MODENCODE DATA ACCESS WEBINAR
"Understanding worm and fly transcriptome data"
Thursday Mar 1, 12:00 EST

modENCODE project aims to provide the biological research community with a comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D.melanogaster. Data Coordination Center for modENCODE is conducting a series of webinars with the next one, "Understanding worm and fly transcriptome data", scheduled on Thursday Mar 1, 12:00 EST (Eastern US time). This webinar will introduce the participant to the transcriptome analysis data generated in Robert Waterston's lab (C. elegans) and Susan Celniker's lab (D. melanogaster), all data sets accessible via www.modencode.org.

Space is limited so advance registration is necessary. Please email helpmodencode.org to reserve your spot. More details and the schedule are at

http://wiki.modencode.org/project/index.php/DCC_Usability_webinars

FlyBase is saddened to announce the passing of Jim Crow, an eminent and long time contributor to Drosophila genetics and evolutionary theory. We note that GENETICS had just begun a series of articles describing Jim’s many contribution to science, teaching and public service. Three of these are linked below as PDF files.

Wisconsin State Journal obituary article

Genetics editorial article (PDF)

Abrahamson article (PDF)

Hartl article (PDF)

FlyBase sadly reports the passing of Art Chovnik a prominent member of the Drosophila community. His contributions to the analysis of gene structure and regulation were numerous and seminal. The following obituary was taken from a web posting noting his passing.

Arthur Chovnick, a pioneer of modern genetic analysis in higher organisms, passed away on Monday, (September 5, 2011), after a long illness. Dr. Chovnick created materials and strategies that shaped the framework of his field for several decades. His breakthrough methods for approaching the analysis of recombination and gene organization using Drosophila melanogaster (fruit flies) rather than micro-organisms (bacteria and phages) allowed a vast expansion of genetic studies. As professor of Genetics and Cell Biology at the University of Connecticut, his intellectual impact continues through the many students and postdoctoral fellows he trained, as well as through his editorial positions at the journals Genetics, Genetical Research, and Fundamental Genetics. His influence extended through his work as director of the Cold Spring Harbor Laboratory (1960-1962), as fellow of the American Association for the Advancement of Science (since 1963), and through his active memberships in the Genetics Society of America and the Connecticut Academy of Science and Engineering, where he was a founding member. Dr. Chovnick contributed ninety articles to respected scientific journals on the topics of organization and control of eukaryotic gene expression, developmental genetics, recombination mechanisms, transposable elements, and transformation. First awarded a National Institute of Health (NIH) postdoctoral research fellowship in 1953, upon earning his Ph.D. in genetics from Ohio State University, Dr. Chovnick proudly maintained the longest continuous grant in the history of the NIH, running from 1953 and past his retirement as Emeritus Professor in 1994. Dr. Chovnick also received an honorary Doctor of Science degree from Guelph University, as well as the University of Connecticut Alumni Association Research Excellence Award. Earlier in life, he interrupted his undergraduate studies at Indiana University to serve in the Navy during World War ll. Arthur Chovnick was born August 2, 1927, in Brooklyn, NY, the son of Fannie and Herman Chovnick. He is survived by his wife, Elinor, of 62 years; his daughter, Lisa of Princeton, NJ, and her husband, Herbert Bibbero; his son, Benjamin, of Willimantic, CT and his wife, Florence Caillard; his brothers Stanley Chovnick and his wife Julie and Arnold Channing; his sister, Lenora Weseley and her husband Martin; his grandchilden Anna, Adam, and Philip; and many nieces, nephews, friends and colleagues.

Memorial donations may be made to the Arthur Chovnick Graduate Fellowship in Genetics at the University of Connecticut. Please make checks payable to: The UConn Foundation noting "Chovnick Fellowship" on the memo line. Send to: UConn Foundation, 2390 Alumni Drive, Unit 3206, Storrs, CT 06269-2410.

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

Since the 2007 publication of the 12 species genomes, the genomes of nine additional species have been sequenced, bringing the total to 21. The UCSD stock center has the strains of the newly sequenced species in addition to a number of other stocks of each of these. Please visit the DSSC website for more information:

https://stockcenter.ucsd.edu/info/welcome.php

FlyBase 2012 Release Schedule

The following are the tentative dates of FlyBase releases in 2012. There will be 6 releases this year.

• FB2012_01 - January 20^th
• FB2012_02 - March 2^nd
• FB2012_03 - May 4^th
• FB2012_04 - July 6^th
• FB2012_05 - September 7^th
• FB2012_06 - November 2^nd

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

On behalf of the entire Drosophila research community, FlyBase congratulates Nobel Laureate Jules Hoffmann. Professor Hoffmann was honored with a share of the Nobel Prize in Physiology or Medicine 2011 for his pioneering work on the innate immune system using Drosophila. Hoffmann and colleagues are in particular cited for having provided the first evidence that Toll receptors mediate the innate immune response.

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 (irvinewaksman.rutgers.edu), Rutgers University, and Amit Singh (amit.singhnotes.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: jffallonwisc.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

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

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.

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 October 10th
• FB2011_10 - November 11th November 18th

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

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.

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

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.

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.

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.