A Database of Drosophila Genes & Genomes

FB2013_03, released May 7th, 2013
 

New in this release

 
 

FlyBase will list here changes and improvements to the website. Changes from releases in previous years can be viewed in the sections labeled by year, below.

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.