Softpedia >Mac >Math/Scientific >Genome Workbench >  Changelog

Genome Workbench Changelog

What's new in Genome Workbench 3.9.1

Jan 9, 2024
  • New Features:
  • Genome Workbench macro editor is rafactored to handle larger submission files more easily
  • Bug fixes and Improvements:
  • Additional improvements to the Editing and Submission package
  • Fixed a bug in recommending compatible views in the Open View dialog
  • Fixed a node property bug
  • Additional minor bug fixes
  • Additional improvements to performance

New in Genome Workbench 3.8.0 (Sep 19, 2022)

  • New Features:
  • CSI index files are now supported for BAM and VCF file uploads
  • Added ability to generate a project with different folders for each input ASN.1 object
  • New alternative start option for using 'ATG/GTG/TTG' start codons in the six-frame translations track in the Graphical Sequence View
  • Added ability to edit steps in the microflow macro editor
  • Bug fixes and Improvements:
  • Fixed a bug preventing pasting a search term in the search box of the Tree View
  • Fixed a bug in locating SNP features using the search function in the Graphical Sequence View
  • Updated code to be compatible with a new PubMed API
  • Additional feature and performance improvements
  • Additional minor bug fixes

New in Genome Workbench 2.12.5 (Feb 9, 2018)

  • 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

New in Genome Workbench 2.12.0 (Feb 9, 2018)

  • 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

New in Genome Workbench 2.11.10 (Mar 22, 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

New in Genome Workbench 2.5.0 (Mar 7, 2012)

  • 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