FB2016_04, released July 28, 2016
 
 

A Database of Drosophila Genes & Genomes

New in this release

 
 

FlyBase will list here changes and improvements to the website, organized according to FlyBase releases, with the most recent release at the top.

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  • July 28 (with the release)
    Gene Snapshots
    Gene Snapshots are short, manually curated summaries aiming to provide a quick overview of the function of a gene's products. We contacted the Drosophila community for expert knowledge and are very grateful for the large number of responses. The new concise summaries appear at the top of each gene page, and will shortly be downloadable to use as an aid in genome-wide analyses and screens. Please see this Commentary for more information.
  • July 28 (with the release)
    R. norvegicus, 3 new algorithms added to Orthologs DIOPT search
    A new model organism species, R. norvegicus, and ortholog prediction algorithms from HGNC, Panther, and ZFIN, have been added to the FlyBase QuickSearch Orthologs DIOPT search.
  • July 28 (with the release)
    Gene Groups update
    Several new groups have been added to the Gene Groups resource, including Glycoside hydrolase family (18 members), Heat Shock Proteins and Potassium channel subunits. Gene Groups can be searched using the QuickSearch tab on the homepage or browsed as a list.
hide FB2016_03
 
  • May 24 (with the release)
    New protein domains GBrowse track
    FlyBase is integrating protein domain data generated by Pfam into our site. As of the May 2016 release, there is a new GBrowse track (Protein domains (PFAM) under the "Aligned Evidence" section of the tracks listing) showing protein domains, where you can see these domains aligned with the genome sequence and protein transcript tracks.
  • May 24 (with the release)
    Transcription start site data
    Transcription start site (TSS) data, as described in Batut et al., 2013 (RAMPAGE) and Ahsan et al., 2009 (machiBase) is now available in GBrowse. These data comprise the mapped 5´ ends of capped transcripts for various developmental stages, as well as over 31,000 discrete TSS calls from the RAMPAGE dataset. Look for RAMPAGE TSS or MachiBase tracks listed under the "Aligned Evidence" section of the track selection page.
  • May 24 (with the release)
    Small RNA-Seq data
    Jaaved Mohammed and Eric Lai have generously provided FlyBase with small RNA-Seq coverage profiles for 13 developmental stage, 5 tissues and 26 cell lines. These coverage profiles have been generated by remapping and consolidating hundreds of RNA-Seq experiments characterizing small RNA species (<30nt). These profiles should be of interest to those studying the biology of miRNA, piRNA and siRNA. Many thanks to the Lai lab for these data, which are available as GBrowse tracks under the "small RNA-Seq" section of the tracks listing. Track names for these data are:
    Developmental stages, stranded small RNA-Seq (Lai lab)
    Tissues, stranded small RNA-Seq (Lai lab)
    Tissue culture cells (Schneider + embryonic), stranded small RNA-Seq (Lai lab)
    Tissue culture cells (imaginal disc), stranded small RNA-Seq (Lai lab)
    Tissue culture cells (CNS, ovary, blood), stranded small RNA-Seq (Lai lab)
  • May 24 (with the release)
    DIS entries updated
    Articles published in Drosophila Information Service (DIS) during the period 2006-2015 (volumes 89-98) inclusive were previously absent from FlyBase, but have now been incorporated as of this release. They can be viewed here. Authors are encouraged to use our Fast-Track Your Paper tool for these articles in order to prioritise them for further data curation and to make associations with the key genes described therein.
  • May 24 (with the release)
    Chromosome maps
    Chromosome map images have been re-annotated and returned to the FlyBase website. Muller elements for twelve Drosophila species can be viewed here.
    The original images of these chromosome maps, as well as many other maps and a useful table of genomic, genetic and cytological coordinates for all annotated D. melanogaster genes can be found in the new "Maps" section of the FlyBase "External Resources" page: http://flybase.org/wiki/FlyBase:Maps
  • May 24 (with the release)
    ID Converter upgrade
    The FlyBase ID conversion tool has been improved to handle new ID types. In addition to FlyBase IDs and symbols, you can now enter PubMed IDs or GenBank/Uniprot/Swiss-Prot/TrEMBL accessions for conversion to FlyBase genes or other data types.
hide FB2016_02
 
  • March 30 (with the release)
    New orthology data and query tool
    FlyBase has incorporated orthology predictions between genes of 8 model organisms from the DRSC Integrative Ortholog Prediction Tool (DIOPT). These DIOPT-derived orthology calls are now shown explicitly within the 'Orthologs' section of D. melanogaster Gene Reports, alongside our exisiting orthology set from OrthoDB that is biased towards species closely related to D. melanogaster. Both datasets are searchable through the new 'Orthologs' tab of our QuickSearch tool.
  • March 30 (with the release)
    miRNA annotation set update
    The FlyBase miRNA annotation set has been updated to correspond with miRBase release 21. This has added a number of new miRNA annotations for D. melanogaster (18), D. virilis (60) and D. pseudoobscura (1). In addition the remapping of the D. simulans miRBase annotations to the new release 2 assembly resulted in the elimination of 16 miRNA gene annotations, primarily removing redundant annotations that were due to assembly artifacts.
  • March 30 (with the release)
    Systematic nomenclature for D. melanogaster tRNA genes
    We have worked with the Genomic tRNA database (GtRNAdb) to systematically identify and assign informative nomenclature to the ~300 nuclear genes encoding cytoplasmic tRNAs in D. melanogaster. These data are best viewed via the new Gene Group page for these genes here.
  • March 30 (with the release)
    P{acman} clones now in GBrowse
    PacMan clones from the Chori-321 and Chori-322 libraries can now be viewed in Gbrowse by selecting those tracks from the 'Other reagents' section on the 'Select Tracks' tab of GBrowse.
hide FB2016_01
 
  • January 14 (with the release)
    External Resources pages
    The FlyBase website contains hundreds of links to useful external sites concerning stocks, antibodies, CRISPR, and more. These links have been gathered together and placed on the FlyBase Wiki as several well-organized lists for easy browsing:  http://flybase.org/wiki/FlyBase:External_Resources
    A prominant new button (External Resources) on the FlyBase home page will take you there, or use the navigation menu at Links → External Resources.
  • January 14 (with the release)
    New video tutorials
    New video tutorials have been made to help you navigate in and use FlyBase. You can find the new videos under Help → Video Tutorials.
  • January 14 (with the release)
    P{acman} clones
    Information on 49422 concordantly mapped P{acman} clones has been added to FlyBase. 12456 of these clones are from the CHORI-321 library (average insert size 83 kb) and 36966 are from the CHORI-322 library (average insert size 21 kb). Construction and characterization of these libraries are described in FBrf0209231. Information on these clones are available in FlyBase in the relevant clone and dataset reports. See the links in the 'External Crossreferences and Linkouts' section of a clone report to determine if a clone is available for purchase from BACPAC resources.
  • January 14 (with the release)
    Histone modification and TFBS data for embryonic mesoderm: GBrowse tracks
    Histone modification data for the embryonic mesoderm are now available (Bonn et al., 2012). These include ChIP-seq genomic occupancy data for H3K4me1, H3K4me3, H3K27Ac, H3K27me3, H3K36me3, H3K79me3 and RNA Pol II (RpII33 subunit) obtained from purified embyronic mesodermal cells. FlyBase offers the ChIP-Seq peak calls in a new GBrowse track, listed under the "Noncoding Features" section of the tracks listing:
    Histone Modifications - mesoderm (Furlong lab, ChiP-Seq peak calls)
    ChIP-chip genome binding data for transcription factors key to mesodermal development are now available. Data for 13 transcription factors at various points of embryogenesis (28 samples in all) have been kindly provided by Eileen Furlong's lab (EMBL), comprising several studies: Zinzen et al., 2009, Bonn et al., 2012, Junion et al., 2012, Rembold et al., 2014 and Ciglar et al., 2014. FlyBase offers the ChIP-chip peak calls in a new GBrowse track, listed under the "Noncoding Features" section of the tracks listing:
    TFBS - mesoderm (Furlong lab, ChiP-chip)
  • December 12
    Community page
    Several community-building resources in the FlyBase site have been consolidated into a new Community page. Sign up for our newsletter or Twitter feed, use the FlyBase People database, or visit the FlyBase Forum. Click on the “Join Our Community” button in the FlyBase home page sidebar.
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hide FB2015_05
 
  • October 28
    RNA-Seq tools re-organized
    The four most-used tools for access to FlyBase RNA-Seq data: GBrowse, RNA-Seq Profile, RNA-Seq Similarity, and RNA-Seq By Region, have several new entry points. FlyBase users can now find these tools gathered under a single menu heading (Tools ⇒ RNA-Seq Tools), and the QuickSearch Expression tab now has a panel with links to each tool. Each of these access points also has a link to a new RNA-Seq tools summary page, where you can learn more about how and when to use each of these tools, with links to the tools and in-depth help.
  • November 20 (with the release)
    D. virilis release incremented
    At the request of the NCBI, 4 rRNA annotations have been removed from the D. virilis genome. The D. virilis release number has been incremented to 1.04.
hide FB2015_04
 
  • September 3 (with the release)
    Fast-Track Your Paper tool upgrade
    The FlyBase Fast-Track Your Paper community curation tool has been upgraded. New features of note include being able to upload a list of genes to associate with your paper, 'sessions' so you can go back and change mistakes in a submission, or even take a break and finish entering data later, and more flexibility in ordering data entry tasks. Please see this Commentary for more information.
  • September 3 (with the release)
    Human Disease Model reports
    The FB2015_04 release of FlyBase includes the addition of Human Disease Model reports, which integrate all the disease-related information from multiple reports in FlyBase. These reports highlight the role of systems modeled in flies on research into human disease and the potential impact of the results on translational research. One of the purposes of this report format is to provide a less specialized entry point for non-Drosophila researchers and for Drosophila researchers newly interested in Drosophila disease model systems.
    Please see this Commentary for more information.
  • September 3 (with the release)
    GBrowse improvements
    Following a recent FlyBase Community Advisory Group survey, several improvements have been made to GBrowse. The default tracks have been updated, a Snapshot feature, allowing you to easily save and view images, has been made more accessible and additional help documentation has been added.
  • September 3 (with the release)
    Changes to FlyBase home page and navigation
    The addition of the new Gene Groups tab to QuickSearch necessitated the partitioning of the QuickSearch tabs into two rows. FlyBase has also restructured the navigation bar and left sidebar.
  • September 3 (with the release)
    Gene Groups data class additions
    FlyBase users can now browse a list of gene groups, or search for Gene Group report pages using the new QuickSearch tab. A new bulk data file is also available here.
  • September 3 (with the release)
    VDRC Vienna Tiles GBrowse track
    FlyBase now offers a GBrowse track to help users browse lines from the VDRC Vienna Tiles (VT) GAL4 collection, listed in the "Other Reagents" section of the GBrowse Track Selection page. The glyphs represent putative enhancers used to generate fly stocks carrying GAL4 transgenic constructs. Clicking the glyph brings up the associated Sequence Feature report - see the "Associated information" section for related genes and constructs (links to stock reports therein): e.g., VT020839. The FlyBase VDRC-VT report offers additional details about the VDRC-VT collection.
  • September 3 (with the release)
    Improved esyN interactions graphic on gene reports
    FlyBase has incorporated a number of improvements to the interactive esyN network graphics. In the gene report, users can now choose to display interactions between neighbors (i.e., interactions between interactors of the gene of interest). To make better sense of complicated networks, three different layout options are available: force directed (default), circle and concentric. These configuration options are shown to the left of the esyN display. FlyBase also now offers esyN displays in the interaction report, where the two subjects of the interaction report are highlighted in pink, and common interactors of the two factors are highlighted in purple. The force directed, circle and concentric layout options are also available in these interaction report graphics. Please note that these new configuration options do not work in older versions of Safari (v5). FlyBase would like to thank the esyN group (http://www.esyn.org/) for making these new configuration options possible.
hide FB2015_03
 
  • June 26 (with the release)
    Protein Domains tab in QuickSearch
    The QuickSearch tool on the FlyBase home page has a new tab for searching genes using InterPro protein domain annotations.
  • June 26 (with the release)
    esyN interaction view in gene reports
    FlyBase gene reports now include an interactions graphic provided by esyN. The network is interactive, and a linkout goes to the same interaction network at the esyN site, where further configuration and editing is available.
  • June 26 (with the release)
    New reports for non-transposable element based insertions
    FlyBase already produces an Insertion Report for insertions of transposable-element based transgenic constructs, e.g. P{GawB}Dllem212. Starting in the fb_2015_03 release, we now also generate an Insertion Report if exogenous DNA is inserted into the genome via non-transposable element-based means. In this case, since no transposable-element ends are present, the ends of the inserted element are designated using 'TI' (for 'transgene insertion') e.g. TI{GAL4}. Please see this Commentary for more information.
  • June 26 (with the release)
    RNA-Seq by Region query tool
    The new RNA-Seq By Region tool reports the average (per base) expression level for a given genomic region in the modENCODE developmental and tissue RNA-Seq transcriptome profiles. This tool allows one to evaluate the approximate expression level of individual exons, parts of exons, introns and/or intergenic regions. It can be accessed from any FlyBase gene report, in the “High-Throughput Expression Data” sub-section of the “Expression Data” section. Please see this Commentary for more information.
    Please note that the tool previously called “RNA-Seq Search” has been renamed to “RNA-Seq Profile Search”; FlyBase hopes this change will prevent possible confusion between the two tools.
hide FB2015_02
 
  • March 1
    FlyBase newsletter launched
    FlyBase users have indicated on surveys that their preferred method of contact is via email. Accordingly, FlyBase will be sending an occasional mailing to our user list, with release announcements, web site updates, and important Drosophila community news. Our first such newsletter went out on March 1 of this year.
    If you would like to subscribe, go to our signup page.
  • May 4 (with the release)
    Gene Group reports
    FlyBase is introducing new ‘Gene Group Reports’, which will bring together genes/gene products that are acknowledged to form a biological group, such as members of a gene family (e.g. Actins, Wnts), subunits of a protein complex (e.g. proteasome, ribosome), or another functional grouping (e.g. Ubiquitin E3 ligases). Gene Groups may be searched via the Simple tab of QuickSearch, or navigated to via the new ‘Gene Group Membership’ section of a Gene Report.
  • May 4 (with the release)
    3 more species genome annotations updated
    Annotations generated by NCBI as part of their GNOMON annotation pipeline will replace the CAF1 generated annotations that have not changed since 2006. Three additional species; D. mojavensis, D. virilis and D. willistoni now have updated GNOMON annotations for a total of 8 species.
  • May 4 (with the release)
    Gene-level genetic interaction data
    A gene-level summary of genetic interaction data for D. melanogaster genes is now being computed each release from the allele-level genetic interaction statements captured by FlyBase (this new summary replaces out-of-date gene-level genetic interaction data that was no longer being maintained). The summary gives an overview of the genetic interactions for a gene, complementing the allele-level statements which give a detailed view of each individual interaction.
    The gene-level genetic interaction data can be accessed in two ways:
    1. The ‘Summary of Genetic Interactions’ section on the Gene Reports contains a table showing the gene-level genetic interaction summary. The table shows which gene(s) have been shown to interact genetically with the gene, together with the nature of the interaction (‘enhanceable’ or ‘suppressible’) and the reference(s) from which the data came in each case.
    2. A bulk file is accessible through the Precomputed Files page (Files menu ⇒ Current release, "Genetic interaction table" under the Genes section). The format is described here.
  • May 4 (with the release)
    NIH Expression data plots added to Dpse gene reports
    The RNA-seq expression data provided by the Oliver group for D. pseudoobscura, and currently displayed in FlyBase GBrowse, can now also be seen in gene reports. Many D. pseudoobscura reports now have an expression plot showing these data, similar to those shown on D. melanogaster reports for modENCODE expression data.
hide FB2015_01
 
  • December 2014
    Wiki page for FlyBase Community Advisory group
    A new Community Advisory Group wiki page has been added, accessible from the Documents section of the homepage. The page includes information about the group, how to join and update your details, and results of the surveys carried out so far.
  • February 24 (with the release)
    5 species genome annotations updated
    For 5 of the sequenced species; D. ananassae, D. erecta, D. pseudoobscura, D. simulans and D. yakuba, the CAF1 generated annotations that have not changed since 2006 are being replaced by annotations generated by NCBI as part of their GNOMON annotation pipeline as described in this paper (http://www.ncbi.nlm.nih.gov/core/assets/genome/files/Gnomon-description.pdf), with additional information at http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/. We have maintained gene, transcript and protein symbol and IDs for GNOMON annotations identified by NCBI as corresponding to existing CAF1 annotations but many models have new identifiers.
  • February 24 (with the release)
    New reference mitochondrial genome assembly
    In FB2015_01, a new D. melanogaster mitochondrial genome assembly derived exclusively from the "iso-1" sequenced strain (NCBI KJ947872.2, RefSeq NC_024511.2) replaces the old mitochondrial genome assembly, which was a composite of sequences from various D. melanogaster strains. See the current release notes for more details on the new mitochondrial genome assembly. FlyBase features have been migrated from the old to the new mitochondrial genome assembly. There have been small changes to the nucleotide sequence of the following genes: mt:ATPase6, mt:Cyt-b, mt:ND1-PA, mt:ND4, mt:ND5, mt:lrRNA and mt:ori. The previous mitochondrial assembly continues to be accessible through the archived FlyBase releases.
  • February 24 (with the release)
    Automatically Generated Summary updated
    The 'Comments on Affy2 ProbeSet' and 'Summary of FlyAtlas Anatomical Expression Data' sections of the Automatically Generated Summary on the gene reports have been removed. These data are still available elsewhere on the website.
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hide FB2014_06
 
  • November 12 (with the release)
    Realigned modENCODE RNA-Seq data
    FlyBase has updated RNA-Seq coverage data for the modENCODE transcriptome datasets, re-aligned to the Release 6 reference genome assembly. RNA-Seq coverage data is now available for new regions of the genome assembly, notably regions of centric heterochromatin and previously fragmented gene annotations that have been properly assembled in Release 6.
  • November 12 (with the release)
    Configurable topoview tracks in GBrowse
    FlyBase GBrowse tracks displayed using the 'topoview' track style are now configurable. Users can choose sample subtrack spacing and offset, select scaling algorithm, and turn individual subtracks on or off.
  • November 12 (with the release)
    New BLAST species
    Two new fly species have been added to the FlyBase BLAST database: Musca domestica (house fly), and Glossina morsitans (tsetse fly).
  • November 12 (with the release)
    PMCID and DOI added to precomputed References file
    The file cross-referencing FlyBase FBrf ID and PubMed ID found under References in the FlyBase Precomputed Files page now also includes cross-references to PubMed Central reference number (PMCID) and to Digital Object Identifier (DOI).
  • November 12 (with the release)
    DPIM data obsoleted
    The DPiM-1 protein interaction dataset has been retired from FlyBase at the request of the data providers. The raw unfiltered protein identification from pull-down experiments that formed the basis of the DPiM-1 data set has been superseded by the DPiM-2 dataset described in FBrf0216491. An explanation for this change is provided in FBrf0222073.
  • October
    Resources, Author Guidelines pages revised
    The Author Guidelines page has been updated to reflect current best practices for publications that authors expect FlyBase to include in our bibliography.
    The Drosophila Network Resources page (accessed from the FlyBase Wiki Resources page) has also been revised and reorganized, and now includes categorized links to well over 150 resource websites.
  • October
    FlyBase Community Advisory Group is launched
    During October we launched our new Community Advisory Group that we plan to consult on a regular basis about upcoming changes and developments in FlyBase. Our aim is to have a representative from every lab that uses Drosophila data in their research. The registration page can be found here: http://flybase.org/static_pages/feedback/community_advisory_group_form.html
hide FB2014_05
 
  • September 9 (with the release)
    GBrowse 2 Megaview
    GBrowse 2 now has a 'MegaView' option, where you can view aberrations, estimated cytological bands, and other large-scale genomic features.
    Select the ' D. melanogaster MegaView' option under Data Source.
  • September 9 (with the release)
    Y-chromosome assembly and annotation improved
    The updated Y-chromosome in genomic release 6 from the BDGP is now 3.667 Mb (a 10X increase from release 5) with the incorporation of new sequence, sequence previously reported as part of the unmapped and unordered U scaffold, plus a small mis-mapped fragment from 3LHet in release 5. Annotation release 6.02 includes significant changes to the gene models on the Y, including those for seven known genes (kl-3, kl-5, WDY, Ccy, Ory, Ppr-Y, and PRY) that were fragmented, incomplete, or unidentified in release 5.
  • September 9 (with the release)
    PubMed Central links
    Links to PubMed Central have been added to the reference reports.
  • September 9 (with the release)
    TermLink is now Vocabularies
    The FlyBase tool for searching genes and more using controlled vocabulary terms is being renamed from TermLink to Vocabularies. FlyBase users may find the new name better conveys the purpose and usefulness of this under-appreciated tool.
hide FB2014_04
 
  • July 21 (with the release)
    D. melanogaster release 6.01
    FlyBase has migrated all D. melanogaster genomic data to release 6 of the BDGP assembly.
    If you have data for which you will need to convert genomic coordinates, the FlyBase Coordinate Converter tool has been updated to convert from R5 → R6 and R6 → R5 coordinates. If you have a large number of coordinates to convert, you may want to consider installing our stand-alone conversion code, posted at FlyBase @ GitHub.
  • July 21 (with the release)
    GBrowse 1 retired
    The migration of FlyBase from GBrowse 1 to GBrowse 2 is complete, and GBrowse 1 will no longer be available through the main FlyBase site.
    With the retirement of GBrowse 1 we will lose Orthoview, which displayed orthology calls between D. melanogaster and other species. GBrowse 1 also supported views of genomic data for a selection of non-Drosophila species; these will no longer be available (the non-melanogaster Drosophila species will continue to be available in GBrowse 2). GBrowse 1 will still be available from inside the archived FlyBase servers.
    In return for these, we gain a number of new features. For a summary, please see this Commentary.
  • July 21 (with the release)
    Chromosome maps removed
    The large aberration map and chromosome map images previously available on FlyBase have had to be retired. The chromosome maps in particular have seen their usefulness degraded by changes in the Google Maps API used to drive most of their features. Both of these map sets were based on Dmel Release 5 coordinate data, which is now obsolete.
    As with all other FlyBase tools that are being retired with the change to Dmel release 6, these maps can still be accessed from within our archived FlyBase servers.
hide FB2014_03
 
  • May 9 (with the release)
    D. albomicans added to BLAST
    Drosophila albomicans has been added to the FlyBase BLAST tool.
  • May 9 (with the release)
    Human disease model data bulk download file
    Human disease model data is now available in a bulk file. This file will be updated with each release, and will be available through the Precomputed Files page (Files menu ⇒ Current release, under the new Human Disease section).
  • April 30
    Anatomy Ontology Updates
    The Drosophila anatomy ontology (DAO) has been extensively revised over the last 4 years, and now comprises over 8500 terms. Particular emphasis has been focused on neuroanatomy, and the DAO now includes ~2000 distinct neurons, over 200 lineage clones (including fruitless ones), and the descriptions and nomenclature for the neuropil regions in the adult brain from the BrainName group (Ito et al., 2014). Please see this Commentary for more information.
  • April 9
    Fly Board & White Papers link
    The FlyBase home page has a new "Fly Board & White Papers" button in sidebar, which links to a new page combining the 'Fly Board' and 'White Papers' pages. Those links have been removed from the News menu.
  • March/April
    Wiki links
    Migration of resource pages to the FlyBase Wiki continues. The 'FlyBase Guides' link under the Help menu, and the 'Stock Collections' and 'All Resources' links under the Resources menu, now link to new pages on our wiki.
  • March 14
    FlyBase ADRC materials
    Slides from our two presentations, and two pamphlets distributed by FlyBase at the recent ADRC in San Diego are now available for downloading from our FlyBase Guides page.
hide FB2014_02
 
  • March 18 (with the release)
    Human Disease Searching
    With the addition of a new human disease ontology, FlyBase data can now be searched using human disease terms. A new Human Disease tab on the QuickSearch form, and additions to the TermLink tool, will provide these new search options.
    FlyBase gene and allele reports also have a new Human Disease Model Data section (located just below the Orthologs section in the gene reports and just below the Nature of the Allele section in allele reports), where gene-specific allele models and interactions data are listed. Download links for these data are located in this section of the gene reports.
  • March 18 (with the release)
    Dpse alignments restored
    Nucleotide and protein alignments to the D. pseudoobscura genome that are provided to FlyBase by NCBI and that had been temporarily dropped as part of the migration to the updated release 3 assembly have been restored in this release. New and updated alignments will be routinely processed as they become available and incorporated into the public FlyBase releases.
  • March 18 (with the release)
    Continued migration of help pages, etc. to wiki
    Users of FlyBase documentation pages will notice that many of our formerly static web documents have been moved to the FlyBase wiki. FlyBase will be moving all similar pages to the wiki over the next few months.
  • March 18 (with the release)
    New Flygut and ApoDroso linkouts
    Flygut and ApoDroso linkouts have been added to the gene reports. You will find them under the general Linkout section at the bottom of the report. Flygut has another linkout under Expression Data → External Data & Images.
    Searching for 'flygut' or 'apodroso' in simple search will find genes with linkouts.
hide FB2014_01
 
  • January 17 (with the release)
    High-resolution wild-type images added to some allele reports
    Many of the allele reports that had high-resolution images added to them in February of 2013 now also have corresponding wild-type (OreR) images for comparison.
  • January 17 (with the release)
    High-throughput expression summary text updates
    High-throughput expression summary statements are now being updated with each release. These statements can be found at the end of the Summaries on Dmel gene reports.
  • December 1
    FlyBase 102 paper
    Members of the FlyBase Consortium have published another paper in the 'tutorial' series in Nucleic Acids Research: FlyBase 102 - Advanced Approaches to Interrogating FlyBase. There is a brief FlyBase News article, and a more detailed FlyBase Commentary, related to this publication.
  • November
    lexA driver collection of Rubin laboratory at Janelia Farm
    The approximately 1400 lexA driver lines in this collection were constructed using the methods described in Pfeiffer B.D., T.B. Ngo, K.L. Hibbard, C. Murphy, A. Jenett, J.W. Truman and G.M. Rubin, 2010. Refinement of Tools for Targeted Gene Expression in Drosophila. Genetics. 2010 186:735-755.  FBrf0212052.html
  • November
    Bin legends added to RNA-Seq Search dataset forms
    Legends showing the expression bin values corresponding to the terms used to describe expression levels used in the RNA-Seq Search tool now appear next to each dataset form.
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hide 2013
hide FB2013_06
 
  • November 4 (with the release)
    Upload/Convert IDs tool
    The Upload/Convert IDs tool (formerly ID Converter) has been renamed to emphasize that it can be used to upload a list or file of IDs or symbols, for conversion into a FlyBase hit list for further analysis.
  • November 4 (with the release)
    QueryBuilder improvements
    The QueryBuilder tool has been modified to separate functions related to querying from functions related to the hitlists generated by queries. The hitlists generated by QueryBuilder now open in a new window/tab, and feature all normal FlyBase hitlist tools, including the "Convert to" menu.
  • November 4 (with the release)
    Twitter, YouTube, email icons
    Icon links to the FlyBase Twitter feed, the FlyBase YouTube channel, and the FlyBase email contact page can now be found in the footer of each page in the FlyBase website.
  • November 4 (with the release)
    Leaflet update
    An updated FlyBase leaflet was handed out at the recent European Drosophila Research Conference in Barcelona. You can print a copy from the link in our FlyBase Guides page. Click on "EDRC Handout October 2013".
  • November 4 (with the release)
    DIOPT ortholog links
    The Orthologs section of FlyBase gene reports now features links to DIOPT (the DRSC Integrative Ortholog Prediction Tool) for seven selected target species (H. sapiens, M. musculus, C. elegans, D. rerio, X. tropicalis, S. cerevisiae, S. pombe).
  • November 4 (with the release)
    SliceSeq longitudinal expression images
    The Expression ⇒ External Data and Images subsection of FlyBase gene reports now includes a set of images from SliceSeq. The images show longitudinal expression heatmaps for embryos at seven stages. For experimental details, see the dataset report SliceSeq_25um.
hide FB2013_05
 
  • September 10 (with the release)
    Gene reports re-organized to emphasize function information
    A FlyBase Commentary discussing the gene report changes can be viewed here.
  • September 10 (with the release)
    FlyORF stocklist added to FlyBase
    The stocklist of FlyORF has been added to FlyBase. FlyORF is a collection of well-characterized transgenic D. melanogaster UAS-ORF lines that can be used for controlled and efficient overexpression of genes in the library.
  • September 10 (with the release)
    GBrowse button on the home page now defaults to GBrowse 2
    The link to GBrowse from the FlyBase home page GBrowse button has been updated to point directly to GBrowse 2. During the 'beta' phase of the migration to GBrowse 2, this button was modified to show several options when pressed, including GBrowse 2 but also several GBrowse 1 views.
    Please note that you can still access GBrowse 1 from the GBrowse 2 page. Links between GBrowse versions will be prominently available for the remainder of the transition period.
  • August 2013
    Feature Mapper improvements
    The FlyBase Feature Mapper tool has been improved in layout, usability, and output.
hide FB2013_04
 
  • June 19
    Updated D. pseudoobscura RNA-Seq data
    Brian Oliver’s group has provided FlyBase with updated RNA-Seq coverage data for D. pseudoobscura.
    For more details, please see this Commentary.
  • July 16 (with the release)
    Feature Mapper improvements
    The FlyBase Feature Mapper tool has had a 'makeover'. The feature checklist in the form has been organized to be analogous to the track groups in GBrowse, and groups can be checked with a single click.
  • July 16 (with the release)
    BLAST links migrate to GBrowse 2
    The link to GBrowse from the FlyBase BLAST results page has been updated to point to GBrowse 2 instead of GBrowse, as part of the ongoing FlyBase GBrowse migration.
  • July 16 (with the release)
    GBrowse topoview popup legend
    The explanatory popup for the GBrowse topoview track now displays a legend for the separate profiles. A link at the top goes to the metadata report corresponding to the track.
    Tip: GBrowse popups disappear after a few seconds unless you move your mouse over them - then they will stay so that you can read them at your leisure.
  • July 16 (with the release)
    GO autocomplete overflow link
    The GO tab in the FlyBase QuickSearch tool has had a new perk added to its autocompletion feature. When the list of matching terms is too long to display all of them, a link to the TermLink tool appears at the end. Follow the link to TermLink to see the entire matching list.
hide FB2013_03
 
  • May 7 (with the release)
    New name and button link for RNA-Seq Search Tool
    The tool formerly known as the 'High-Throughput Expression Profile' tool has been renamed the RNA-Seq Search Tool. A new seventh button link for this tool has been added to the array at the top of the FlyBase home page.
  • May 7 (with the release)
    RNA-seq RPKM data bulk download
    FlyBase has extended its initial gene-level analyses of RNA-seq throughput data from modENCODE and others. The algorithm for RPKM (reads per kilobase per million mapped reads) has been refined, additional datasets have been analyzed, and these data are now available for bulk download.
    Bulk data files can be accessed from the Precomputed Data Files page (menu: Files → Current Release). Look in the Genes section; the item line is 'RNA-Seq RPKM values'. You can download the file directly by clicking here.
    For more details, please see this Commentary.
  • May 7 (with the release)
    QuickSearch Help link
    The 'QuickSearch help' link in the upper-right corner of each tab form has been replaced with a '?' help icon next to the QuickSearch heading. The layout of the Expression tab has also been altered to move the link to the RNA-Seq Search tool to the top of the form.
  • May 7 (with the release)
    Precomputed Data Files name and format changes
    Inconsistencies in file format and naming on the Precomputed Data Files page have been addressed. Several files linked through this page have had their compression formats changed, with consequent changes to their names. During the next several releases these changes will be migrating to the Archived Data files page. The FlyBase FTP site files will also be affected by these changes.
    Automated download scripts may need updating to accommodate these changes.
hide FB2013_02
 
  • February 8
    Hi-Res D. melanogaster Mutation Images
    A beautiful set of almost 300 high-resolution images exemplifying mutations of D. melanogaster has been added to the images database within FlyBase. These images will now appear in the Allele Reports for the depicted mutants.
    The contributors have also created poster-quality collages of these images for eye color mutations [pdf|tiff], bristle mutations [pdf|tiff], eye shape mutations [pdf|tiff] and body color and wing shape mutations [pdf|tiff].
    Please see this Commentary for more details.
  • March 6
    FlyBase Archives in The Cloud
    FlyBase data is now available on the Open Science Data Cloud (OSDC). Data from all FlyBase releases are available including GFF, FASTA, XML, precomputed files, Chado PostgreSQL dumps, and more.
    Please see this Commentary for more details.
  • March 8 (with the release)
    GBrowse 2 Beta
    FlyBase has implemented a beta installation of GBrowse 2. The Gene Reports now have a button link to GBrowse 2 in the Genomic Location section, near the existing 'View in GBrowse' button link.
    Please see this Commentary for more details.
  • March 8 (with the release)
    Dpse release 3 assembly
    The Drosophila pseudoobscura genome sequence has been updated to the release 3 assembly produced by the HGSC group at the Baylor School of Medicine. Please see this Commentary for more details.
  • March 8 (with the release)
    Recalculated RPKM values for HT expression data
    The expression values calculated from the modENCODE RNA-seq experiments and used to generate expression histograms on the Gene Reports and to power the High-Throughput Expression Search tool, have now been normalized to account for read lengths. The binning scheme which allows searching has been altered appropriately for the recalculated values.
    A slight reorganization of the Expression Data → High-Throughput Expression Data section of the Gene Reports accompanies these data updates. Users can now find links to corresponding dataset metadata reports for each dataset, and the reference links have moved to more appropriate locations.
  • March 8 (with the release)
    Batch download for ortholog data restored
    The Batch Download functionality for ortholog data is now available for OrthoDB version 6.
hide FB2013_01
 
  • mid-November 2012
    Informative Commentaries
    FlyBase adds several informative commentaries to the rotation on the front page, covering topics from Learning About FlyBase Through Our Publications to introductions to several of our favorite tools, new as well as tested.
    The commentaries now change in rotation several times each minute. We hope this gives our visitors a chance to see commentaries that they might not otherwise notice.
  • January 23 (with the release)
    Reporter Expression
    FlyBase gene reports have a new subsection under Expression Data; Expression Deduced from Reporters.
  • January 23 (with the release)
    SignaLink linkouts
    Linkouts to the SignaLink database of protein-protein and protein-miRNA interactions can now be found in FlyBase gene reports under Interactions & Pathways → External Data.
  • January 23 (with the release)
    OrthoDB upgraded to version 6
    The orthologs shown in the FlyBase gene reports from OrthoDB have been updated to reflect the newest OrthoDB release, version 6.
  • January 23 (with the release)
    GO expression location information now appears in 2 places in gene reports
    The 'Cellular Component' information in the Gene Ontology section of the FlyBase gene reports is now duplicated under Expression → Polypeptide Expression, in a section called GO Subcellular Localization.
  • January 23 (with the release)
    Button links to FlyBase Genewiki on gene reports
    The Summary Information section of FlyBase gene reports now has a User Contributed Data subsection. A button there links you to the corresponding gene page on FlyBase gene wiki site. Once there you can edit, add to, or re-write the gene summary. Summaries edited by users on the wiki will be reproduced in the User Contributed Data section in future releases.
  • January 23 (with the release)
    Alternative expression search result lists
    Expression search gene result list pages now have button links at the top of the page to go to alternative result lists of insertions or recombinant constructs instead of genes.
  • January 23 (with the release)
    New GBrowse tracks
    Two new stranded expression tracks have been added to GBrowse. The L3 CNS neuron and L3 CNS neuroblast tracks can be found in the Expression/Regulation GBrowse view, within the Expression Levels: RNA-Seq by Tissue track group.
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hide 2012
hide FB2012_06
 
  • mid-October
    Improvements to the GBrowse glyph for transgenic insertion sites
    The glyph now includes a small arrow indicating orientation, when it is known. Insertion sites for which the location is not known exactly are now indicated by dashed lines flanking the icon.
  • November 6 (with release)
    Feature Mapper
    FlyBase introduces a new way to gather feature data by genomic region; Feature Mapper. The Feature Mapper tool can be accessed via a link in the Tools⇒Genomic/Map Tools menu.
  • November 6 (with release)
    The Drosophila Species Stock Center (UCSD) stock list has been updated.
  • November 6 (with release)
    Expression search upgrade
    Several new datasets have been added to the high-throughput expression search tool. FlyBase genes can now be searched using data on expression by anatomy, treatments, and cell lines. Joint searches using two or more expression datasets simultaneously are supported as well.
  • November 6 (with release)
    OMIM and HGNC links for inferred human gene orthologs
    The 'Orthologs' section in the gene reports now has a 'Human Orthologs' subsection, which highlights the human orthologs inferred from the OrthoDB Ortholog Groups. Information about the human genes and disease associations can be found via the links to corresponding HUGO Gene Nomenclature Committee (HGNC) and Online Mendelian Inheritance in Man (OMIM) gene reports.
  • November 6 (with release)
    NIG-FLY RNAi constructs
    All RNAi constructs available from NIG-FLY have been added in the form of construct and allele reports; the genomic extent of the targeted segment can be viewed on GBrowse. A dataset report for the NIG-FLY project is also available (FBlc0000491).
hide FB2012_05
 
  • August
    Transcription start sites
    A new TSS track has been added to the GBrowse Expression/Regulation view (Aligned Evidence track group).
  • September 7 (with release)
    Reference reports have been reorganized for improved clarity.
  • September 7 (with release)
    Four newGO evidence codes are available for use by FlyBase curators, and will begin to appear in gene reports in the Gene Ontology section, under "Terms Based on Predictions or Assertions". The new codes are:
    • inferred from biological aspect of ancestor
    • inferred from biological aspect of descendant
    • inferred from key residues
    • inferred from rapid divergence
hide FB2012_04
 
  • July 6 (with release)
    Interactions
    New interactions from the Spiros lab have been added to FlyBase. The new data appears in the gene and interaction reports, and can be browsed using the Interactions Browser.
  • July 6 (with release)
    RNAseq expression plots
    New high-throughput RNAseq data from modENCODE have been added to FlyBase. Gene reports now include plots for expression variation across different cell lines, different treatments, and in different tissues.
  • July 6 (with release)
    The Files menu of the FlyBase website navigation bar has been reorganized and simplified.
hide FB2012_03
 
  • May 1
    The Drosophila Board has released theReports on Community Resources and Projects from the 2012 Board meeting agenda. A link to a PDF of this report has been added to the 'Fly Board' page on our website. (A link to the Fly Board page can be found under the News menu.)
    You can also access this report here.
  • May 11 (with release)
    New and improved orthologies (see this Commentary for details)
  • May 11 (with release)
    High-Throughput RNAseq expression data update
    The modENCODE RNAseq expression by developmental stage data (used by GBrowse, and the HT Expression Profile tool,) will now be updated each release to account for changes to gene models.
  • May 11 (with release)
    The QuickSearch Simple tab now has a species filter, similar to filters already in place for the Expression and Data Type tabs. Default behavior for 'simple' searches will now be to exclude non-melanogaster search results (with a few exceptions). To include other Drosophila species in your search, tick the 'include non-Dmel species' checkbox.
hide FB2012_02
 
  • March 2 (with release)
    modENCODE high-throughput RNA-seq expression data can now be used to query FlyBase records using an expression profile. See the query tool here.
hide FB2012_01
 
  • January 4
    The 'How to cite FlyBase' page was updated to reflect publication of a new user guide paper by FlyBase.
  • January 20 (with release)
    HD2 and HFA amplicon libraries have been updated. Updates can be viewed in the GBrowse Stocks and Reagents view (RNAi Reagents and Data track group), and in the sequence feature reports (linked from the library names above).
  • January 20 (with release)
    A new RNA Editing Sites track has been added to the GBrowse Expression/Regulation view (Noncoding Features track group).
  • January 20 (with release)
    A new file relating FlyBase FBrf numbers and PubMed IDs is now included in the 'References' section of the Precomputed Files page, as well as on the FlyBase FTP site (in releases → [release num] → precomputed_files).
  • January 20 (with release)
    Gene expression cluster data from the modENCODE Consortium can now be found under Expression → Expression Clusters in the gene reports. modENCODE defines each of these groupings as "a cluster of genes with similar mRNA expression dynamics across development."
    FBrf0213979
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hide 2011
hide FB2011_10
 
  • November 18 (with the release)
    Views and tracks in GBrowse have been reorganized. See this Commentary for more details.
  • November 18 (with the release)
    New species have been added to the FlyBase BLAST tool.
hide FB2011_09
 
  • October 10 (with the release)
    Correction notice: The coordinates for the 5-state chromatin domains of Filion et al. (2010) were incorrectly converted by FlyBase from release 4 of the D. melanogaster genome scaffold to the current release 5 build. The authors have informed us that the data, generated on release-4-based microarrays, were already converted into release 5 coordinates upon deposition in the GEO data repository. The coordinates for the GBrowse chromatin domains track are now correctly displayed.
  • September 14
    ExpreS2ion Biotechnologies has developed "an improved drosophila S2 insect cell expression system"; a link to their site has been added to the FlyBase Resources page.
  • September 12
    The beta version of tabbed QuickSearch is available for evaluation. See this Commentary for more details.
hide FB2011_08
 
  • September 2 (with the release)
    New transcription factor binding site tracks have been added to GBrowse. See this Commentary for more details.
  • September 2 (with the release)
    Expression data for each gene will no longer appear in a separate report. All available expression data has been folded back into the corresponding gene reports.
hide FB2011_07
 

All of the changes made to FlyBase during this release period were incremental.
See the FB2011_07 Release Notes for details.

hide FB2011_06
 
  • June 24 (with the release)
    New data tracks have been added to GBrowse. A new "origin of replication" data track has been added to the tracks available for the "D. melanogaster" Data Source (in the "Mapped features" track section). Stranded RNA-seq data for expression under various treatments, cell lines, and for selected tissues and developmental stages, have been added to the tracks available for the "D. melanogaster RNA-seq Data" Data Source; (in the "Other RNA-seq data" and "RNA-seq data, expression by tissue" track sections). See this Commentary for more details.
hide FB2011_05
 
  • Apr 14
    The text autocompletion feature of QuickSearch and other tools has been improved to support multi-term searching.
  • Apr 22
    Origin of replication features added to GBrowse and sequence feature reports.
  • May 12
    The minutes of the 2011 meeting of the North American Drosophila Board have been posted on the Fly Board page.