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

2016
FB2016_05
  • October 18 (with the release)
    JBrowse beta
    FlyBase is deploying a JBrowse instance; a 'beta' version is now available here. About half of the full set of FlyBase tracks have been imported into this instance; some of the more complex tracks (i.e., RNA-Seq topoview) will come later. A JBrowse link now appears in gene reports next to the current GBrowse link.
  • October 18 (with the release)
    Gene Groups update
    A new video tutorial on 'Finding related genes in FlyBase: Gene groups' is available now on FlyBase TV. Several new Gene Groups have also been added in this release, including spliceosomal complexes, tetraspanins and nonaspanins.
  • October 18 (with the release)
    New antibody linkouts
    The antibody section of the Gene Reports page has been updated with the addition of links to the Developmental Studies Hybridoma Bank (DSHB). Our current collection of DSHB links exist across ~240 Gene Reports and is derived from their Drosophila-specific antigen list.
FB2016_04
  • 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.
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.
FB2016_02
  • March 29 (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 29 (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 29 (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 29 (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.
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 via Gbrowse and 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.
2015
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.
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.
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.
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.
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.

For earlier New In This Release items going back to 2011, please visit one of our archive servers.