Melanie 9.2.0 (2019.6.13.0)
This page describes the new features, changes and fixes that were introduced in the Melanie software since the release of Melanie 9.1.1 (2018.4.5.0).
You can learn about the installation requirements and instructions for Melanie 9.2.0 (2019.6.13.0) in its Readme file.
All modules (Classic, DIGE, Coverage)
- The Project report feature automatically generates a comprehensive PDF report that summarizes all essential quality control checks, workflow parameters, results, images, tables and plots in a single document. If desired, a detailed spot measurements report can be generated as a referenced appendix. The coverage analysis report comprises results for the entire experiment, so there is no need to produce a separate report for each image pair. The expression analysis report integrates information from all open analyses (e.g. two-factor analysis, one-factor analysis, PCA), for all or selected spots, with spot details including 2D or 3D views as visible in the software.
- In the Edit pI/MW screen, it is now possible to use one of the predefined IPG strip definitions (linear and nonlinear) for pI calibration, or to define, save and reuse a custom strip. After correct positioning of the two ends of the strip, pI values are automatically calculated for all spots in the experiment.
- Tabular reports can now be saved in PDF format.
- Images can now directly be imported from TWAIN scanners.
HCP Antibody Coverage Analysis (Coverage module)
- The Coverage quadrants and associated reports (Quadrant histograms and Quadrant matrix) help evaluate the coverage of your antibody for different size and charge categories of proteins.
- The Coverage range (displayed behind the coverage percentage) indicates the range within which your coverage will fall if you only edited the uncertain spots, considering that each uncertain spot could either be absent or present. The coverage range can help you gauge the stability/robustness of your coverage analysis and tells whether a detailed spot review is relevant. Simply report the coverage range instead of coverage to save time, avoid the subjectivity of spot status editing and integrate the notion of uncertainty in your results. The coverage range is also shown as black intervals in coverage histograms. Note that it is only calculated and displayed if there are uncertain spots.
- The Presence summary recaps the absence/presence information of each spot on every image in the experiment. It lets you review and edit spot presence while viewing spots across all images, select proteins that were detected with a certain frequency in specific image subsets (e.g. all, primary or secondary images), identify spots for which presence state was edited and verify the congruency of edited spot presence state with the presence filter thresholds.
- The Presence plot helps you review if coverage status edits are reasonably congruent with the thresholds set in the Presence filter.
Differential expression Analysis (Classic and DIGE modules)
- For columns that contain ratio data (e.g. Fold, levels in Expression ratio table), there now is an option Show ratio as color that automatically applies default thresholds and color schemes to quickly show which spots are up- or down-regulated by a factor of 2 or more.
- In some tables, especially in the Classic and DIGE modules, Filter by values now proposes default filter criteria.
- Small improvements in the Create project window.
- It is now possible to create Coverage DIBE/DIGE projects where the stain/label for the Primary image (revealing all HCP antigen proteins) can be different for each blot or gel.
- To allow clarification and generalization, messages and constraints related to the assignment of images as primary or secondary have been reviewed.
- For projects of type Coverage (non DIGE/DIBE), after making changes to primary/secondary image assignments, the alignment setup is updated to reflect the new image relations. However, non-default alignment setups are not modified.
- Preliminary detection in the Alignment step was optimized for images with background noise.
- Validation, annotation and spots set columns were added in the PCA – Spots as observations report.
- The Coverage table now includes a Status edited column indicating whether a spot’s automatically assigned presence status was modified (ticked box) subsequent to spot editing or a user edit.
- In the Coverage summary table, the columns Spots, Primary, Secondary, Common, Uncertain, Formula and Coverage type are now shown by default.
- In most tables, pI and MW columns are now visible by default.
- The size of the 2D and 3D images in reports can now be adjusted as Small, Medium or Large by going to the report’s Options icon and selecting Image size.
- When saving reports and exports, the choice of columns to be included has been improved.
- Display value > Show as color settings are now conserved when switching between analysis sheets.
- It is now possible to choose (in General options/Display/Display image background in 3D View) whether the hidden areas in the 2D view are shown in white or with image background in the 3D view.
Performance and usability
- Improvements in how edits are managed in all steps of the workflow (Undo/Redo/Save/Reset).
- Error in raw image conversion when opening images with inverted flag and lookup table.
- Crash after adjusting contrast of inverted images (white spots on a black background) in Edit images, and then returning to Quality control.
- Crash when opening coverage analysis after deletion of previously analyzed images.
- In the Image edition screen, it was sometimes necessary to click the Crop tool twice to re-activate it.
- The number of pI/MW markers in the Edit pI/MW drop down in Quality control could be inconsistent with the number of markers mentioned in the Edit pI/MW screen (when some markers were outside the crop area).
- Renaming of groups in the Alignment setup corrupted the matches.
- In Alignment setup, saving of changes failed when there was a space at the end of a file name.
- Warping was not always updated after match edits.
- Minor correction/adaptation of position of spot centers.
- For Coverage DIGE experiments, when Intra align in the advanced Workflow options was ticked and the change confirmed, the option disappeared (one couldn’t untick it again later on).
- Changes in detection parameters were not applied in particular circumstances.
- For Coverage DIGE experiments, the Detection input in the Detection step was always reset to the default after returning to Alignment to edit some matches.
- When editing the Detection input on a previously detected project, the software displayed a wrong error message.
- The background computation option, in the advanced Workflow options for Detection, was not stored in the project’s settings.
Spot edition / Review
- Matches could get corrupted after particular spot edits. This fix includes a mechanism to repair projects affected by the corruption.
Review – Spot normalization
- In Spot Normalization, the “within” option was not managed in Undo/Redo.
- Changing detection parameters removed the Presence filter thresholds that were previously set.
- Crash when creating a new project while being in the Coverage summary tab.
- Coverage diagrams were not properly centered.
- After collapsing the Review status section, switching to another tab and then returning to the original tab, the Review status section could not be expanded.
- Match vectors and alignment in Picking were lost when switching to the Alignment step and then back to Picking.
- The pI and MW columns in the Spots to pick table displayed wrong values (whether pI and MW markers were defined or not).
- In tables, there was a shift of the boxes that appear in the table toolbar after Show… options on columns are successively selected and then again closed.
- For DIGE experiments, the Vol Ratio could not be displayed in the Spot table.
- OK and Cancel buttons covered part of the tools in the “Choose color for [spot set or validation column]” window.
Annotations, spot sets, validation columns
- Spot sets were not properly saved during the session where they were created.
- The Warp image option was not applied to images that were not directly aligned to the global reference.
- In 3D View, it was not possible to select a spot by clicking on its saturated area.
- White spaces at the beginning or the end of project names, gel (DIGE) names or image names could cause data loss. Additional tests on those names have been introduced to avoid inconsistency with Microsoft Windows behavior.
- When renaming a project, primary reference (for Coverage experiments) and pI/MW information was lost.
- Reset modifications did not work correctly for particular sequences of operations.
- Options icon on Cursor information window did not have a tooltip.