Release Notes for Genome Workbench 3.0.1 (August 20, 2019)

New Features

Bug Fixes and Improvements

  • Database: VDB gate indexing fixed
  • MSA view: expanded features issues fixed
  • Assembly: assembly table going blank fixed for MacOS
  • Graphical Sequence View: Assembly Accession selection fixed
  • Editing Tools: fixed crash in Remove All Features
  • Add Publication: fixes for DOI lookup
  • Sequences: fixes for Add Assembly Gaps to Sequence
  • Editing Tools: fixed crash in Convert Features
  • Editing Tools: fix for Retranslate Coding Regions improperly adjusting mat-peptide spans

Release Notes for Genome Workbench 3.0.0 (July 3, 2019)

New Features

  • In this version NCBI releases a new extension package to create and edit genomic submissions for GenBank. This new package is supposed to replace NCBI Sequin (see Feature comparison between Sequin and Genome Workbench for more details)
  • Documentation for Genome Workbench Editing
  • Sequence Editing Package: improved support for GFF3 import files for feature annotation
  • New menu items to add, edit, and remove individual features on sequences, functionality to manipulate sequence data. New validator with ability to check against GenBank submission standards and fix problems found.
  • Added support for clients working via Windows Remote Desktop
  • Extended support for X-Windows protocol, Genome Workbench can now display graphics in X-Windows configuration, tested with X2Go client and other servers
  • MacOS: Added build for MacOS Metal graphics to reflect Apple plan to discontinue support for OpenGL in new versions of MacOS

Bug Fixes and Improvements

  • Tree View: fixed crash with tree re-routing
  • BAM files: fixed SRR accession validation issues in the Open Dialog
  • MSA View: fixed minor flickering issues on Windows

Release Notes for Genome Workbench 2.13.0 (March 20, 2019)

New Features

  • Graphical Sequence View: new SNP tracks released
  • Graphical Sequence View: improved alignment statistics table (Alignment statistics settings: Show A, G, T, C and Gaps) to correctly account for introns (graphics now include intron row)
  • Graphical Sequence View: Alignment tooltips now also report introns separately from gaps

Bug Fixes and Improvements

  • Graphical Sequence View: fixed bug with incorrect vector graphics (PDF) export in case when default settings were changed
  • Graphical Sequence View: improved BAM / SRA renderings of D/N CIGAR specified gaps
  • Graphical Sequence View: fixed bug in context menu action “Zoom to Selected Object(s)”
  • Text View: fixed crash in Flat File (GenBank) mode, crash was happening because of incorrect handling of diacritic symbols
  • Tools MAFFT: fixed issues with running it on MacOS and Windows
  • Tools BLAST: Improved MacOS interface to pick blast database file location
  • Improved import of FASTA sequences via clipboard

Release Notes for Genome Workbench 2.12.10 (August 20, 2018)

New Features

  • Graphical Sequence View: created category for proteomics tracks

Bug Fixes and Improvements

  • Fixed some memory consumption issues
  • Fixed hang up and freeze when loading project items first time on cold cache
  • Graphical Sequence View: fixed display of alignments when local (non GenBank) molecule was BLASTed with NCBI database
  • Graphical Sequence View: fixed errors in CDS tooltip (incorrect product sequence)
  • Graphical Sequence View: fixed display of variation features imported from a GFF file
  • Graphical Sequence View: fixed issues with HMM alignment tooltips and variants features
  • Graphical Sequence View: fixed issues with rendering of short introns
  • Graphical Sequence View: improved consistency of visual range synchronization options
  • BAM/VDB format compatibility: fixed critical errors and crashes
  • BAM file format: improved user interface and chromosome names re-mapping logic to be better compatible with NCBI molecule accessions
  • Multiple Sequence Alignment View: fixed bug with garbled labeling of projected proteins
  • File Import: fixed regression when input file is zip compressed
  • File Import: improved with more common file extensions

Release Notes for Genome Workbench 2.12.8 (February 14, 2018)

New Features

  • BAM Files: added WIG export for coverage graph

Bug Fixes and Improvements

  • Text View: fixed crash showing GenBank format
  • Text View: improved FASTA format view GUI (context menu) added “Expand All” option
  • Graphical Sequence View: fixed disappearance of gene container of tracks on project update
  • Graphical Sequence View: fixed crash when moving views (also applies to Multiple Sequence Alignment View)
  • Graphical Sequence View: fixed various rendering issues for BAM alignments
  • Graphical Sequence View: fixed issues last base not shown when zoomed in
  • Graphical Sequence View: improved rendering of internal unaligned regions, showing the dashed line and number of unaligned bases
  • Graphical Sequence View: improved info and help usability
  • Graphical Sequence View: fixed crash in tooltips when clicked on unaligned base
  • Graphical Sequence View: fixed crash on assembly/chr open-close scenario
  • Multiple Alignment View: improved consensus rendering speed
  • Reworked registry update mechanism for better stability
  • Search View: fixed crash when selecting from results
  • Tree View: fixed crash in Force layout mode
  • Tree View: fixed rendering bug when colored selection set disappeared after subtree deletion
  • FASTA Loader: improved handling of local ids
  • GTF/GFF import: fixed various errors and conflicts in format readers
  • Open View Dialog: improved to remember width of columns
  • File Open Dialog: better format file names when adding to project to better reflect name and the type of bio-object
  • Export: improved usability to automatically open the target folder, so user can quickly find the exported file
  • Export: added warning if system is about to overwrite a file
  • Installer: removed confusing settings for network PROXY environment, use automatic detection when possible
  • Removed workspaces from the GUI as a non-essential concept
  • BAM format: improved restore/removal of BAM data loader module on project close/re-open
  • Fixed crash in situations when Genome Workbench home folder got accidentally deleted from disk
  • Fixed bug in Windows OS version reporting
  • Linux: fixed shutdown message typo

Release Notes for Genome Workbench 2.12.5 (September 18, 2017)

New Features

  • BAM Files: added WIG export for coverage graph
  • Text View: FASTA mode – implemented sequence selector
  • Graphical Sequence View: new navigation tutorial
  • Open Dialog: implemented logic to recognize and load Genome Assembly Accessions as GenBank accessions

Bug Fixes and Improvements

  • MacOS-X: fixed crash with PDF editing
  • ProSplign tool: fixed issues with local sequences
  • Graphical Sequence View: performance optimizations of BAM data tracks
  • Graphical Sequence View: fixes in selection mechanism when switching between different views
  • Graphical Sequence View: matching (identical) bases in alignments now rendered clearer
  • Graphical Sequence View: fixed broken links on SNP tooltips
  • Graphical Sequence View: fixed incorrect display of nucleotide to protein alignments
  • Graphical Sequence View: improved tooltips for non-coding genes, removed incorrect links
  • Graphical Sequence View: fixed inconsistent display of identical bases with linked-mate pairs
  • FASTA export of pairwise alignments improved not to produce multiple copies of alignments
  • FASTA import: improved import of organism information
  • Improved display of SRA files pointing to local sequences (de-novo assemblies)
  • Search View: fixed component search incorrect display in Graphical Sequence View
  • Tree View: fixed issues with sometimes missing labels
  • Tree View: improved collapse of nodes
  • Tree View: fixed issue in collapse nodes in Slanted Cladogram layout
  • Multiple Alignment Viewer: fixed potential feature duplication
  • GTF file format: fixed crash and other export issues
  • ORF finder: fixes in length calculations
  • MacOS: fixed automatic loading of project files (*.gbp) on double click
  • Generic Table View: improved clipboard copy of selected column
  • Fixed descriptions of Alignment Summary View and Multi-Pane Cross Alignment View

Release Notes for Genome Workbench 2.12.0 (June 22, 2017)

New Features

  • Integrated new popular Multiple Alignment tools: KAlign, MAFFT, Clustal Omega
  • Export of Multiple Alignments in FASTA Alignment format, compatible with third party tools and viewers
  • New reworked FASTA import for sequences and alignments
  • BAM files: project interface now allows sequential adding multiple BAM files or SRA accessions to view side by side in Graphical Sequence View
  • Open Dialog: can now open files via HTTP and FTP protocols
  • Open Dialog: it is now possible to add NA (annotation submitted to NCBI) to the project and then open Text View on that NA to inspect the content

Bug Fixes and Improvements

  • Graphical Sequence View: improved track handling, fixed major issues with unexpected track appearance/disappearance, fixed issues with saving tracks and options over the restart
  • Graphical Sequence View: fixed crash in tooltips at max zoom for NG alignments with propagated features
  • Graphical Sequence View: fixed processing of histogram settings
  • Graphical Sequence View: improved opening/initialization time
  • Graphical Sequence View: fixed false mismatch issues in alignments
  • Graphical Sequence View: improved BAM pileup graph rendering
  • Graphical Sequence View: improved label for non-gene features (regulatory, protein_bind, misc_feature, repeat_region, and a few others)
  • Graphical Sequence View: fixed discrepancies in graphs RNA exon coverage
  • Multiple Alignment View: fixed hang if alignment referred to some unknown molecule
  • Multiple Alignment View: improved compact mode not to show titles for groups of tracks
  • Gene Model Tool: fixed crash
  • Tree Viewer: fixed crash with zooming in circular layout
  • Tree Viewer: improved rendering of collapsed subtrees, made it more visible
  • Improved performance and usage statistics collection to provide better quality of service
  • Fixed issue with intermittent incorrect validation of molecule ids (required restart of the program to restore the function)
  • Fixe issues with GFF import
  • BAM files: fixed issues related to BAM import, when no reference sequence was selected for adding into the project
  • BAM files: added option to filter sequences on load
  • Project Tree View: improved handling of non-actionable menu items (disabled when not handled)
  • Dot Matrix View: fixed issues with selection broadcasting processing
  • Search View: ORF search – fixed incorrect tooltips
  • MacOS: improved crash detection and handling

Release Notes for Genome Workbench 2.11.10 (March 10, 2017)

New Features

  • Critical improvement in HTTPs protocol communication with NCBI
  • Graphical Sequence View: improved track configuration dialog, improved classification, search, more tracks are now available
  • New manual for search in bio-trees
  • Multiple Alignment View: implemented new coloring scheme: conservation

Bug Fixes and Improvements

  • MacOS: fixed issues with downloading and using masking files
  • Multiple Alignment View: fixed a crash
  • Graphical Sequence View: fixed crash in zooming to some areas
  • Graphical Sequence View: fixed issues with tracks disappearing
  • Graphical Sequence View: corrected sequence for projected features found on protein to DNA alignment
  • Graphical Sequence View: fixed “Go to sequence” dialog on MacOS
  • Graphical Sequence View: performance improvements for displaying large alignments
  • Graphical Sequence View: improved initialization time when opening a second instance
  • Graphical Sequence View: improved the display default to link mate pairs
  • Graphical Sequence View: fixed cosmetic issue in grayscale mode
  • Tree View: fixed issues with not displaying tooltips
  • Tree View: improved work with collapsed nodes/sub-trees
  • Tree View: performance optimizations for Force Layout
  • Multiple Alignment View: fixed logic in tooltips
  • Improved cache management
  • Fixed crash when user removes Active Object Inspector
  • MacOS: fixed issues with windows floating on top of some dialogs

Release Notes for Genome Workbench 2.11.7 (December 29, 2016)

New Features

  • Critical improvement in HTTPs protocol communication with NCBI
  • Graphical Sequence View: improved rendering for translation discrepancies
  • Graphical Sequence View: improved handling of tracks, added new data
  • Text View: improved robustness when showing data from incomplete projects, when some links to local data cannot be loaded

Bug Fixes and Improvements

  • Graphical Sequence View: fixed crash when two views are open and use track range broadcasting
  • Graphical Sequence View: improved protein alignment rendering to pick more precise translation table
  • Graphical Sequence View: improved tooltips formatting and positioning
  • Text View: fixed issue on MacOS with disabled “Select All”

Release Notes for Genome Workbench 2.11.5 (November 14, 2016)

New Features

  • Use of encrypted HTTPs protocol for back-end communication for VDB/SRA based annotations
  • Multiple Alignment View: reworked to use feature renderings from Graphical Sequence View
  • Multiple Alignment View: added consensus option to BLOSUM coloring methods
  • Open File: implemented loading multiple feature tables at once (used to be only first file)
  • Open File: implemented reading of ‘Text Alignment’ format (FASTA Alignment) used by third party tools like MUSCLE
  • Graphical Sequence View: Six-frame translation track – new option "Left-to-right translations" now correctly works if we flip orientation
  • New tutorial for Coloring methods in Multiple Alignment View
  • Readers: improved FASTA reader messages, modified GFF3 reader to keep GFF3 alignments as single alignments

Bug Fixes and Improvements

  • Text View: fixed bug of not opening certain files
  • Search View: fixed crash trying to run tools directly on searched objects without adding to the project
  • Tools Dialog: fixed issue with incorrect molecules shown due to errors in selection processing
  • Graphical Sequence View: fixed issue showing some extra amino acid in ProSplign alignment in intron part
  • Graphical Sequence View: fixed rendering of protein/DNA alignments across splice junction
  • Graphical Sequence View: fixed alignment drawing (bug was to extend it one position farther sometimes)
  • Graphical Sequence View: corrected tooltip wordings for ORF
  • Graphical Sequence View: fixed expansion of features in dbvar track
  • Alignment Span View: fixed issue with incorrect Exon/Intron boundaries for amino acids encoded across a splice junction shown
  • Sequence Text View: fixed appearance issue on MacOS (text overlap with Find label)
  • Tree Viewer: search query performance optimized
  • Open Dialog: fixed issues with posting BLAST RID from NCBI web site (it was shown as hyperlink, not text)
  • Generic Table View: export improved to quote text fields to be more compatible with data, which includes commas and improve import into Microsoft Access
  • Readers: handling the precursor_RNA feature bug fixed in GFF3

Release Notes for Genome Workbench 2.11.0 (October 6, 2016)

New Features

Bug Fixes and Improvements

  • BLAST Search: fixed incorrect processing of queries based on selected range
  • Improved stability in situations when it works standalone, without any network
  • Text View: fixed Select All on MacOS
  • NG Aligner Tool: added sort options to for Query and Subject sequences
  • Graphical Sequence View: fixed event handling freeze for two coordinated views
  • Graphical Sequence View: improved tooltips to avoid duplicate information, better formatting of mate pairs
  • Graphical Sequence View: graph track rendering improved to better reflect areas with no values
  • Graphical Sequence View: improved rendering of features to avoid overlap with strand indicator
  • Tree View: fixed broken tree label editing
  • Tree View: improved performance of bounding box tree markup
  • Tree View: add “do not sort” option to Sort menu
  • Dot Matrix View: improved to better combine alignments together to open in one view
  • Export improved to better classify possible variants available with or without data type conversion
  • Improved BED format import: added support for feature coloring instructions
  • BAM support: improved graph generation time, added various optimizations

Release Notes for Genome Workbench 2.10.7 (June 24, 2016)

New Features

Bug Fixes and Improvements

  • Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
  • Tree View: layout updated to better accommodate nodes of different sizes
  • Table Import Dialog (MacOS): fixed issue with table visibility
  • Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
  • Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
  • Graphical Sequence View: fixed protein coloration methods
  • Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
  • Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
  • Search View: ORF Finder – fixed incorrect protein lengths
  • Fixed bug with not opening project file (.gbp) on a click
  • Fixed issues in GVF import
  • Fixed BLAST Search tool against NCBI databases not working
  • Fixed tblastn (protein BLAST) not working in standalone mode
  • Fixed GTF export failure

Release Notes for Genome Workbench 2.10.5 (April 25, 2016)

New Features

  • New ProSplign tool integrated with Genome Workbench (Tutorial, Video)
  • New export function for BAM/cSRA coverage graphs (Tutorial)
  • New export function for alignments GFF3 format ((Tutorial))
  • Tree View: implemented new export mode based on selections (tutorial coming)
  • Tree View: added support for distance based circular trees
  • Tree View: new rooting mode (Midpoint Root) results in more balanced trees (Tutorial)
  • Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" – to re-root at mid-branch (Tutorial)

Bug Fixes and Improvements

  • Alignment Table Export: fixed selection of correct alignment objects for export
  • Text View: fixed incorrect display for SNP/variation feature after a feature search
  • Sequence Text View: fixed crash on text search
  • Open File Dialog: fixed MacOS crash in File Import if user attempted to delete existing open items
  • Graphical Sequence View: fixed issues with alignments coloration for protein to nucleotide alignments
  • Graphical Sequence View: tooltips for SNPs freeze fixed for MacOS
  • Graphical Sequence View: improved retrieval of segment map for sequence
  • Graphical Sequence View: new feature 'Project features from aligned sequences' allows to see protein when zooming in to sequence level on CDSs
  • MacOS: fixed random crash on exit
  • Search View: fixed crash when adding a gene to a project
  • Run Tool Dialog: fixed object selection issues
  • Run Tool Dialog: improved to offer a full parent molecule (not just a selected range), similar to Active Object Inspector
  • Run Tool Dialog BLAST: improved to remember column widths in tables
  • Windows: fixed issues with not being able to use more than 2GB of memory on 64-bit OS
  • Improved taxon label retrieval to be non-blocking
  • Phylogenetic Tree Builder: improved to use accessions of molecules, not GIs
  • New mechanism for new version update notification
  • Alignment Span View: fixed export to CSV

Release Notes for Genome Workbench 2.10.0 (January 19, 2016)

New Features

  • BLAST tool reworked to support search in local BLAST databases
  • Tree View: new functionality to collapse multiple nodes based on selection or a query

Bug Fixes and Improvements

  • MacOS-X: fixed crash related fonts and mouse event processing
  • Generic Table View: fixed issues with opening sequences when viewing assemblies
  • Generic Table View: CSV export now allows to select export columns
  • Performance improvements loading WGS (Whole Genome Sequencing) molecules
  • Improved compatibility with GFF format (format reader)
  • Multiple Alignment View: fixed crash in setting Master sequence
  • Multiple Alignment View: fixed issues with showing previously hidden rows
  • Multiple Alignment View: fixed terminology for amino acids for protein alignments
  • Graphical Sequence View: improved track names to better synchronize with the annotation labels coming from the data loaders
  • Graphical Sequence View: fixed labels side overlap on some narrow views, fixed feature overlap
  • Graphical Sequence View: improved alignments renderings to make gaps visible on small scale zoom level
  • Graphical Sequence View: fixed issue with marker failed to disappear (just moves to position 1)
  • Tree View: improved newick format compatibility
  • BAM format support: improved index file name recognition
  • FASTA import: fixed regression with processing ids of local molecules
  • Search View: improved to better provide organism names
  • Search View: fixed crash on opening search results
  • Search View: fixed incorrect label for SNPs
  • Alignment Span View: fixed issue with mixed alignments
  • Text View: fixed cursor wait state
  • Linux: Fixed visual glitch in PDF export dialog
  • Project Save Dialog: fixed defaults for multi-project save (workspace)

Release Notes for Genome Workbench 2.9.5 (August 26, 2015)

New Features

  • MacOS-X: added support for the MacOS 10.10 (Yosemite)
  • Graphical Sequence View: added ruler for protein coding regions
  • Dot Matrix View, Multi-pane Cross Alignment View: added Save to PDF export feature

Bug Fixes and Improvements

  • MacOS-X: added support for the latest MacOS versions
  • BAM file format support: fixed crash, improved exception and error handling when opening incorrect BAM files
  • BAM format support: fixed crashes on loading certain accessions
  • Alignments display: fixed issues with alignments referring to certain
  • Fixed crash on startup in situations when network access to update service is unavailable
  • Fixed remote access to certain type of accessions and annotations (VDB storage type)
  • Graphical Sequence View: fixed “loading…” text in generated PDF
  • Graphical Sequence View / Alignment Views: implemented a new color scheme for ATGC colors, it is now coordinated with SNPs. New color scheme is more friendly to certain types of color blindness
  • Graphical Sequence View: improved performance of alignment rendering, scrolling of views
  • Graphical Sequence View: fixed bug in export of alignments
  • Tree View: fixed bug with node highlighting, when user cycles through the search results
  • Tree View: improved performance of tree sorting when many views are open
  • Tree View: improved tree-to-tree comparison (broadcasting selections)
  • Search View: search of Genome assemblies improved to get more consistent results, which can be added to the Project.
  • Broadcasting Options Dialog: fixed issues with saving options
  • Project Tree View: improved performance of large projects (selections, actions on selected items, search, etc)

Release Notes for Genome Workbench 2.9.0 (May 05, 2015)

New Features

  • Tree View: implemented custom selections and coloring for queries and clusters
  • Graphical Sequence View: combined VDJ-segments and C-region features into the gene model track
  • Graphical Sequence View: graph track improved to show negative numbers
  • Tree View and Generic Table View: added support for wildcard search and phonetic search
  • Tree View and Generic Table View: implemented broadcasting between Tree and Table if both views are open on the same data
  • Project Tree View: new function to hide the disabled content

Bug Fixes and Improvements

  • Fixed visualization glitch on showing certain BAM files
  • Graphical Sequence View: improved renderings of recognition sites
  • Graphical Sequence View: fixed SNP gray-scale rendering
  • Open Dialog: Improved performance
  • Open Dialog: improved saving locations (accessions with range)
  • GFF load: improved column parsing algorithm, added more meaningful project items
  • WIG load: improve spec correctness
  • Tree View: fixed issues with not remembering custom label settings
  • Tree View: fixed issues with visual area jumping to a new location after search, even when search target is already visible
  • Fixed crash on empty tree file
  • Active Objects Inspector: fixed bug on not showing selection size
  • Active Objects Inspector: improved performance in Brief and Full mode
  • SPLIGN Tool: added function to add accession manually
  • BLAST Tool: improvements and fixes to eliminate crash on run
  • Implemented "Reset" button for SPLIGN, Find Overlap, BLAST Search and BLAST Sequences
  • Tools/Options: added new option to change or disable the auto save interval

Release Notes for Genome Workbench 2.8.10 additional build (February 05, 2015)

Bug Fixes and Improvements

  • Fixed crash on MAC OS X 10.10 (Yosemite)

Release Notes for Genome Workbench 2.8.10 (January 16, 2015)

New Features

  • Added support for Ubuntu 14.04
  • Implemented automatic project save and restore on restart (if software crashes)
  • Implemented saving of windows positions (docked and floating)

Bug Fixes and Improvements

  • Fixed crash on Ubuntu 14.04 when selecting a range in graphical sequence view
  • Fixed crash when vertically stacking views
  • Fixed issue with windows move, not redrawing correctly
  • Linux and MacOS – fixed issues with on-exit hanging
  • Tree View: fixed crash with stack overflow of large trees
  • Tree View: fixed issue with queries, going into loop (with blinking screen visual effects)
  • Tree View: fixed broadcasting between same tree open in different views
  • Tree View: improved settings save and restore after restart
  • Tree View: improved PDF output to consider left/right top/bottom margins
  • Tree View: Settings dialog layout fixed not to clip dialog controls (transparency factor)
  • Graphical Sequence View: fixed crash on moving tracks in Multi-level mode
  • Graphical Sequence View: fixed display issues with Clinical variants track
  • Graphical Sequence View: improved feature (depth) discovery algorithm
  • Graphical Sequence View: improved PDF renderings of markers, fixed issue with unnamed markers
  • Graphical Sequence View: improved rendering of links in tooltips
  • Graphical Sequence View: fixed bugs with disabled alignments sometimes remained visible as a track
  • Sequence Text View: fixed crashes in rendering and color changing
  • Text View: fixed hanging issues when searching
  • Text View: fixed crash on some keyboard + mouse combinations
  • Text View: fixed crash on Linux when user tries to paste something
  • Text View: improved toolbar usability
  • Multiple Alignment View: fixed issue with columns visually overlapping
  • Newick tree format import – fixed format detection algorithm (was misdirecting as BED format)
  • Open View Dialog: fixed issues with being unresponsive after data conversion
  • Open View Dialog: fixed search/filtering functionality

Release Notes for Genome Workbench 2.8.0 (August 18, 2014)

New Features

Bug Fixes and Improvements

  • Genome Workbench upgraded to use new version of wxWidgets 3.0.1, fixed some MacOS issues
  • Search View: fixed issue with loss of Strong Kozak signals
  • BED reader: fixed crash on certain files
  • GFF reader: fixed some compatibility issues
  • Cross Alignment View: fixed crash
  • Fixed crash on Linux and Mac on minimization of some views
  • File related dialog – added extra checks for file/path validity
  • BLAST Search Tool: performance optimization of dialogs opening, better handling of long tasks
  • Open Dialog – Genomes: fixed bug with showing duplicate items
  • Run Tools dialogs: performance optimization
  • Text View: ‘Find’ improved hot-key processing (Ctrl+A to select all)
  • Open Dialog: MacOS fixed access to recently used projects and workspaces

Release Notes for Genome Workbench 2.7.19 (June 03, 2014)

New Features

  • Text View – improved searching, added case sensitivity search option
  • Open Dialog – added history list for opening GenBank molecules by accession

Bug Fixes and Improvements

  • Graphical Sequence View: fixed crash on competing multi-threaded redraw
  • Fixed network connection issues on certain networks not reporting correct DNS address
  • Improved GFF3 import
  • Fixed BAM/cSRA files opening when BAM file is located on Windows local or network mapped drives
  • Sequence Text View - fixed crash on color change
  • Fixed crash with dragging Project Tree Window
  • BED file import – improved remapping using information from genomic assemblies
  • Tree View – improved broadcasting mechanism with Tree View and Generic Table View
  • Tree View – improved wait cursor for certain operations that may take a long time
  • Tree View – fixed bug with viewport and scrollbars render incorrectly after maximizing or un-maximizing a window
  • Tree View – fixed bug in Search function (it required two clicks to start)
  • Tree View – PDF export, fixed bug with missing labels when working using Remote Desktop
  • Active Objects Inspector – improved display of selected rows from Generic Table View
  • Dot Matrix View – fixed crash
  • Open View Dialog – fixed issue with unnecessary extra rows when selecting regions for display
  • Multiple Alignment View – fixed OpenGL issue on Intel integrated graphics card
  • Generic Table View – improved search function to better search for phrases
  • Text View – fixed issues with non-displaying ASN.1 types when switching to and from the ASN mode
  • About dialog – design change, use hyperlink to open the website

Release Notes for Genome Workbench 2.7.15 (February 14, 2014)

New Features

  • Multiple Alignment View: implemented adaptive feature display when zooming in
  • Active Objects Inspector replaces Selection Inspector. New View should offer an improved selection context examination. See Using Active Objects Inspector tutorial for more details.
  • Binary packages for Linux OpenSUSE 13.1 are now available

Bug Fixes and Improvements

  • Fixed major issue with OpenGL overlay/scrolling. Could cause crashes or view scrolling irregularities
  • Multiple Pane View: fixed crash on loading BLAST results
  • Graphical Sequence View: fixed crash on zooming in and out, related to SNP track
  • Graphical Sequence View: fixed Go To Position dialog to give better diagnostics in case of a user error
  • Graphical Sequence View: PDF export fixed rendering of Markers with commas in the name
  • Text View / Flat File: fixed Mac OS rendering issues
  • Text View / Flat File: performance optimization, extended capabilities of real-time rendering of molecules to tens of thousands
  • File Import: optimization improvement to speed up load of files containing multiple project items
  • File Import: remapping stage now shows accession.version and description of molecules, instead of plain GI numbers
  • Mac OS: improved tooltips for toolbar buttons
  • Phylogenetic Tree Builder Tool: improved diagnostics of errors
  • Multiple Alignment View: optimizations to avoid main GUI freezes
  • Open Dialog: removed duplicate elements in table of genomes (load Genome)
  • PDF export: fixed issue with XREF table errors
  • Tree View: fixed issues with showing Force Layout progress on Mac OS
  • Tree View: PDF export fixed issues for showing labels of collapsed nodes
  • Tree View: added an option to stop layout
  • Tree View: broadcasting mechanism fixed not to accumulate selected nodes

Release Notes for Genome Workbench 2.7.12 (December 16, 2013)

New Features

  • New improved GFF format reader
  • New Tree Renderer with improved speed
  • Data import redesigned to support molecule id mappings from local to NCBI accessions using genome assemblies
  • Open View dialog now implements filtering/search, making it easier to find the right object (for example alignment)
  • Graphical Sequence View: implemented visualization for map data records representing restriction maps or other non-sequence based maps such as MAP_000012.1. For more details see Graphical View legend

Bug Fixes and Improvements

  • Fixed crash on unloading/renaming/moving of project items
  • MacOS: fixed failure to run BLAST in standalone mode
  • Improved BED import
  • Tree View: improved custom label to be set separately for each tree (it was a global setting before)
  • Tree View: fixed crash in Force Layout display mode
  • Tree View: improved label pattern parsing to avoid incorrect labels
  • Improved OpenGL rendering compatibility with regard to various drivers
  • Fixed OpenGL bug with access to rendering prior to context creation
  • Multiple Alignment View: fixed crash with alignment coloration (Column Quality Score)
  • Multiple Alignment View: fixed issue with graphics scale factor with column resize
  • Multiple Alignment View: improved tooltip content, implemented new sticky tooltips
  • Multi Pane Cross Alignment View: fixed crashes and failures to open
  • Improved GTF export dialog and code
  • Sequence Text View: fixed crash by better handling of internal exceptions
  • Improved system response on bulk deletion of project element (a potential crash fixed)
  • Fixed issues with generation of project item labels for imported data
  • Graphical Sequence View: fixed bug with displaying scaffold and component maps
  • Graphical Sequence View: fixed incorrect tooltip pointer for flipped strand display mode
  • Graphical Sequence View: PDF export, fixed bug with missing empty tracks in the final
  • Graphical Sequence View: Fxed bug with opening wrong alignment despite the cursor selection
  • Graphical Sequence View: tooltip improvement to show “comment”
  • MacOS: fixed some cases of program freezing on pasting data
  • Improved compilation for OpenSUSE
  • Windows/OpenGL: fixed critical problem with incorrect zoom after showing dialogs
  • Generic Table View: improved to show sequence ids as a column
  • Improved error message diagnostics for tools
  • Find Overlap tool: improved stability, logging and canceling
  • PDF export: fixed interaction issues with PDF Save dialog
  • Improved file format detection for compressed (gzip) files (file import)
  • Linux: fixed Drag and Drop for Open Dialog

Release Notes for Genome Workbench 2.7.6 (June 3, 2013)

New Features

No new features were added during this release.

Bug Fixes and Improvements

  • Graphical Sequence View: Fixed issues with missing feature track “Others”/”Misc”
  • Graphical Sequence View: Fixed issues with displaying unaligned tails
  • Graphical Sequence View: PDF export fixed coordinated bug when setting range, fixed issues on Linux
  • Graphical Sequence View: six frame translation track – fixed translation table for mitochondrial sequences
  • Graphical Sequence View: Improved alignment statistics in the tooltips now showing both base count and base percentage
  • Find Overlap Overlap Between DNA Sequences tool: fixed instability, correctly implemented tool cancel function
  • Fixed crash on cleaning internal cache database
  • Table Import: improved handling of invalid values
  • Create Gene Model tool: improved error handling
  • Tree View: Fixed rendering issues on with some Linux drivers, force linux to use standard source alpha blending as we also do for OpenGL 1.1
  • Tree View: fixed transparency factor settings dialog
  • Multiple Alignment View: fixed tooltip window size to better fit text on Linux

Release Notes for Genome Workbench 2.7.5 (May 13, 2013)

New Features

Bug Fixes and Improvements

  • Graphical Sequence View: improved marker details dialog
  • Search View (MacOS): improved tooltips to correctly display full data description
  • Search View (Linux): fixed autocomplete selection
  • Linux: fixed application freeze related to status bar update
  • FASTA Load: fixed critical bug which prevented multi-entry FASTA files to be loaded
  • Generic Table View: fixed crash working with empty table
  • Graphical Sequence View: fixed alignment score coloration issues
  • Graphical Sequence View: fixed pseudo feature rendering
  • Graphical Sequence View: fixed/improved tooltips (extra line break, SNP tooltips content, etc)
  • Graphical Sequence View: fixed failure to group RNA and CDREGION features if gene is absent
  • Graphical Sequence View: fixed tooltips generation of alignments with references on unresolved local sequences
  • Graphical Sequence View: added support of whitespace as sequence position
  • Multiple Alignment View: fixed tooltip
  • Fixed bug in visible range broadcasting
  • Fixed thread race crash related to caching taxonomic labels
  • Table Reader: improved recognition of column delimiters
  • Open View Dialog (MacOS): fixed “Command+A” key combination to select all objects
  • BAM/cSRA compatibility: improved diagnostic messages for cases when sorting/indexing cannot work because of permissions and other restrictions
  • ASN.1 files import: added support for direct opening of gzipped files (without need to decompress)
  • NG Aligner tool: number of fixes and improvements
  • Generic Table View/SNP View: fixed sorting of numeric (RSID) fields

Other notes

  • Ubintu 10.04 and Genome Workbench builds for it are no longer supported

Release Notes for Genome Workbench 2.7.0 (March 18, 2013)

New Features

  • New, reimplemented SNP Table View (SNP Table View Tutorial)
  • Graphical Sequence View: implemented new persistent markers on sequences (Sequence View Markers Tutorial)
  • Implemented reader of 5-column feature table format
  • Text View: Implemented search
  • Genome Workbench project can now be opened as Table (Project Tree View, project context menu / Open Table View). New feature allows user to sort and search project content.

Bug Fixes and Improvements

  • Multiple Alignment View: added new column “Organism name” (taxonomic name)
  • Multiple Alignment View: fixed issues with BLAST results with multiple queries
  • BLAST Search: improved Blast DB selection from the most recently used list
  • BLAST: improved parameters selection interface not to allow mutually exclusive options
  • Graphical Sequence View: fixed crash with protein alignments
  • Graphical Sequence View: fixed crash with visualization of pile-up graph for alignments
  • Graphical Sequence View: improved 'Project features for aligned sequences' mode for alignment tracks
  • Graphical Sequence View: fixed display of alignments with local ids
  • Graphical Sequence View: restored defline as part of sequence track label, sequence track tooltip improved to be pinnable
  • Graphical Sequence View: implement 5’ end visual tagging (sequence track)
  • Splign tool: fixed crash
  • Table Import: improved recognition of DOS/Unix line breaks, various small issues fixed
  • OpenGL support: resolved issues with some limited functionality graphics drivers, improved work with Remote Desktop
  • Tree View: improvements and fixes for PDF printing
  • Generic Table View: implemented support for Copy from cell function
  • Generic Table View: added support for disabled rows
  • Table Views (all): added pop-up tooltip to show full content of extra long cells
  • VCF support: improved label generation for VCF imported variants
  • Alignment Summary View: fixed number of bugs and issues
  • Text View: implemented molecule separation in Flat File mode
  • Create Gene Model Tool: added option to propagate ncRNA features
  • Status Bar: added explicit warning, when relaxed molecule id comparison is used in broadcasting
  • BAM support: fixed crash working with network paths and some incorrect path locations
  • Open Dialog: number of small GUI cleanups and improvements, improvements of MacOS copy and paste
  • Broadcast Options dialog: save settings for program restart

Release Notes for Genome Workbench 2.6.5 (November 14, 2012)

New Features

  • Add Tools Quick Launch items to context menu
  • Graphical Sequence View: implemented separation graphs into sub-tracks based on meta-information title

Bug Fixes and Improvements

  • Updated VCF and GFF readers, fixed issues with checking sequence ids
  • Connection issues resolved for users running international versions of Windows or MacOS
  • BLAST tool dialog freeze for a long time loading list of available BLAST databases
  • BLAST RID load: fixed to automatically import both alignments and local sequences
  • MUSCLE tool integration: fixed alignment coordinate remapping(shift error)
  • Graphical Sequence View: fixed display of tracks with alt-loci alignments
  • Graphical Sequence View: fixed fixed alignment score coloration for SRA
  • Graphical Sequence View: tooltips improved alignment statistics and positions
  • Graphical Sequence View: fixed indels rendering in protein-to-genomic alignments
  • Graphical Sequence View: fixed empty tooltip lines (sequence)
  • Multiple Alignment View: fixed tooltips to be displayed only over sequence part
  • Linux: improved README for users building custom Genome Workbench
  • Search View: fixed failures handling multiple sequence ids
  • Search View: Kozak patterns updated
  • BAM/cSRA support: fixed Open File masking for MacOS and Linux
  • Text View: fixed crash in Flat File mode
  • Tree View: fixed view title after tree sort operation
  • MacOS: fixed opening projects from network paths/mappings/mountpoints
  • MacOS: fixed issues with pasting into Open View dialog
  • HTTP connection component: fixed "User-Agent:" self-identification to better conform standards
  • Improved logging and Feedback reporting not to collect potentially sensitive information

Release Notes for Genome Workbench 2.6.0 (August 31, 2012)

New Features

  • Search View: Implemented SNP Search (search by NCBI rs id)
  • File Open: implemented support of direct file open from compressed formats .gz and .bz2
  • Generic Table View and Tree View now remember old queries and search terms
  • Generic Table View: new context menu option to filter on this cell
  • Tree View: implemented broadcasting of taxonomic ids (tax-id property) to facilitate interactive comparison of trees
  • Multiple Alignment View: new tooltips with detailed statistics for row and column

Bug Fixes and Improvements

  • Format auto-detection for opening multiple files improved. First file is used for format detection analysis.
  • Graphical Sequence View: major improvement in speed of rendering of BAM/cSRA alignments
  • Graphical Sequence View: when selecting a region by mouse show exact boundary coordinates to improve position accuracy
  • Graphical Sequence View: "Go to Sequence Position/Range..." fixed bug with focus in the dialog
  • Graphical Sequence View: various fixes and improvements displaying of alignments
  • Search View: fixed crash on feature search (“Select Feature Types”)
  • Search View: fixed crash on closing the view while search in progress
  • SPLIGN Tool: exposed more parameters for the algorithm
  • Improved Drag-n-Drop of files into Project Tree
  • Graphical View and Alignment Span View discrepancy fixed (rows selection made visible in Selection View)
  • MacOS-X: improved windows docking
  • MacOS-X: Application specific data now put into more conventional location for Mac platform
  • MacOS-X: fixed bug with scroll bar disappearance in Graphical Sequence Viewer
  • ORF/Kozak finder: fixed crash related to multi-threading
  • File Open Dialog: improved layout to fix some cosmetic issues
  • Tree View: Fixed bug with OpenGL rendering of mini-map (“m” key)
  • Tree View: fixed issues in scaling of bounding boxes (cladogram mode)
  • Window Manager: fixed number of issues which could cause crashes and incorrect window layouts
  • Genome Assemblies – Generic Table View: added new columns: 'Assembly unit' and 'Patch type'
  • Genome Assemblies – Grahical Sequence View: added support and visualization of of alignments coming with assembly
  • Run Tool Dialog: improved default selection of target project for result
  • Text View: fixed crash
  • Feedback tool: improved e-mail address validation
  • BLAST Search Tool: new improved categorization of available BLAST databases
  • NG Align tool: algorithm rework and code cleanup
  • Added support of new types of molecule accessions
  • Linux: fixed number of dialogs where radio buttons did not work
  • File Open/Import: improved default naming of project items, added meaningful track title for Graphical Sequence View
  • File Open/Import: filename validation improved to be more responsive when used for slow network drives or locations
  • Generic Table View: format of accession columns changed to include version number
  • Generic Table View: fixed bug in query language, causing string interpretation of certain numeric types (like distance between nodes)

Release Notes for Genome Workbench 2.5.5 (May 17, 2012)

New Features

  • Graphical Sequence View: saves markers and visual ranges (positions) on the sequence in the project file, reopening project now restores the context, making it easier to navigate.
  • Graphical Sequence View: New rendering for clone features
  • RMO format: added support for RepeatMasker RMP files (Feature Table)
  • VCF format: added as supported file format for Open Dialog
  • Implemented multiple-column sort option for tables (Search results, etc)
  • BAM/cSRA: added support for SRA accessions in the Open Dialog
  • Tree View: Search now supports wildcard espressions ‘?’ and ‘*’

Bug Fixes and Improvements

  • Fixed multiple issues in processing and displaying alignments, due to switch to the new Alignment Manager (C++ Toolkit)
  • Open Dialog (Genomes): fixed crash opening certain genomes like 'Escherichia coli'
  • Open Dialog (Genomes): improved discovery of certain genomes (GRCm38)
  • MacOSX:  Fixed bug when you click on list icon Float/Minimize/Close options are disabled when docked
  • MacOSX: Fixed bug with menu items not always available
  • MacOSX, Windows: certain command shortcuts changed to better satisfy platform standards
  • MacOSX: Solved stability issues related to OpenGL on dual GPU MacBook Pro machines
  • MacOSX: solved drag-n-drop issues between Project Tree elements
  • MacOSX: fixed a major issue in windows layout
  • File Export: added default extensions for files of different formats
  • Tree View: performance optimization for various versions of OpenGL
  • Linux: Fixed compatibility issues, related to various versions of libpng and its APIs
  • Project Load: load of large project can now be canceled using context menu
  • Labels generation: fixed crash
  • Labels generation: improved performance of taxon labels bulk retrieval
  • FASTA import/export: fixed bug with exporting duplicate sequence ids (which prevented opening the exported file)
  • Graphical Sequence View: Fixed bug in selection broadcasting for results of Component Search
  • Graphical Sequence View: improved rendering of backgrounds for mRNA features
  • Graphical Sequence View: fixed direction of transcription are drawn backwards in alignments
  • Graphical Sequence View: more options for alignment height
  • Graphical Sequence View: improved rendering of mixed strand alignments
  • Graphical Sequence View: improved rendering of protein to genomic alignments
  • Graphical Sequence View: fixed bug with ProSplign alignments don't project up from NT to NC
  • Graphical Sequence View: fixed crash related to hotkeys and local menu
  • Generic Table View: added export into a separated file, readable by MS Excel (use context menu)
  • SPLIGN Tool: crash fixed
  • Tree View: fixed rendering of area markup
  • Tree View: fixed crash if node is deleted in one tree and user goes to another tree
  • Tree View: improved broadcasting of certain local sequence ids
  • Multiple Alignment View: fixed crash on certain BLAST alignments
  • Search View: fixed issues with server-side compatibility sometimes showing empty columns
  • ORF Search: crash fixed
  • Genome Workbench now uses wxWidgets 2.9.3, fixing lots of issues on various platforms
  • Close Workspace Dialog: layout fixed
  • Alignment Summary Report: fixed to show 1-based coordinates (was: 0-based)
  • BED Import: improved compatibility with BED format

Genome Workbench 2.5.0 Release Notes (1/11/12)

New Features

  • Added support of Genomes (user can now search and load genome information (collection of sequences) from NCBI into project.
  • BAM files loader now integrated with genome information from NCBI
  • Added support for a new cSRA file format
  • MacOS-X 64-bit build added to our distribution list

Bug Fixes

  • GFF reader optimized for better performance, file size and memory footprint
  • Improved communication protocol for clients working with certain versions of not so standard firewalls
  • Graphical Sequence View: improved clone feature rendering
  • Graphical Sequence View: fixed incorrect selection broadcasting
  • Multiple Alignment View: fixed memory leak causing major slow down or crash on large data
  • Text View: can now show ASN.1 type information
  • Text View: fixed bug in range display for FASTA format
  • Tree View: fixed crash on entering letters for cluster ids
  • Tree View: improved performance and fixed some issues with radial layout
  • Improved performance of generating a meaningful description for sequences
  • Export of annotations in ASN.1 format: fixed issues of files written incorrectly, so binary ASN cannot import back to Genome Workbench
  • Generic Table View: implemented cell de-selection, improved object broadcasting
  • Generic Table View: accessions and locations made clickable
  • Search View:  fixed bug with incorrect row selection when sorting
  • Search View: fixed bug on searching for components
  • New version notification dialog: improved UI to offer a clickable URL
  • BAM file loader: fixed file permission issues on MacOS-X
  • BAM file loader: allow to select more than one file at once
  • Open Dialog: improved performance opening a project item with large number of objects (like Genome collection)
  • Open File Dialog: fixed issue with sometimes incorrect file opening on Windows
  • FASTA load: performance optimization
  • Project Save and Load: improved progress reporting, so Genome Workbench does not look dead while it is just busy

Genome Workbench 2.4.5 Release Notes (10/18/11)

New Features

  • Open Dialog now implements a default view functionality, user can now open default view with a mouse double click in the project tree
  • Generic Table View: implemented search function and query language
  • Generic Table View: implemented new option to open trees as tables
  • Tree View: implemented distance (scale) bar for trees with distances (like phylotrees)
  • Graphical Sequence View: improved tooltips, links to RefSeq Gene, Entrez WEB pages added
  • GFF3: major version upgrade for GFF reader
  • Text View: implemented data types display for ASN.1 mode

Bug Fixes and Improvements

  • Multiple Alignment View: fixed memory consumption and crashing issues
  • Graphical Sequence View: optimization of density graph computation
  • Graphical Sequence View: fixed tooltips popup when dialog is shown
  • Graphical Sequence View: fixed duplicate genes when project items annotate gene twice with an additional location
  • Graphical Sequence View: fixed function of Undo-Redo buttons
  • Graphical Sequence View: Fixed rendering issues of alignment statistics graphs at certain zoom levels
  • BAM files compatibility:
  • Tree View: improved search function
  • Tree View: fixed crash when large tree is viewed with a change of layouts
  • Tree View: fixed some sizing errors when certain trees become not fully visible after changes in zooming mode from vertical to proportional
  • Tree View: fixed layout calculations and display of small single-node trees
  • Tree View: fixed function of Undo-Redo buttons
  • Tree View: fixed issues with nodes expand-collapse actions
  • Tree View: fixed rendering issues with not always cleaning the view port area
  • Local data caching: fixed bug in the internal SQL statements causing old data to stay in the database longer than expected
  • Selection Inspector: fixed bug with scope selector disabled on MacOS
  • Project Tree View: fixed crash when project item moved from one project to another
  • Improvements and fixes of communication protocol to better work with older version semi-compliant proxy servers. This improvement results in better connection to NCBI data servers.
  • Search View: MacOS version fixed autocomplete prevented entering new data
  • Open View dialog: fixed location duplications
  • FASTA export for BLAST alignments, fixed issues with showing incorrect locations in dialogs
  • FASTA loading performance optimizations, use more advanced memory mapped I/O where possible
  • Generic Table View: fixed graphical rendering issues (extra vertical lines) on MacOS
  • Text View: now saves view settings (fonts, etc)
  • MacOS: fixed various GUI issues related to keyboard commands and zooming using main menu, About not working, etc

Genome Workbench 2.4.0 Release Notes

New Features

  • Tree View: implemented tree filtering using query language with logical expressions
  • Implemented a brand new view: Alignment Summary to display various alignment properties (Identity %, Coverage %, mismatches, gaps, e-value, etc) in form of a tabular grid
  • Implemented new column options for all table views to show/hide column, specify sorting and sort order
  • Graphical Sequence View: ergonomics improvement, view now preserves collapse/expand state of track during Genome Workbench execution session
  • Search Tool: overhaul of ORF Finder and Kozak Scan algorithms
  • Graphical Sequence View: implemented context menu item Rename me to change track name
  • Graphical Sequence View: user interaction improvements: '+' or '-' sign clickable on the left side of a track title bar, implemented track cloning
  • Graphical Sequence View: 6-frame translation and protein translation are now context aware and can use alternative genetic code tables
  • Graphical Sequence View: implemented alignment summary and statistics graph for alignment tracks (like BAM)
  • Graphical Sequence View: implemented easy access to help and documentation

Fixes

  • Fixed bug with incorrect taxonomic id when searching for a nucleotide in NCBI public databases
  • Fixed Merge Alignment tool to use the same engine as Cleanup Alignment only with more exposed parameters
  • Fixed bug with BLAST tool not honor multiple query sequences
  • Fixed bug with tooltips sometimes stealing focus from views, so keyboard shortcuts may not work as a result
  • Implemented new BLAST results retrieval from NCBI to improve stability over unfavorable network conditions
  • Graphical Sequence View: fixed display of component map in multiple level layout
  • Graphical Sequence Viewer: fixed bug in reading self-alignments, which caused alignments visualization duplication
  • Graphical Sequence View: fixed rendering of multi-location fuzz rendering
  • Graphical Sequence View: fixed alignment coloration mismatch
  • Graphical Sequence View: fixed freezing opening more than one view at the same time
  • Graphical Sequence View: fixed crash in six frame translation track when switching between multiple layout mode and default mode
  • Fixed bug in reading alignment segments, which in some cases manifested as failure to open Multiple Alignment View
  • MacOS-X: fixed bug with loading local caching plugin
  • MacOS-X: fixed crash on drag-n-drop project items
  • MacOS-X: fixed WindowMasker tar file download creates incorrect file permissions on Mac and Linux
  • Selection View: fixed coordinate discrepancy bug
  • Open View Dialog: fixed object grouping mode (feature tables failed to open)
  • Open View Dialog: fixed "attempt to access NULL pointer" error
  • Alignment Views: fixed view opening to better categorize alignments
  • Fixed serious issues in layout and windows management
  • Tree View: fixed crash on closing
  • Search View: fixed thread races crash
  • Search View: fixed issues with buttons Start and Stop became enabled simultaneously
  • Search View: fixed component search coordinate error (it was giving +1)
  • Search View: improved stability of ENTREZ search
  • Search View: column width changes are now saved
  • BAM reader: fixed bug opening files on network drives
  • BAM reader: fixed issue with canceled opening tasks stays on in the Task View
  • GTF/GFF import: incorporate better reader

Genome Workbench 2.3.2 Release Notes

New Features

  • Sequence Viewer: implemented fake end rendering for clone features
  • ORF Search: implemented new column (Start Context), showing residues preceding and following ATG

Fixes

  • BLAST and Windowmasker cannot start on Windows (missing manifest files)
  • Sequence Viewer: fixed Marker navigation direction issue (Alt+left arrow)
  • Tree View: performance optimization for large tree label assignment

Genome Workbench 2.3.1 Release Notes

New Features

  • BAM/SRA format support. Please see tutorial 6
  • CLUSTAL execution added (as an external tool).
  • Tree View: implemented image export to assemble panorama images and/or printing
  • Tree View: implemented support for Zoom to Selection
  • Implemented progress indicator when Genome Workbench accessing network services.
  • Implemented progress indicator and cancel for View Open function (if it takes too long to convert objects)
  • Graphical Sequence View: multiple rendering improvements to better visualize large clusters of features (icicles), improve rendering of component color maps
  • Graphical Sequence View: Improved six frame translation track, better codon detection, and visualization parameters
  • BLAST tool: new option to link related hits together (for better visualization).
  • Options dialog: checkbox to quickly enable/disable use of PROXY (for roaming users)
  • Linux binary build is now based on Ubuntu 10.04 LTS (Lucid Lynx)

Fixes

  • Multiple Alignment Viewer: fixed crashes on opening certain alignments with version-less accessions, fixed tooltip crashes.
  • Fixed crash with View opening (improperly sent notifications)
  • Graphical Sequence View: fixed crash in tooltips at the end of a sequence
  • Window Masker directory path now saved between Genome Workbench executions
  • Selection View fixed crash related to internal event races
  • Tree View: fixed rendering for trees with negative distances
  • Export Alignments: crash fixed
  • BLAST tool: fixed algorithmic crash related to incorrect location mapping
  • Newick tree loader: improved standard conformance
  • Tooltips: made multiple improvements to better conform to standards of target platform (Windows, Linux, MacOS)
  • Windows manager: fixed issues in panel configuration, making impossible to resize things to invisibility (and loss of GUI control), fixed bugs on loading incorrect configurations
  • On-disk cache: improved automatic recovery if database got corrupted.
  • MacOS support: cosmetic fixes in the status bar
  • MUSCLE tool: fixed execution failure if path includes spaces

Genome Workbench 2.2.2 Release Notes

New features

  • More advanced network traversal for clients behind restrictive firewalls
  • Documented Graphical Sequence Viewer rendering styles (Sequence Viewer legends)
  • Tree View: Implemented new markup styles (Adding a Phylogenetic Tree View)
  • Search for Repetitive Sequences Tool: integrated with Window Masker stats files
  • Improved support for opening files located in directories containing international symbols
  • Improved progress messages to inform user if Genome Workbench needs to run a network transaction and may look frozen

Bug Fixes and Improvements

  • BLAST tool execution: advanced parameters are better understood by in-core BLAST
  • Feature Table View: improved functionality to show features on chromosomes (used recursive lookup for features if annotations are placed on components)
  • Open Dialog: improved performance for clipboard pasting long list of accessions
  • Dot Matrix Viewer: fixed bug with combining certain alignments into one view
  • Dot Matrix Viewer: fixed cases when open dialog shows empty list
  • Dot Matrix View: fixed bug with opening objects (in some cases view incorrectly complained "Please select at least one object")
  • Graphical Sequence Viewer: fixed crash on mouse over certain alignments
  • Fixed cache database corruption, when running multiple Genome Workbench instances
  • Fixed incorrect handling of certain Trace Archive Ti accessions
  • Tree Viewer: fixed minimap corruption
  • MacOS-X: cosmetic improvements in look and feel
  • Open Dialog fixed number of copy-paste issues when working with large accession lists and on Linux
  • Tree Export: added default file extension to file selection dialog

Genome Workbench 2.2.1 Release Notes

Genome Workbench version 2.2.1 was an internal NCBI only release.


Genome Workbench 2.2.0 Release Notes

New features

  • New tool: NCBI Genomic Aligner (also known as NG Aligner)
  • Feature Table View reworked to support more input types (locations, annotations, sequence ids)
  • BLAST tool (local): implemented integration with WindowMasker, user can download a WindowMasker statistics from NCBI FTP and use it as a filtering option in Genome Workbench
  • Tree View: implemented sticky tooltips. Genome Workbench now implements dialog to automate masks download
  • Graphical Sequence Viewer: implemented meta-information load to quickly discover NAs (named Annotations), improved performance, reduced memory footprint
  • Graphical Sequence Viewer: new tooltip system with sticky tooltips (works as a bookmark)
  • Graphical Sequence Viewer: improved alignment tooltips to reflect PolyA and Unaligned tails
  • Multiple Alignment View: added a new column sorting option: non-sorted
  • Open Dialog: implemented ability to open data from Genbank (Accession) with a selected region
  • SPLIGN tool: added "Max Intron Size" option (user defined Maximum Genomic Extent limit)
  • Text View: supports opening with a molecule range (selection in Graphical Sequence View) to show list of features in flat GenBank mode

Bug Fixes and Improvements

  • Tree View: fixed broadcast selection to better support various alternative sequence ids (GIs, accessions)
  • Tree View: fixes and improvements in GUI switch to black-and-white color scheme
  • Tree View: fixed zooming inconsistencies
  • Tree View: fixed bug with failing to create a sub-tree with one single node
  • Tree View: MacOS X: removed hard-coded font size, fixed size issue in Properties dialog, fixed empty space above scrollbar, lack of background color in search bar, incorrect button sizes
  • Graphical Sequence View: fixed bug to show features (genes) that contain seq-loc with multiple seq-ids
  • Graphical Sequence View: fixed display for trans-splicing (exons are on mixed strands). Example: AE014297.2, gene name: mod(mdg4), transcript name: CG32491-RT
  • Graphical Sequence View: fixed massive feature duplication when user loads a local feature into the same workbench project
  • Multiple Alignment View: fixed compatibility issues with alignments produced by MUSCLE, fixed crashes
  • Multiple Alignment View: optimization to quickly stop background data processing if view closes or user collapses a row
  • Dot Matrix View: fixed issue with unnecessarily opening multiple views, better support for multiple alignments display in one view
  • Dot Matrix View: fixed bug with opening (not opening) certain types of alignments (Sparse-segs for multiple sequence)
  • Text View: fixed FASTA mode crash on certain incorrectly formulated data (non-existing local accessions) (Supercontigs from Broad)
  • Text View: Fixed flat file display for single feature (was: "feature not found")
  • Text View: memory footprint reduced up to 30%
  • Gene Model Tool: removed "Copy other features from record" option (disabled)
  • Gene Model Tool: fixed crash in the algorithm
  • BLAST tool (local): fixed bug in running tBLASTn (protein to nucleotide) in standalone mode
  • BLAST tool (local): tuned parameters of BLASTn to make it more like MegaBLAST (failed to find certain hits before)
  • Remote BLAST load: fixed thread race crash when loading results from an NCBI BLAST farm
  • Sequence Search tool: Fixed bug with unimplemented reverse complement search
  • Sequence Search Tool: Fixed bug with search in selected range
  • Fixed GUI long lock on view closing
  • Tooltips: fixed multiple bugs related to cross platform tooltip implementation (Linux, MacOS-X)
  • Open Dialog: fixed bug with incorrect accession list save between Genome Workbench sessions
  • Feedback report: Improved internal diagnostics to better track time of certain events
  • Improved performance of saving options and settings
  • Window Manager: restore minimized view by a single mouse click (ergonomics improvement)
  • MS Windows build: discontinued support for Visual Studio 2005, base build platform becomes VS 2008

Genome Workbench 2.1.2 Release Notes

Special Thanks

We are especially indebted to the NCBI C++ Toolkit team, whose patience and help in establishing a capable network setup and in establishing a baseline for Windows 7 installation was invaluable. We are particularly indebted to Aaron Ucko for his help with FASTA parsing issues; Eugene Vasilchenko for general help with object manager issues and debugging memory consumption issues; Anton Lavrentiev and Sergey Satsky for help in improving network setup; Vladimir Ivanov for help with Windows 7 setup; and Denis Vakatov for general support and dealing with our compressed schedule.

New features

  • Added special build for 64-bit Windows 7, enables more views to be opened simulteneously.
  • Graphical Sequnece Viewer:
  • new rendering styles for feature qulity characteristics
  • new feature to center view around marker position (available through context menu)
  • Tree View:
  • added black and white color scheme
  • added mouse dragging and panning for trees
  • added font size customization
  • Multiple Alignment View:
  • anchor row interaction improved to allow selection/expansion

Bug Fixes and Improvements

  • Added an option to run BLAST as standalone, out-of-process program, fixes a lot of Genome Workbench stability issues.
  • Graphical Sequnece Viewer:
  • fixed hang on selection of certain CDS fetures
  • fixed crash in tooltip for exon feature
  • Reduced memory consumption of highly repetitive alignments
  • BLAST search:
  • fixed passing Repeats argument to NCBI server
  • fixed error reporting from BLAST farm to client
  • Fixed various errors related to GFF import
  • Improved network connectivity test for clients behind firewalls with closed high ports
  • Search tool: fixed error when searching for incorrect or misspelled words
  • FASTA import/export: improved compatibility with gene export FASTA files or files with non-standard symbols in defline
  • Improved local data cache corruption detection, implemented automatic recovery
  • Tree View:
  • fixed bug in edge color customization
  • fixed Undo/Redo
  • fixed issues with minimap drag
  • fixed issues with search

Genome Workbench 2.1.1 Release Notes

New features

  • Implemented network availability diagnostics, report issues if Genome Workbench cannot connect to NCBI servers
  • Graphical Sequence Viewer: added new tracks (OMIM genes, CCDS genes, pseudogenes, ncRNAs and non-protein-coding genes)
  • Graphical Sequence Viewer: implemented '..' as a delimiter for sequence ranges
  • Graphical Sequence Viewer: multiple improvements in variation features coloring
  • Graphical Sequence Viewer: improved labels layout (side labels) for alignments and component maps
  • Graphical Sequence Viewer: major improvements in component map visualization and coloring
  • Tree View: implemented mouse based scroll/pan, improved user interaction consistency between grapghical sequence view and tree view
  • Tree View: implemented sub-tree extraction
  • Tree View: new rendering mode to highlight collapsed sub-trees (Ctrl-L)
  • Search: Added sequence location to results
  • MUSCLE tool: added support for the newer version 3.8
  • Installer: improved installation for users without admin priviledges

Bug Fixes and Improvements

  • Fixed crashes related to threading and multi-tasking
  • Graphical Sequence Viewer: bug fix in rendering conceptual translation relative to protein product
  • Tree View: fixed tree attributes and labels inconsistency for (Phylogenetic Tree and Common Tax Tree)
  • Tree View: fixed crash on Undo
  • Fixed crash on shutdown if user closes application immediately after start
  • Dot Matrix View: fixed issues with displaying self-alignments
  • Dot Matrix View: fixed issues related to lost high score hits (floating point rounding errors)
  • Text View: fixed crash when displaying certain features
  • Text View: fixed bugs with not showing protein sequences in Flat File mode
  • Fixed issues with tooltips over OpenGL graphics for Linux and MacOS X
  • Multiple Alignment View: [+] button now works for the Master row
  • WindowMasker tool: improved stability
  • Selection Inspector: fixed crash on switching between modes
  • Selection Inspector: fixed MacOS X compatibility issues (support for Apple key)
  • Project Tree View: improved MacOS X compatibility for tree elements editing

Genome Workbench 2.1.0 Release Notes

New features

  • New Tree Viewer rendering with improved labels visibility, better support of clusters (coloring), function to load external attributes, node selection broadcasting (based on sequence id)
  • Improved Tutorial
  • Added integration with external MUSCLE tool
  • Graphical Sequence View: feature quality visualization (rendering styles for .partial., .pseudo.,
  • Graphical Sequence View: support for non-consensus splice sites
  • Alignment Span View: support for
  • Graphical Sequence View: mouse over alignment reports sequence base position in tooltip
  • Graphical Sequence View: new rendering for parent-child feature relationships
  • Graphical Sequence View: New content options for Gene Model Track to show/hide genes distribution histogram
  • Linux build: added 64-bit Linux build (Ubuntu 8.4 Hardy), implemented DEB distribution file creation
  • File Open Dialog: Implemented dead item removal from most recently used list
  • Implemented Common Taxonomic Tree for sequences tool, with support of FASTA files as a legitimate data source for sequence ids
  • Project Tree View: Folder open/closed state preserved in the project file
  • File Open dialog: added list of recently open files
  • Graphical Sequence View: added support for the new Clone feature subtype
  • BLAST search tool: added RID (task id) for the details box, implemented copy-paste for easier WEB integration
  • Alignment Span View: added support for unaligned head-tail, support Introl-Exon(In/Del) (splign alignments)

Bug Fixes and Improvements

  • Fixed GUI logic in the Project Save dialog
  • Graphical Sequence View: fixed Zoom handler behavior (.z. key processing)
  • Improved Windows installer and plugin loading mechanism to be Windows Vista and Windows 2003 compatible
  • Graphical Sequence View: Fixed serious performance degradation when zoomed to sequence level
  • Graphical Sequence View: corrected positions for CDS translation and protein sequence
  • Fixed disappearing scrollbar (windows manager)
  • Fixed Project Item description editing / saving
  • Fixed Needleman-Wunsch aligner
  • Multiple Alignment View: fixed thick lines rendering issue
  • Graphical Sequence View: fixed View redraw in multi-level mode after a project change
  • Improved alignment labels for Spliced Alignments
  • ASN export: improved file name validation
  • Graphical Sequence View: Fixed Disc alignment rendering
  • Project Tree View: Folder Delete/Cut/Paste/Drag-n-Drop function fixed
  • Open File Dialog: fixed bug when Back button was showing empty or incorrect page
  • Graphical Sequence View: fixed bug in alignment statistics (coverage) displayed in tooltips
  • Fixed crash when editing label for unloaded project
  • MacOS-X Color Picker Dialog: fixed dialog to correctly apply color changes
  • MacOS-X: Implemented About box dialog
  • Graphical Sequence View: fixed crash in flipped strand mode
  • Search Edit Box: fixed upper-lower case history editing
  • Tree View: fixed context menu radio button display to better reflect changes in the layout
  • Multiple Alignment View: fixed unnecessary redraw happened on unrelated change in the project
  • Feature Table View: fixed crash when the view is closed before loading content
  • Text View: fixed crash in renderer
  • Fixed GUI stalls generating labels for objects containing multiple alignments
  • Fixed crash in Search Panel
  • Fixed multiple issues related to internal thread/task processing
  • Fixed selection inspector update/refresh related to multi-pane alignment viewer

Support Center

Last updated: 2019-08-20T14:46:28Z