respondents who had contacted us for help found our response very good or good (88%). For a detailed breakdown of the results please see the acompanying PDF.

More importantly, your responses have been key in setting our priorities for the future, and we urge you to continue to give us suggestions for how we can improve the ability of FlyBase to assist your research. We need to understand FlyBase users' needs in order to make best use of our limited resources. We received too many suggestions to discuss all of them in this summary, and although all the points that were raised are being considered by the FlyBase team, we would like to highlight here a few of the lessons we learned from the survey.

• Formalizing the structure of the data can result in reports that are not easy to read and understand. On the one hand users want to find out the basics of what is known about a gene from a short summary written in plain English. On the other hand using "controlled vocabularies" or "ontologies" is essential to produce a database that can be effectively searched (if different terms are used to describe the same thing, then to find all the entries for that thing, you would have to search with all possible terms; if you always use the same term, then one search is comprehensive). These contrasting needs were also reflected in the responses we received, for example when we asked "Are there data that are difficult to interpret because of formatting or presentation?" we received these two opposing responses:
  • "The automated descriptions of gene function are very poor. I reckon that's because GO doesn't work. GO and controlled vocabulary is great for informatics, but awful for the average grad student wanting to do genetics."
  • "The textual descriptions of gene expression are utterly useless for the computational community. Someone should sit down and translate them into the official vocabulary."
  We recognize that both approaches are essential: controlled vocabularies for effective searching and textual descriptions for summarizing subtle aspects of genetic, phenotypic and expression information. We have realized that no single approach will solve all problems, so we will be providing a variety of summaries. We will transfer "Red Book" summaries for the classical markers and visible phenotypes in the adult. Many users found Tom Brody's Interactive Fly a good source of information, and he has kindly agreed to supply FlyBase with his gene summaries. In addition we will set up a gene wiki, so that users can contribute to gene summaries, both in an attributed way or adding to a collective summary. We are investigating other approaches as well and welcome your further suggestions.
• We are currently working hard to eliminate the problem that one can click on a data topic only to discover there is nothing in that category (empty matryoshka). If you haven't already noticed it, you can use Profile Manager to set your own configurations of which parts of the gene report are open by default.
• We are significantly accelerating literature incorporation into FlyBase. We will describe our detailed plans separately, but one important feature will be to seek your help, by asking authors to give us key bits of information from the paper on a data entry web site. A number of users also asked for protein interaction data and information about useful reagents, such as antibodies. We will begin to incorporate these data types in the next several months.
• The phenotypic and expression data need to be improved, and methods developed to improve our ability to search for genes with similar phenotypes or expression patterns.
• Many of you would like FlyBase search tools to guess, "like Google", at what you are looking for when you type something that is not in the database. FlyBase provides the equivalent of Google spell-checking for symbols by including in the database extensive symbol synonyms. If you search for a known variant of a gene or other symbol, the record will be found. We plan to provide additional help by offering Google-style suggestions based on extension of the letters you have already typed. We will not, however, be able to provide search tools that test for all possible variants of what you have typed (even Google doesn't do that).
• Information about orthologs and gene families need to be improved. We are replacing the current ortholog identifiers with gene symbols, and if possible names, from the other species. We are also evaluating optimal ways to present alignments and relationships amongst orthologs and gene families, and we expect the first results of these efforts to be publicly accessible in the next several months.
• We had been concerned that those FlyBase users at great distance from our servers in Indiana might have much slower access to FlyBase; if so, this would have argued for the establishment of FlyBase mirrors around the globe. Here is the perception of the speed of the website from those countries with substantial numbers of survey respondents:
   

  Total

  Fast

  Acceptable

  Slow

  Canada

  29

  13 (45%)

  13 (45%)

  3 (10%)

  France

  58

  20 (34%)

  36 (62%)

  2 (3%)

  Germany

  52

  23 (44%)

  26 (50%)

  3 (6%)

  Spain

  32

  14 (44%)

  17 (53%)

  1 (3%)

  UK

  116

  41 (35%)

  61 (52%)

  14 (12%)

  USA

  481

  138 (29%)

  276 (57%)

  63 (13%)
  It can be seen that there is no correlation between the speed of FlyBase site and the country of access; therefore we concluded that mirrors would not improve speed of access to FlyBase. Rather, we expect that the speed of access reflects a complex set of issues such as local network conditions, capacity and configuration of individual desktops, browser choices and other issues that are largely out of our control.

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).

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.

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.

Dear Fly Person,

Every two years the Drosophila Board, together with extensive input from the fly community, revises and publishes the Drosophila Board White Paper. This document is extremely useful for informing NIH and NSF of our top research priorities. 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 White Paper is scheduled for an update this year, and I am writing to ask for your input.

Please download and read the latest version of the White Paper:

http://flybase.org/static_pages/news/whitepapers/DrosBoardWP2007.pdf

• Which projects on the list remain high priority?
• What are the bottlenecks to current research using Drosophila?
• What do you see as the emerging projects or technologies that should be encouraged or supported?

Your input to this process is essential for maintaining and expanding our research tools. Please take the time to send your comments and ideas so that our stated priorities accurately represent the fly community for the next few years. Respond to me, to your regional Representative on the Board, or to any member of the Board. Our email addresses can be found at:

http://flybase.org/static_pages/news/board.html

Thank you for your help,

Carl Thummel
President, Drosophila Board

The award will be presented at the upcoming Drosophila Research Conference in Chicago on March 5th, 2009.

The Image Award recognizes the important role that compelling images have played in Drosophila research.  To encourage and celebrate this role, finalist images will be displayed throughout the conference, and 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 2008 are eligible.  Submissions can be made electronically to imageawardlists.berkeley.edu. Please see www.Drosophila-images.org for more details and complete instructions for submission, as well as for images of past winners.

This year, we will be accepting submissions of videos as well as still images.  These will be considered in a single competition - there will not be a separate category for videos. See the website for size and format for submission.

We encourage you to submit your work for consideration. Submissions are open until Jan. 15, 2009.

Sincerely,

The Drosophila Image Award Committee:

Michelle Arbeitman
David Bilder
Ross Cagan
Brian Calvi
Peter Lawrence

NHGRI announced the Data Release Policy agreed for the ENCODE and modENCODE Projects.

The modENCODE White Paper [PDF] proposes

• "The sequencing of 8 additional fruitfly and 7 nematode species selected specifically for their potential to enhance modENCODE's goal of complete functional annotation of DNA elements in the genomes of Drosophila melanogaster and Caenorhabditis elegans."

The NHGRI would like input from the fly community on the draft Data Release Policy that has been developed for the ENCODE and modENCODE Projects.

NHGRI has updated the data release plan for the ENCODE (Encyclopedia of DNA elements) and model organism ENCODE (modENCODE) Projects (see http://www.genome.gov/ENCODE and http://www.genome.gov/modENCODE, respectively), which are designed to identify all functional elements in the genomes of human (ENCODE), and Drosophila melanogaster and Caenorhabditis elegans (modENCODE). NHGRI has designated both ENCODE and modENCODE as "community resource projects." Accordingly, the data release plan is based on the principles set forth in the Fort Lauderdale agreement (http://www.genome.gov/Pages/Research/WellcomeReport0303.pdf). This update provides more specificity to the data release guidelines.

The Fort Lauderdale agreement noted that the success and utility of community resource projects is based on mutual and independent responsibilities for the production and use of the resource by the resource producers, the resource users, and the funding agencies. The update of the ENCODE/modENCODE data release plan has been developed in consultation with the members of the ENCODE and modENCODE Consortia, and with the External Consultants Panel for the projects. As the plan is intended to take into account the needs and responsibilities of the resource users, we would like to offer the research community an opportunity to provide feedback on the proposal before the plan is finalized. Comments on the plan should be sent to Encodemail.nih.gov by Wednesday, October 15, 2008.

The Drosophila Genetic Reference Panel White Paper 2008 [PDF] proposes

• "The sequencing of a D. melanogaster genetic reference panel of 192 wild-type lines from a single natural population which have been inbred to homozygosity, and for which extensive information on complex trait phenotypes has been collected. This will create: (1) A community resource for association mapping of quantitative trait loci. Within this project we will demonstrate such mapping and provide candidate quantitative trait polymorphisms for traits relevant to human health. (2) A community resource of common Drosophila sequence polymorphisms (SNPs and indels) with a minor allele frequency (MAF) of 0.02 or greater. These variants will be valuable for high resolution QTL mapping as well as mapping alleles of major effect, molecular population genetic analyses, and allele specific transcription studies, among others. (3) A 'test bench' for statistical methods used in QTL association and mapping studies for traits affecting human disease."

FlyBase congratulates Allan Spradling on receiving the Gruber 2008 Genetics Prize

Are you in the academic lineage from Thomas Hunt Morgan? The Drosophila Researcher Genealogy begun by Keith Maggert has been expanded and incorporated into the Academic Tree Project. You can now log in and add yourself, your students, your advisors, and collaborators to the tree for Drosophila researchers. The Fly Tree currently includes over 1200 people. Put yourself on the tree at http://www.academictree.org/flytree/

Questions and comments can be directed to Mike Dietrich at: Michael.DietrichDartmouth.edu

The family of Ed Lewis has finished a project that Ed Lewis started before his death: to publish the amazing artwork of his wife, Pam. An on-line version of this book can be accessed at http://www.fruitfly.org/lewis/Site/Back.html. Several of her pen and ink and watercolors have been used in posters for scientific meetings. The Lewis family invites you to enjoy them.

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.

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_mackayncsu.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