FlyBase: News and Announcements

FB2011_03, released March 21st, 2011
 
FlyBase News
show FlyBase Wishes to Thank Our Visitors at the ADRC ... Apr 2011

FlyBase would like to thank all the ADRC attendees who visited us at this years' meeting in San Diego, CA. Your input is extremely valuable to us, and we will be considering all the questions and comments you brought to us in the coming weeks.

If you didn't have a chance to stop by, you can download copies of our posters, pamphlets, and presentations on our FlyBase Guides page. If you have a question or comment about FlyBase that you didn't get to ask us please feel free to Contact FlyBase.

show Developmental Dynamics call for Drosophila papers for a Special Issue ... Feb 2011

The following is a reproduction of an announcement by Developmental Dynamics:

Call for Papers for a Special Issue in DEVELOPMENTAL DYNAMICS on “Drosophila as a Model for Understanding Development and Disease”

We are pleased to announce a call for papers for a Special Issue of Developmental Dynamics celebrating the importance of research on Drosophila in development and disease. The issue will be guest-edited by Ken Irvine (irvine@waksman.rutgers.edu), Rutgers University, and Amit Singh (amit.singh@notes.udayton.edu ), University of Dayton.

Drosophila investigators are invited to submit papers to Developmental Dynamics for a special issue of the journal to be published in late 2011 or early 2012. Papers should be submitted no later than June 15, 2011, for consideration for the special issue. Research articles exploring mechanisms of development, Technique articles describing new techniques of broad impact, or Disease Connection articles describing novel models/preparations/approaches for understanding the developmental basis of disease are welcomed. Ideas for appropriate Reviews articles are also encouraged (contact the Reviews Editor, John F. Fallon: jffallon@wisc.edu). All articles undergo thorough peer review to determine their merits for publication.

Developmental Dynamics is committed to publishing papers of central importance to the developmental biology community. All special issue articles are open access immediately upon publication, allowing your work to be disseminated widely throughout the scientific community. There are no page or color charges, and Developmental Dynamics is fully compliant with the open access policies of NIH, HHMI, and the Wellcome Trust.

Manuscripts should be submitted online at: http://mc.manuscriptcentral.com/dvdy-wiley

Author Guidelines can be found at:
http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0177/homepage/ForAuthors.html


We look forward to receiving your submissions.

Best wishes,
Gary C. Schoenwolf, Ph.D.
Editor-in-Chief, Developmental Dynamics

show In Memoriam: Victoria Finnerty ... Feb 2011

We sadly announce that Dr. Victoria Finnerty, Professor of Biology at Emory University, has passed away at the age of 73. She remained a fully active faculty member until the end of last year. She was in Chicago with her son and his family during the last few months. After her graduate and postdoctoral studies with Art Chovnick at the University of Connecticut, Vickie came to Emory in 1976 where she maintained an active lab throughout her career. Her early seminal work focused on the use of high resolution recombinational analysis of the maroon-like gene to understand gene structure in Drosophila. Her interests then shifted to understanding the molecular function of the maroon-like gene in the production of a molybdenum-containing cofactor required for the activity of xanthine dehydrogenase (rosy) and other enzymes. Vickie was well-known as a gifted teacher and mentor, and during the last several years of her career she focused most of her efforts on undergraduate education in the Emory Biology Department. Her kindness, warmth, dedication and even-tempered manner will be greatly missed by her many friends in the Drosophila community. She was loved by all who knew her.

Respectfully,
Barry Yedvobnick, Janis O'Donnell & Bill Gelbart

show modENCODE project publishes integrative analysis papers ... Jan 2011

FlyBase is pleased to note the publication on December 22, 2010 of an extremely important set of papers from the modENCODE project, including two integrative papers (one on Drosophila melanogaster and the other on Caenorhabditis elegans DNA elements) as well as a series of companion papers. The complete list of papers is available through the modENCODE website (http://blog.modencode.org/papers) and the major impact of the work is summarized in a press release from NHGRI (http://www.genome.gov/27542795).

On behalf of the Drosophila research community, we wish to acknowledge and thank NHGRI for its generous support of this major community resource project. FlyBase is in the process of working with the modENCODE project to incorporate the summary results of these studies into FlyBase. As data sets are incorporated, we will post notices describing the new data on FlyBase.

show FlyBase 2011 Release Schedule ... Oct 2010

FlyBase 2011 Release Schedule

The following are the tentative dates of FlyBase releases in 2011. There will be 10 releases this year with no releases in August and December.

  • FB2011_01 - January 21st
  • FB2011_02 - February 18th
  • FB2011_03 - March 18th March 21st
  • FB2011_04 - April 22nd
  • FB2011_05 - May 27th
  • FB2011_06 - June 24th
  • FB2011_07 - July 22nd
  • FB2011_08 - September 2nd
  • FB2011_09 - October 7th
  • FB2011_10 - November 11th

Please feel free to Contact us with any questions or comments.

show Zotero Support ... Jun 2010

FlyBase has added support for Zotero to our reference reports and any search result that returns references.

To utilize this functionality you need to use Firefox and have Zotero installed. After you have satisfied those requirements you should see a Zotero icon in the Firefox location bar any time you view a FlyBase reference report or a search result. This icon indicates that you can import the current citation or list of citations into your Zotero database by clicking on it.

For more information about Zotero please see http://www.zotero.org/.

If you have a question or comment about FlyBase please feel free to Contact FlyBase.

show New X Duplications ... May 2010

Dear Drosophilist,

The Duplication Consortium, comprised of members of the Kaufman, Bellen and Hoskins labs, has used and is using the 83 kb P[acman] libraries (Nat Methods (2009) 6:431-434) to generate a set of duplications to cover the X chromosome. The initial set of these duplications are now available at the Bloomington Drosophila Stock Center and will soon appear on the GBrowse maps at FlyBase.

The specific coverage of each of these duplications can be viewed on the Pacman Resources website at http://pacmanfly.org/dups.php as well as on the BDSC web site http://fly.bio.indiana.edu/Browse/dp/DC-Dps.php. As more duplication lines are made they will be deposited at the BDSC and they will be added to these sites. Our goal is to provide, as far as is possible, complete coverage of the euchromatic X Chromosome. We hope those of you who may need them will find them useful. Any feedback about the stocks, will be appreciated.

Sincerely,

The Duplication Consortium

show Resumption of Fly-TILL Services ... May 2010

We announce the resumption of the Fly-TILL reverse-genetics service. Fly-TILL first opened in 2005 as a non-profit service supported by user fees to discover point mutations in genes of interest for the Drosophila community. Fly-TILL uses a mismatch detection strategy developed at the Fred Hutchinson Center with NSF funding, and introduced as a service for the Arabidopsis community in 2002. The method was later applied to screening balanced Chromosome 2 and 3 lines that had been produced and maintained by Charles Zuker and colleagues at UCSD. About 200 allelic series averaging ~9 mutations per order were discovered and reported to users by the Seattle TILLING Project at the University of Washington and the Hutch (Cooper, Greene, et al. Genetics 180:661-7, 2008; Cooper, Till, et al. Fly 2:300-2, 2008), and mutant lines were distributed by the Zuker lab. Fly-TILL was suspended at the end of 2008 when the Zuker lines were no longer maintained. However, new EMS-mutagenized populations of balanced Chromosome 2 and 3 lines have been established by the Hawley group at the Stowers Institute, and DNAs have been prepared and tested for screening in collaboration with the Henikoff group at the Hutch.

We are pleased to report that the Hawley lines are more densely mutagenized than were the Zuker lines, which will allow us to maintain and screen fewer lines at lower cost to deliver a suitable allelic series. In addition, no culling of lethals was carried out on the Hawley lines, as was the case for the Zuker lines, so that a broad range of EMS-induced mutations should be present. Based on our screening and quality control tests thus far, we expect that the average allelic series will yield 7-8 mutations, of which 50% will be missense, 5% truncation and 45% silent. Because this is random mutagenesis, we cannot predict the mutation frequency and distribution of any single allelic series. A user fee of $1750 per allelic series will cover the cost of screening ~1500 DNA samples derived from the Chromosome 2 or 3 lines at the Hutch, and stocks will be distributed by the Hawley lab upon request. Former Fly-TILL users who wish to have the Hawley lines screened for same amplicons used on the Zuker lines will be billed $1500 per allelic series.

We anticipate reopening Fly-TILL service on Monday June 14, 2010, at which time orders will be processed on a first-come, first-served basis. Orders placed before then will be put in the queue, and orders in the queue will be billed and processed when Fly-TILL reopens, capacity permitting. Please note that we will not be able to maintain these beyond July 1, 2011. To learn more about Fly-TILL or to put orders in the queue, go to http://tilling.fhcrc.org/fly/. The Web site describes how TILLING works, what Fly-TILL expects to deliver, answers to frequently asked questions and user policies.

show modENCODE Survey ... Mar 2010

The people who run the modENCODE web site have asked for input from the Drosophilia community. The ENCODE and modENCODE Data Coordination Centers (DCC's) are sponsoring a joint survey to assess the usability of their sites and to solicit suggestions for the future. Please take a few minutes to complete the survey at this URL:

http://www.surveymonkey.com/s/XV666V5

They are trying to determine the extent to which the site is or is not making modENCODE data available to the fly research community — please participate. Bear in mind that the survey covers both ENCODE (the human project) and modENCODE (the fly and worm project); the two projects operate separate web-sites, and the questions on the survey are project-specific.

show FlyBase part of GO Consortium project ... Feb 2010

FlyBase is currently participating in the Gene Ontology Consortium's Reference Genome Project, a collaborative project to comprehensively annotate gene function for twelve 'Reference Genomes': D. melanogaster, H. sapiens, M. musculus, R. norvegicus, G. gallus, D. rerio, D. discoideum, A. thaliana, C. elegans, S. cerevisiae, S. pombe and E. coli. The Reference Genome project aims to improve the breadth and depth of GO annotation for participating genomes as well as provide reference annotations for newly sequenced or previously unannotated genomes.

For more information, please see the GO Reference Genome Annotation Project and this paper: PLoS Comput Biol 2009 5(7):e1000431.

show GenBank Release ... Jan 2010

An update to the Drosophila melanogaster annotations was published by NCBI on December 18, 2009. This update is reflected in GenBank, RefSeq, and Entrez Gene records. This GenBank release corresponds to release 5.22 of the D. melanogaster genome annotation except for the few changes noted below. We plan to continue to submit D. melanogaster annotation updates to NCBI approximately twice 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 December 18, 2009 GenBank annotations and those in release 5.22 of FlyBase:

  1. Annotation CG40626 is not present in the GenBank submission and was subsequently deleted in annotation release 5.23 of Dmel in FlyBase as it corresponds to a redundant fragment in the unordered scaffold U.
  2. Annotations CG15364, CG4040, CG33224 are not present in the GenBank submission as they were present in release 5.22 only due to an incomplete merge of these annotations into CG42388 that occurred in a previous release.
  3. The mRNA and protein genome location for CG41561-RA and CG41561-PA were included in the GenBank submission and in subsequent FlyBase releases as it was unintentionally deleted from release 5.22.
  4. EcR-RF and EcR-PF were renamed to EcR-RG and EcR-PG, respectively in the GenBank submission and subsequent FlyBase releases as the RF/PF suffix had been previously used for different isoforms in a previous GenBank submission.
  5. CG32573-RB and CG32573-PB were renamed to CG32573-RC and CG32573-PC, respectively in the GenBank submission and subsequent FlyBase releases as the RF/PF suffix had been previously used for a different isoform in a previous GenBank submission.
show FlyBase 2010 Release Schedule ... Oct 2010

FlyBase 2010 Release Schedule

The following are the tentative dates of FlyBase releases in 2010. There will be 9 releases this year with no releases in July, August, and December.

  • FB2010_01 - January 22nd
  • FB2010_02 - February 19th
  • FB2010_03 - March 19th
  • FB2010_04 - April 23rd
  • FB2010_05 - May 28th
  • FB2010_06 - June 25th
  • FB2010_07 - July 23rd- Canceled 1
  • FB2010_07 - September 3rd
  • FB2010_08 - October 8th - Delayed until October 13th
  • FB2010_09 - November 12th - Delayed until November 19th

Please feel free to Contact us with any questions or comments.

1. The July 23rd release has been canceled so that we can focus on a few new features and data types.

show Gene Ontology section changes ... Jul 2009

FlyBase uses Gene Ontology (GO) terms to describe the function, biological role and subcellular location of gene products. This release sees a number of improvements to the Gene Ontology section of the gene report pages.

The major change, in response to user feedback, is that all GO terms supported by experimental evidence1 in primary research papers are now grouped in a separate section. This will allow users to distinguish more readily characteristics that have been experimentally verified in Drosophila from those that are predicted based on similarity to other gene products or asserted in papers without the supporting experimental data being shown. The new sections are labelled 'Terms Based on Experimental Evidence' and 'Terms Based on Predictions or Assertions' - we indicate how many terms appear in each (note that the same term may appear in both sections).

Capturing all data from the vast Drosophila literature is a slow process and we do not yet have GO terms assigned for all genes. We have become aware that there is some confusion in distinguishing gene products that are truly uncharacterised from those that have no terms because they have not yet been thoroughly examined by a curator. To address this, for gene products where we can't find any evidence for GO terms for one or more aspect of GO, we have added a new section at the top of the gene ontology section with an explicit statement to that effect 2. We also include a date to indicate when a curator last reviewed all information for the gene product.

GO terms for Drosophila gene products are often predicted based on homology to other sequences, the presence of a well-characterised protein domain or inferred from other assigned GO terms (e.g. if a gene product has transcription factor activity we could infer it is found in the nucleus). To make it easier to see the basis of such term assignments, we have added links to the relevant sequences, domains and GO terms. Where possible we also indicate the species of the homologous gene products.

Finally, not all GO terms are assigned to Drosophila gene products by FlyBase. We now acknowledge the source of external contributions, most notably from UniProtKB, in the evidence column of the GO section.

If you have any suggestions or comments regarding the GO terms assigned to your favorite genes or how this information is presented please contact FlyBase.

(1) Note: Experimental evidence comprises of terms assigned with the evidence codes: 'inferred from direct assay', inferred from genetic interaction', 'inferred from mutant phenotype' and (the infrequently used) 'inferred from expression pattern'.

(2) Note: In the precomputed gene_association.fb file these 'known unknowns' will continue to be annotated with the most general (root) GO terms 'molecular function', 'biological process', or 'cellular component' as appropriate using the 'no data available' evidence code.

FlyBase Announcements
show 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.

show 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
show Szeged Stocks Transferred To Kyoto ... Feb 2010

Szeged Stocks Transferred To Kyoto

Following the closure of the Szeged stock centre in June 2009 the majority of the stocks have now been transferred to the DGRC in Kyoto (http://kyotofly.kit.jp/stocks).

Among the stocks now available are the complete set of molecularly-defined ED deletions and 1500 of the RS3 and RS5 lines, from the DrosDel consortium (http://www.drosdel.org.uk/). More RS lines will become available soon.

(Note: the RS insertions carry FRT sites which, for example, can be used as docking sites for FLP-mediated transgene remobilisation, using the split white + marker strategy. For review see Venken and Bellen (2007) Development 134:3571-3584.)

The RS lines are listed here:


and the ED deletions here:
show D. santomea genome release ... Jan 2010

Release of a first draft of the Drosophila santomea genome sequence (v1.0)

D. santomea was first described by Lachaise et al (2000) as a new melanogaster-group sister species endemic to the island of São Tomé off the coast of West Africa. D. santomea is most closely related to D. yakuba and the two species diverged ~0.5 Mya (Cariou et al. 2001; Llopart et al. 2005; Bachtrog et al. 2006). The species has a number of derived characters relative to D. yakuba, including highly reduced pigmentation and mating and temperature preferences, making it fertile ground for studies of the evolution of novel characters (Llopart et al. 2002; Coyne et al. 2004; Carbone et al. 2005; Llopart et al. 2005; Mas and Jallon 2005; Moehring et al. 2006; Jeong et al. 2008; Matute and Coyne 2009). The species is only partially reproductively isolated from D. yakuba, facilitating the genetic dissection of the factors underlying reproductive isolation and other derived phenotypic traits of interest.

The current draft genome represents a bwa (http://bio-bwa.sourceforge.net/bwa.shtml) assembly of 65.9 million 54 bp Illumina sequence reads to the D. yakuba reference genome sequence (release 1.3) yielding an average coverage of ~10X. Further updates are expected soon, including higher coverage with paired-end reads and a de novo assembly in collaboration with Mike Eisen at UC Berkeley.

This first release can be downloaded at this website:

http://genomics.princeton.edu/AndolfattoLab/Links.html

We hope this will stimulate evolutionary genetic research on D. santomea and other Drosophila species - enjoy!

  • Peter Andolfatto
  • Tina Hu
  • Kevin Thornton
show The 2010 Drosophila Image Award ... Dec 2009

Dear Drosophila Colleagues,

This is the ONLY call for submissions for the 2010 Drosophila Image Award. The award will be presented at the upcoming Drosophila Research Conference in Washington D.C. on April 8th, 2010.

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 2009 are eligible. Submissions can be made electronically to imageawardlinklists.berkeley.edu. Please see www.Drosophila-images.org for more details and complete instructions for submission, as well as for images of past winners.

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. 30, 2010.

Sincerely,

The Drosophila Image Award Committee:

Michelle Arbeitman

David Bilder

Ross Cagan

Brian Calvi

Anne Ephrussi

show John Sisson Memorial ... Nov 2009

Dear Colleagues,

It is with sadness that FlyBase notes the passing of John Sisson on October 27. To honor John, and to have an opportunity for his friends to gather and share their memories of John, there will be a memorial event and reception at the UT Alumni Center Connally Ballroom on Sunday, November 22, 1:00 pm to 4:00 pm. All who knew John are welcome. All are welcome to share memories of John, and there will be an audio/visual set up for this purpose. If you are likely to attend or would like to send stories about John (written or recorded) or photos, please let Paul Macdonald (pmacdonaldlink mail.utexas.edu) know.

show Drosophila Board White Paper 2009 ... Oct 2009

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 other funding agencies of our top research priorities. Past White Papers have helped to justify support for valuable community resources such as insertion mutations, stock centers, cDNA collections, and FlyBase.

The White Paper has undergone extensive revision this year. We have discontinued the third section in the 2007 White Paper (“high priority needs that may best be met by R01 support”) in an effort to emphasize community needs rather than attempting to predict which R01s should be supported. The current document has two main sections: (1) basic resources and (2) support for functional analysis of the Drosophila genome – with specific goals outlined in each section.

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

http://flybase.org/static_pages/news/whitepapers/DrosBoardWP2009.pdf

Do you have any suggestions for improving this document? 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
Past-President, Drosophila Board

show Reactome Pathway Database User Survey ... Sep 2009

Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools.  With this in mind, we are actively soliciting comments from the fly research community in order to assess community needs.   We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools.

You can access the survey at: http://tinyurl.com/l48zzq.

show DPGP announcement ... Sep 2009

DPGP announces the availability of Release 1.0 of "50 D. melanogaster genomes"

The Drosophila Population Genome Project released today the reference version (Release 1.0) of the initial sample of Drosophila melanogaster genomes sequenced by the DPGP using first generation (single-end and 36 bp) Solexa/Illumina technology and assembled using maq 0.6.8.

The sample consists of the sequences for the 5 major chromosome arms (X, 2L, 2R, 3L and 3R) for 37 inbred genomes from Trudy Mackay's set of inbred lines sampled in Raleigh, NC and a set of sequenced chromosomes (7 chrXs, 6 chr2s and 5 chr3s) from a sample of Malawi isofemale lines that were inbred using balancers. The data for each chromosome arm are in FASTQ format and list of the regions of residual heterozygosity and identity by descent are attached. Repeated sequence are filtered (set to "N"). The "raw data" are available in the NCBI Short Read Trace Archive. The average coverage of the unique portions of all these genomes is >10X.

Release 1.0 data can be accessed at http://www.dpgp.org.

show Sharing prepublication data ... Sep 2009

Please see the forum on sharing prepublication large-scale data at Nature.

show Szeged Closure ... Jun 2009

Szeged Drosophila Stock Centre will terminate its activity by June 30, 2009. Some of the collections will be transfered to other centers, while others will not be available in the future.

For more information please contact Peter Maroy, University of Szeged.

show 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