Version 0.3.1

By October 23, 2009Release Notes From Blog

Changes in version 0.3.1 (Oct 23, 2009)

New Functionality

  • Kamino now supports simulating and printing agarose gels using 1-4 enzymes using various templates in up to 8 lanes.
  • You can now zoom in on a portion of a sequence. Toggle zooming using the new button at the lower left. Quickly zoom in on a region of interest by first selecting it before toggling on zooming. Use the various zoom controls to zoom in and out, pan back and forth, or manually specify a range to view. You can adjust the zoomed range using the miniature map and clicking and dragging the zoomed window or its endpoints. Zooming limits the portion of the sequence shown in Map and Sequence views, while the zoomed window is highlighted on the root node in History view.
  • Notes view has been replaced with a streamlined Notes Panel that is accessible while using any view by toggling the checkbox at the lower right. You can now mark sequences that you have confirmed experimentally. Just check the checkbox under the notes panel and you’ll get a green check mark at the top right when viewing that document.
  • Kamino now supports limited rich formatting (bold, underline, italics) and easy insertion of Greek letters for feature and primer descriptions and sequence comments.
  • Kamino now supports lower case DNA letters. Quickly convert the case for large blocks of DNA by selecting them and using the new “To Upper” and “To Lower” Edit menu actions.
  • You can now print multiple views at once. When invoking “Print” you’ll be presented with a “Print Options” dialog which allows you to select which views you’d like to print.
  • Kamino now checks for updates and automates their installation.

Enhancements

  • When using the “Remove Restriction Fragment” and “Insert Restriction Fragment(s)” dialogs, Kamino now lists all fragments that will be produced using the enzymes specified. This now includes fragments that bounded by only one of the two enzymes specified. Fragments that would only be produced by changing the sequences methylation are no longer shown. In other words, the fragments listed are the same ones you’ll see when using the Simulate Agarose Gel dialog.
  • From the “Insetions” tab of the primer dialogs you can now insert stop codons.
  • After inserting DNA into a primer sequence, the cursor is now placed after the insertion. Thus you can now quickly build long primer sequences simply by choosing what to insert and clicking insert over and over again.
  • When clicking on blocked sites, Kamino now informs you why the site is blocked and suggests changing the sequences methylation to enable it.
  • Kamino now uses an enhanced fixed width font, for example when using Sequence view or viewing primer and enzyme recognition sequences.
  • Added a “Print” button to the Non cutters dialog on Mac.
  • You can now use various Edit menu actions from with modal dialogs like the Edit Feature and Edit Primer dialogs.
  • Various textual, painting, and alignment enhancements
  • Various optimizations

Bug Fixes

  • Fixed a bug that might prevent Kamino from realizing a primer sequence could bind if hybridization parameters were relaxed in some circumstances.
  • Fixed a bug that prevented Kamino from indicating mismatched primer bases in red within the PCR and other primer related dialogs.
  • Fixed a bug that prevented a sequence’s modified date from being updated when features or primers were created, edited, or removed.
  • Updated the “Enzyme Website” links for SibEnzyme supplied enzymes in the Restriction Enzymes dialog.
  • Fixed a bug that prevented the amplified fragment from always being selected in the PCR dialog.
  • Fixed a bug that prevented primer lengths from being erased after a primer is cleared within the PCR dialog.
  • Fixed a bug that prevented the Kamino uninstaller on Windows from removing all traces of Kamino.
  • Fixed a bug that could cause tick marks in enzymes view to disappear entirely under some circumstances.
  • Codons are now listed in the proper order in the insertions tab of the primer dialogs.
  • Fixed a bug where if a sequence has a unspecified strain the wrong entry is shown when using the Change Methylation dialog.
  • Fixed a bug that prevented preference changes from sticking when toggled by clicking the label associated with a button under the display options tab.
  • When no accession number is specified, the “Assession” label is now black and will not respond to clicks within the Notes Panel.
  • Fixed a regression that prevented copying recognition sequences from within the Restriction Enzymes dialog.
  • Fixed a bug that caused the Preferences window to always show up on top.
  • Fixed a bug where topology and sequence length were not always cleared when cloning and PCR dialog templates were reset.
  • Fixed a bug that prevented the File→Open Recent menu from refreshing when documents were opened within the PCR and Mutagenesis dialogs.
  • When loading open documents within the PCR dialog, Kamino now properly shows the most up to date phosphorylation, methylation, counting from, default genetic code, and chosen enzymes.
  • Fixed a bug that resulted in no enzymes from being shown when loading old files that used an older Kamino file format from within the PCR and Mutagenesis dialogs.
  • Fixed a bug that prevented error messages from being cleared from the list box within cloning dialogs when changing the template.
  • Fixed a bug that prevented properly inserting restriction fragments into a linear vector with sticky endpoints.

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