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GasPedal Changelog

The user benefits are described in the What's New document.

GasPedal 1.1

1.1.0 Final 02 (201811202254)

Improvements

  • The manual is now up to date.
  • Accuracy when calculating fusion images has been increased.
  • Your choices on which attribute and group measures the statistics table should be based on are now saved.
  • You can now choose whether or not you want to apply calibration on calculating fused images.
  • GasPedal can now import data files directly into your project, is able to recognize known samples (list of samples visible in 'Images -> image Attributes...' in file names of imported files, to create / rename groups according to the samples recognized, and to sort images into the respective groups.
  • Importing images now first shows images already imported into your pool, but not yet used in the current project, and if there are none of these, opens the Import Wizard.
  • A new visualisation now shows at a glance in the Project Explorer, the Light Table and the Warping Setup, which sample, gel and channel are assigned to your images. And when pointing on this visualisation, a tool tip tells you details.
  • The job manager now shows automatically if you create jobs by defining automatic warps for the first time in the session.
  • The progress of an autowarp job now shows even if the job was started implicitely by clicking on "Warp" or "Find Match Vectors" in the Dual View.
  • Now you can change the warp mode also in the context menu if exactly two images are selected in the Project Explorer.
  • When clicking on "Review" of one of your image pairs in the Work Flow pane, the Dual View now activates the match vector tool automatically.
  • A new column called "Labels" is available on every Quantitation Table and shows labels from ALL images of the current project, not only those being visible in the current table. With its filters you can control the labels of which images you want to see or hide, regardless of the visibility status of the images themselves, and also regardless of whether the spots of these images are included in the total spot set or not.
  • On spots having labels also on matching spots on other images, the labels are now sorted corresponding to the sorting of the images of their origin in the project manager. This way, by moving the images up or down in the project manager, you can control their sequence in the combo box of the table rows yourself.
  • A new report, "debug.py", was included to enable in case of problems also end users to create debugging output, which can be saved and sent via email to support@decodon.com.
    When GasPedal is running, it can be produced by clicking on the link:
    http://127.0.0.1:2007/GasPedal/debug.py
    Please use your browser function (press the keys CTRL + S simultaneously on your keyboard) to save the report.
  • Administrators in regulated environments, where e.g. CFR-compliance is relevant, can now benefit from syslog based audit trails.

 

Reports

  • If you defined filters in the Quantitation Tables, the report now applies these first, and uses its own defineable filters if not.
  • The report now validates your project setup on calculating results, and tells you, if something is not as it should be.
  • You now have the option to only show image pairs with the same gel.

 

Fixes

  • A problem with the overlay rollup was fixed, where switching back to automatical visibility of spot or label layers did not always work.
  • Several rarely occuring NPEs were fixed.
  • Small cosmetical issues, typos etc. were corrected.
  • The native look-and-feel under Mac OS X was recovered by updating the involved libraries.
  • The job manager now refreshes more accurately and empties and populates its list and controls accordingly when closing and opening projects or the complete application.
  • When clicking on the status button in the Dual View and an image pair with automatic warping is opened, where the match vectors are not yet calculated, GasPedal now does not start finding match vectors any more.
  • A deadlock could occur on importing images.
  • Some problems with the workflow links to open images etc. have been fixed.
  • Some problems with calibration curves are now fixed, e.g. they are now deleted together with their image.

Note: version 1.1.0 Final 1 was not released.

GasPedal 1.0

1.0.6 Final 02 (201712211203)

  • Fixed an error message occuring under rare conditions when opening a quantitation table.
  • Improved handling of calibrations on importing images.

1.0.6 Final 01 (201712142020)

  • Fixed a problem with grouping characters in MGF exports, which could be misinterpreted in NIST search.
  • Added interpretation of attributes, which can sometimes be found in CDF files: 'scale_factor' and 'add_offset' for m/z and intensity values.
  • Spectra comparisons do not offer 'Create Match Vector' if it does not make sense, e.g. on indirectly warped images.
  • Fixed a problem sometimes occuring when alternatively computing spectra for many different CDF files.

1.0.5 Final 02 (201712072026)

  • Memory handling is strongly optimized, with dramatic effect:
    • Performance has improved significantly.
    • GasPedal can now handle much bigger files in much bigger projects with less available memory.
    • Freezes caused by memory outage have been eliminated.
  • Every quantitation table now can show an extra column with all labels linked to spots originating from all images (even hidden ones), and let the user choose which labels from which images to be shown (filter label origins).
  • The description of the spot detection dialog in the manual has been corrected.
  • Small cosmetic issues related to branding are fixed.

Note: version 1.0.5 Final 01 was not released.

1.0.4 Final 03 (201711262012)

  • Internal handling of spectra has been changed to improve performance in big projects.

1.0.4 Final 02 (201711211812)

  • A problem with hanging on batch import was fixed. [7971]
  • The manual has been updated.
  • The label column in the statistics table now has a filter to select the images to provide labels. [7375]
  • The delete button for image attributes like gel, sample and channel is now enabled again. [7968]
  • The labels in the statistic table are now sorted by image order in project explorer (hidden images last). [7928,7375]
  • The selected statistics spot attribute is now used in reports. [#136]
  • In the Spot Album Report the barchart size in barchart thumbnail is now maximized.

1.0.3 Final 01 (201709272249)

  • New Feature: now you can set the reference values of spots for project wide statistics individually for every project to:
    • Normalized Volume
    • Absolute Volume
    • Average Grey Value
    and save along with each project. It can be changed in
    • Project properties
    • Statistics Table
  • Updated shipped Java version for Windows and MacOS to Java 8 Update 144

1.0.2 Final 03 (201709111543)

  • New Feature: The Dual View now shows the mouse position also as RT1 / RT2 in the status bar.
  • In the "Image and Table Column Visibility" dialog the header check box now also reflects partial selections of the columns.
  • Fixed a problem, where GasPedal could hang when importing batches of CDF files multiple times.

1.0.2 Final 02 (201709070126)

  • Now all decimal places for modulation period and time offset specified on image import are shown in image properties.
  • On importing data, the image height is now more consistent with respect to the number of scans per modulation period.

1.0.2 Final 01 (201709042332)

  • New Feature: Now you can "Find Spectrum" everywhere in the context menu of any image to locate specific spectra. (Obviously, this refers only to images containing spectra, and not to those without spectra, e.g. Fused Images)
  • On importing data, the modulation period now can be specified with up to 10 decimal places.
  • Fixed a problem in the "Image and Table Column Visibility", where the header check box already was checked, if any box in that column was checked. Now it will only be checked, if all rows in that column are checked.

1.0.1 Final 02 (201708312241)

  • Increased precision in spectra info for RT, RT1 and RT2 to 3 fractional digits.
  • Fixed a problem where spectra charts were opened initially with different m/z ranges.
  • Fixed a problem where spot profiles in rollup were not refreshed correctly after changes in spot normalization set.

1.0.1 Final 01 (201708181325)

  • Adapted reviewed normalization by introducing calibration curves to consider huge differences in absolute Total Ion Count levels between data sets.

1.0 Final 25 (201708161941)

  • Fixed a NPE when opening the spectra comparison for a match vector on an inverse pair. [7956 resp. 7955]

1.0 Final 24 (201708152319)

  • Fixed a problem, where exporting a project did not include spectra artifacts.

1.0 Final 23 (201707211722)

  • Zoomed region in spectrum chart now stays in the selected zoom state when selecting another chart to display (when clicking on another thumbnail)
  • When opening the spectrum chart with the label tool by clicking on a label named with the spectrum number, choosing another spectrum from the thumbnails and clicking on "Snap", the label will change its name to the number of the new spectrum it was moved to.

Note: version 1.0 Final 22 was not released.

1.0 Final 21 (201707191738)

  • Changed behaviour when zooming into spectrum charts (thumbnails now zoom in as well)

1.0 Final 20 (201707182227)

  • Initial public release

Note: The versions 1.0 Final 01 to 1.0 Final 20 have not been released.

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