Melanie 9.1.0 (2018.3.27.0)

This page describes the new features, changes and fixes that were introduced in the Melanie software since the release of Melanie 9.0.0 (2017.8.10.0).

New features

Exports

  • The export options in the software have been made more extensive and consistent. All images (2D views, 3D views, Display area, Application window), graphical reports, tabular reports and project data can be saved to disk, printed and copied to the clipboard.
  • The following objects can now also be exported: Project list, Factor table and Experimental design view in the Experimental design step, Normalization factor table in the Spot normalization screen, Analysis summary table in the Results step, the application window, 3D views of images (when visible), 2D views of images in the Quality control and Experimental design steps.
  • A new interface enables to tweak the export options for tabular reports and project data. The user can choose to export:
    • Selected rows or all rows
    • All columns, visible columns or a specified subset of columns
    • Project description
    • Extended headers (factor level assignment of images)
    • Colors of the cells as they appear in the table
  • The software conserves the export parameters for the duration of the session, as well as the last file type and file path used.
  • Graphical information in tabular report cells (e.g. bars, histograms, 2D views, 3D views, coverage status) are exported as images in HTML and Excel file types.
  • Images can now also be saved in JPEG format.

Spot edition / Review

  • The Group table now includes an Edited column. Spots that were edited (except Delete and Move) appear ticked in this column and can therefore easily be selected for review.

Display area

  • Saturated areas can be visualized in all workflow steps, using the option Saturation in the Options of the Toolbar.

Compatibility

  • Support for computer mice with enhanced high-resolution mouse wheel.

Changes

Quality control

  • Dots ‘.’ are now allowed in file names (except at the end of the name).

Experimental design

  • When the first factor is created manually, i.e. not via the Experimental design wizard, the Experimental design view now automatically shows at the creation of the factor, and a One-factor analysis is created in Results.

Coverage

  • The Overview window can now be docked at the right of the Coverage table.

Results

  • In the PCA sheet, it is now possible to choose whether to select spots or gels on the PCA plot.
  • In the PCA sheet, the display options for the PCA plot have been simplified and moved to the Options icon at the top right of the plot’s window.

Display area

  • The Group images option is now stored for each workflow step/screen (where the option is available).
  • The default Modes for the various workflow steps/screens have been reviewed.

Tables and plots

  • The toolbar of tabular reports now has a Settings icon that gives access to the Column settings and several tools that were previously only available by right-clicking on a column header (Best fit, Show group by, Show cumulative histogram, Show 2D plot for columns, Select value, Display value).
  • The Cumulative histogram and 2D plot, both available from the Settings icon in tabular reports or by right-clicking a column header, have been improved. The column(s) used for their axes can now be changed easily on the plot and in the report toolbar.
  • The display settings of graphical reports can now be accessed by clicking the Options icon at the top right of the plot’s window.
  • For some reports, Filter by values now proposes a default filter. The default significance level for filtering p-values can be set in the Quantification tab of the General options.

Exports

  • When exporting (Save, Print, Copy to clipboard) spot sets, validation columns, coverage States and coverage Status, the software now exports descriptive text instead of numerical codes.

Fixed bugs

Quality control

  • Crash after adding an image, then renaming it, removing it, and undoing the last operation.
  • Import of .ds files failed for Coverage DIGE/DIBE experiments.
  • For DIGE with internal standard projects, files with the extension .img were missing from the All Image Files filter in the Add images window.
  • Import and grouping of DIGE images (other than .ds files) could fail depending on the structure of the image names. The image grouping algorithm has been further optimized to avoid this.
  • The character ‘&’ in file names is no longer interpreted as an underline.
  • For DIGE experiments, it could happen that the small pI/MW icon marking the image used for pI/MW calibration didn’t appear left of the image name.
  • In the Edit pI/MW screen, when defining pI or MW markers on an image, displaying the Grid, and then switching to a new Image for pI/MW (that didn’t have any markers yet), the latter image could show a non-relevant Grid.
  • When duplicating a project, the information about what image to use as the reference for pI/MW calibration was lost.

Alignment setup

  • It was not possible to change the reference group of a DIGE project.
  • In rare cases, a change in the alignment setup (hierarchy and reference images/groups) could cause some matches to become inconsistent.

Alignment

  • Spots became deactivated after Reset modifications in the Alignment step, and then closing and reopening the software.
  • Error or crash after Undo/Redo of alignment operations following edits of the Workflow options.
  • For some images, typically images with very high resolution, the software shows a warning message when the number of spots in the alignment is too high and gives the possibility to adjust the detection parameters used in the alignment step. The software could crash depending on the chosen options and new detection parameters.

Detection

  • When gel and project names were identical, Reset modifications in Detection removed all spot groups (matches).
  • Error or crash after Undo/Redo of detection operations following edits of the Workflow options.

Spot edition / Review

  • Matches could get corrupted when undoing and then redoing ‘Create spot’ or ‘Split spot’.
  • In some cases, the Save modifications and Reset modifications options could become inaccessible after Undo/Redo of spot editions.

Spot normalization

  • For DIGE experiments, the content of the Markers column in the Normalization table was not reinitialized when switching between images. As a result, the wrong spots could be tagged as markers.

Coverage

  • Images and spot selections were not synchronized when switching between Coverage tabs that had no images in common.
  • Undo ‘Edit coverage’ reset coverage status of all spots to the default (based on presence filter), instead of undoing only the last spot status edit.
  • Undo of Reset spot qualification and Add/Remove targeted coverage was not managed.
  • Crash after removing an existing coverage target positioned after the currently displayed coverage target.
  • Crash on second double-click on one of the histograms in the Coverage summary.

Results

  • For projects of type Single stain and Multiple stain without internal standard, the ratios shown in the Expression ratio table didn’t adapt to the selected Display ratio as option (Usual, Signed, Log10, Log2) in the Quantification tab of the General Options.

Picking

  • Export of pick list to GE Healthcare Ettan (Text) was encoded in Unicode (instead of the correct ANSI format) and indicated the coordinates -1,-1 for the Ettan markers (instead of 0,0).

Display area

  • When reopening DIGE projects, the 3D view of certain images could be completely flat.
  • When the 3D view was displayed and the reference image was exported to the clipboard, the 3D view of the reference image became completely flat.
  • Group images in one pane only worked after another Group images option was applied first.

Tables and plots

  • It was not possible to save the results of a filter (Filter by values) on an existing spot set.
  • For Single stain, DIGE with internal standard or Multiple stain without internal standard projects, the computed pI and MW values in the reports could be based on the pI and MW markers of another image than the one selected by the user (the software selected an image based on the image order in the alignment hierarchy).
  • Crash while displaying a tooltip on a report with the Group by option activated.

Exports

  • Crash when Data from a Coverage project was exported in Excel format.

General

  • Image and project files were not properly managed when the system’s Document folder was located on a network server.
  • When using the software on a computer system with multiple screens, some parts of the application window could be clipped.
  • For the Projects screen and Create project window, the link to the offline documentation in the Help tooltip was wrong.