2.0.0-alpha.6

Version 2.0.0-alpha.6 of the Unipept Desktop application introduces support for building custom protein reference databases from UniProtKB Reference Proteomes.

New features / enhancements:

• Build custom databases from UniProtKB Reference Proteomes (#234)
• Cache release notes in order to save API calls to GitHub API (#233)

2.0.0-alpha.5

The latest version of the Unipept Desktop application provides a fix for some more bugs and issues that were reported by our users.

New features / enhancements:

• Automatically configure memory limit for Docker database construction (#229).
• A new warning is shown when a database folder is trying to be used that does not exist (#225).

Bug fixes:

• Release notes were not rendered correctly on the start page of the application (#218).
• Progress was not correctly reset when rebuilding a database (#219).
• Restart button for database construction was sometimes wrongly disabled (#224).
• Analysing samples using a local database did not work on Linux due to host.docker.internal not being known (#231).

2.0.0-alpha.4

This release of the Unipept Desktop Application provides a fix for a list of bugs. None of these bugs are "crucial" (meaning that they don't cause issues with the analysis results or crashing the app), but were the cause of some annoying inconveniences. Note that this is still an early alpha-release of our application and that the analysis results should still be interpreted with caution.

Enhancements:

• The host is prevented from going to sleep during the construction of a database (#214).

Bug fixes:

• Assay names that were too long in the sidebar are now abbreviated with an ellipsis (#207).
• List of existing databases is now also available when no active Docker connection is available (#211).
• Copying an existing database did not work properly (#212).
• Old versions of the Unipept Docker images are now automatically removed (#213).
• Disk size and disk free space did not always work (especially not on macOS) (#216).
• Start time of analysis was incorrect during start-up phase of an analysis (#217).

2.0.0-alpha.3

This is a hotfix release that provides a solution for incorrect analysis results in specific situations. Upgrading to this version from older v2.0-versions of the Unipept Desktop Application is highly recommended.

Bugfixes:

• Cached network requests where not always correctly invalidated when the underlying custom database was switched (#205).
• Improve Unipept logo to better match native OS logos (#206).

2.0.0-alpha.2

This is a hotfix release that provides a solution for only one bug in particular. The location for temporary file storage (which is required during the construction of a custom database) was not correctly set causing the application to ignore this setting. This release provides a fix for this issue.

Bugfixes:

• Directory for temporary file storage was not correctly mounted in database Docker container (#204)

2.0.0-alpha.1

This release fixes some bugs that were present in the previous alpha-release of the Unipept Desktop application. The following issues have been taken care of:

Bug fixes:

• The default storage location for custom databases was not reset or incorrect in some situations (#200)
• Analyses crashed because the web container did not use the correct database port (#202)
• Clicking outside the "create assay" dialog made it impossible to reopen the dialog again (#199)

Known issues:
Since this is still an alpha release of the application, the following issues are still present in this version of the application and are known by our development team:

• Duplicating an assay does not work
• Cancelling the analysis of an assay does not work
• Start time of analysis is not always correct
• Errors that occur during the construction of a custom database are not always correctly reported
• The user interface of the application is not final yet and will be improved over the coming weeks / months

2.0.0-alpha.0

This is the very first alpha release of version 2.0 of the Unipept Desktop application! This is a very exciting release since it's the first one that allows our users (you!) to test completely new features that are the result of our hard work from the past two years 🎉

It is now possible to construct a custom protein reference database (based upon UniProtKB) to perform analyses with. This allows you to perform a metaproteomics analysis on a subset of all organisms that are found in UniProt, which can lead to a higher accuracy of the analysis results and better performance of the analysis. This is also a first major step in the right direction towards fully supporting proteogenomics analysis (combining the information of both a metagenomics and metaproteomics experiment in order to improve analysis results).

Existing installations of the Unipept Desktop application will not be upgraded automatically to this version (since it still is a alpha release). The stability of this release can not be guaranteed and upgrading is not recommended at this time if the application is being used in production environments.

This version of Unipept Desktop requires Docker Desktop to be installed if you want to build custom protein reference databases. Docker Desktop can be downloaded from this link if it's not yet installed on your system.

New features / enhancements:

• Support for constructing custom protein reference databases (#176)
• Peptides can now also be imported from files for manual assay creation (#176)
• Updated homepage and improved user experience (#176)
• Updated analysis page and improved user experience (#176)
• Updated Electron from v11 to v19 (#176)
• Redundant or useless settings have been removed from the settings page (#176)

Bug fixes:

• Native file picker was not always used on some Linux distros (#176)

Known issues:
Since this is still an alpha release, there are some things that are known not to work at this point in time. This is a non-exhaustive list of all issues that are currently known, but note that there are probably more (that are currently still unknown).

• Duplicating an assay does not work
• Cancelling the analysis of an assay does not work
• Start time of analysis is not always correct
• Errors that occur during the construction of a custom database are not always correctly reported
• The user interface of the application is not final yet and will be improved over the coming weeks / months

1.2.6

Release 1.2.6 of the Unipept Desktop app provides a fix for some minor issues that were reported by users.

Bug fixes:

• When creating a new assay, a press on the enter-key was required when trying to update an assay's name (#181)
• A study was not always removed from the project explorer view upon clicking "delete" (#182)

1.2.5

Release 1.2.5 of the Unipept Desktop application brings some very important refinements to the app. This release was mainly focused on improving the robustness of the analysis process. A new cache that sits between the application and our servers allows for some handy new features. If an analysis fails, you don't need to restart from nothing again next time, but the application will resume where it last stopped. Analyses are also resumed if you close the application during the analysis progress and reopen it again (this still works if you wait a few days before reopening the app).

New features / enhancements:

• Analyses are resumed when application is closed and reopend during analysis in progress (#174)
• The application now tries to recover an analysis session if the internet connection stops working for a short amount of time (#174)
• Improved the information provided about the export of peptides after an analysis (#165)
• Improved error handling for single peptide analysis (#170)

Bug fixes:

• Fixed color settings option not working in Sunburst (#169)
• Resetting Treeview or Treemap was not working (#166)

1.2.4

Release 1.2.4 of the Unipept Desktop application provides more fixes for bugs that have been reported by users. We would like to thank everyone that reported these to us (please do not hesitate to contact us at [email protected] in case you encounter a problem).

Bug fixes:

• Fixed a bug that made it impossible to rename studies in some situations (#163)
• Fixed a bug that caused the demo project to fail during opening (#164)