GenomeView 1.7.1 released

Today we release version 1.7.1 of GenomeView, our genome browser and curator.

This release features a number of improvements:

  • When loading features with the same sequence ID as an already loaded sequence, the features are added to this sequence.
  • GFF3 parser now correctly assembles CDS fragments with the same parent into a single Feature.
  • Save dialog now notifies which file will be overwritten.
  • It is now possible to switch between the SequenceView and the main application.
  • The CDS overview now behaves better, but there is still room for improvement.

GenomeView 1.7 released

GenomeView 1.7 is the latest release of GenomeView. The main new feature in this release is the BioMoby support to communicate with BOGAS.

Features

  • Improved human-readability of some labels
  • Improved search dialog: nucleotide, amino acid and keyword search.
  • Improved BioMoby support
  • Authentication for BioMoby

GenomeView 1.6.9 released

GenomeView 1.6.9 has been released!

This release is only supported as webstart application. We need to sort out the BioMoby libraries before we can support a stand-alone version again.

GenomeView 1.6.9 offers a lot of bug fixes and a number of new features.

  • Partial locations are properly parsed and displayed
  • Save to fasta and gff3 now work properly
  • Each save dialog is now associated with the correct GenomeView instance
  • A number of GUI improvements and naming improvements
  • Added support for gzipped files
  • Parsers ignore lines they don't recognize instead of crashing GenomeView
  • ChromosomeView is back in business, better than ever
  • BioMoby support should be operational, though still a bit experimental
  • Show warning when information may be lost during save

GenomeView 1.6.8 released

GenomeView 1.6.8 offers a lot of bug fixes and a number of new features.

New features

  • When clicking a gene in the annotation panel, it is also selected in the CDS overview table
  • Internal BioMoby support, expect to hear from this more in the next release
  • Several new configuration options
  • Data sources (files, web sites, biomoby services) are now handles uniformly
  • Features can be displayed and saved based on their origin.
  • Expanded save capabilities with more options
  • Added support to copy sequences to the clipboard (ctrl+c)

GenomeView 1.6.7 released

GenomeView 1.6.7 brings a number of new features and fixes some bugs

New features

  • You can hide gene structures that you don't want to see. This can be done by selecting them from the menu 'Selection' or by clicking the last column in the gene structures overview table.
  • Improved some labels throughout the GUI to be more human readable.
  • The module system is replaced by the JPF framework (http://jpf.sourceforge.net/).

DNA physical property module

This module provides graphs that represent the physical properties of DNA.

At the moment 16 different properties are implemented.

Download

GenomeView 1.6.6 released

GenomeView 1.6.6 brings a number of new features and fixes a bug.

New features

  • Motif search is available from the navigation menu
  • Logging to a file can now be configured in the configuration panel
  • Goto nucleotide is available from the navigation menu
  • It is now possible to blast the sequence of a selected region

GenomeView 1.6.5 released

GenomeView 1.6.5 brings a number of bug fixes and some new features

Features

  • Visibility of the 3 panels can be set from the command line on start-up
  • A configuration file can be specified on the command line, this configuration will override the default and user configuration
  • Double clicking a feature centers the view on that feature
  • By default all evidence tracks are visible and expanded
  • You can use mouse wheel to zoom in and out in the evidence and structure panel
  • You can use the mouse to navigate in the evidence panel
  • The structure panel moves when you try to select something outside the visible area
  • It is now possible to remove a single location from a feature

GenomeView 1.6.4 released

Since the major redesign in GenomeView 1.6.3 we solved a number of bugs and added some requested features.

The loading and saving of data has been redesigned in order to make is more easily extensible.

Features

  • The order of tracks in the evidence panel can be changed if desired
  • The output which would normally go to the console is logged to a file to make it easier to diagnose GenomeView crashes
  • Version number is displayed in the program window

GenomeView 1.6.3 released

GenomeView 1.6.3 has been released. This release features a complete redesign of the internal data structures, with loading and saving mechanics. Furthermore we split of the syntheny part of the application, which we live in a new project from now on. GenomeView will only focus on being a genome curation tool.

Some highlights

  • All libraries have been removed in favor of the new custom made data model. This reduces the size of the application from over 60 Mb to less than 1 Mb.
  • The new data model has build-in undo and redo functionality. Basically the old system has been integrated in the data model.
  • Supporting new data formats and data sources is build-in by design in the new data model

Because this is a massive redesign some features may be broken, please report this to us.

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