Recent Releases of unipept-desktop
unipept-desktop - 2.0.2
Release v2.0.2 of the Unipept Desktop application provides support for using the new suffix array based backend of Unipept (see this post for more information on what changed internally).
This means that missed cleavage handling is always enabled (cannot be disabled anymore) and is much faster than before. Please note that the Windows version of Unipept will not automatically update to this release. It is recommended to download the installer here and install the newest version manually on Windows.
- Pep8
Published by pverscha over 1 year ago
unipept-desktop - 2.0.1
Release v2.0.1 of the Unipept Desktop application improves robustness by checking if a new release for the static database actually exists before trying to download one. This should overcome issues that arose prior to this release due to a failed server-side update.
Bug fixes: * Fixed an issue where a non-existent static database was trying to be downloaded (#269, #270)
- Pep8
Published by pverscha about 2 years ago
unipept-desktop - 2.0.0
This release is a major milestone for the Unipept Desktop application. Version 2.0 of the application now provides support for the construction of targeted protein reference databases. This means that from now on, databases can be build that only contain proteins that are associated with a predefined list of taxon, supporting the analysis of proteogenomics datasets.
All documentation and info about this new release can be found on our website: https://unipept.ugent.be/desktop.
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.
- Pep8
Published by pverscha about 3 years ago
unipept-desktop - 2.0.0-beta.0
This is the first beta release of Unipept Desktop v2.0.0. Not much will change now between this beta version and the stable release of Unipept Desktop v2.0.0, which is expected to launch very soon.
Bug fixes: * Update title of the application from "unipept-desktop" to "Unipept Desktop"
- Pep8
Published by pverscha about 3 years ago
unipept-desktop - 2.0.0-alpha.12
This release provides a fix for issues that could occur while exporting Unipept results and bumps the Electron version that's being used to Electron v21 (previous version was Electron v19).
New features / enhancements: * Bumped Electron to v21 (#262)
Bug fixes: * Fixed an issue where exported files contained too many columns (#263)
- Pep8
Published by pverscha about 3 years ago
unipept-desktop - 2.0.0-alpha.11
This release provides a hotfix for an issue where SVG downloads of the Unipept visualizations where corrupted. Upgrading to this version is recommended.
Bug fixes: * Fixed an issue where SVG's got corrupted during download (#260)
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 2.0.0-alpha.10
This releases of the Unipept Desktop app introduces a new function that allows users to add custom Unipept endpoints. These endpoints include (un)official mirrors of the online Unipept service that are set up by us or third parties.
New features / enhancements: * Add custom endpoint services that can be used for the analysis of a sample (#259).
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 2.0.0-alpha.9
This release provides a hotfix for an issue that was supposedly fixed in the previous version of the Unipept Desktop app, but that did pop up again on some machines. Upgrading to this newest version is recommended.
Bug fixes: * Improved fix for an issue where exporting functional annotations summaries was not possible (#255, #257)
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 2.0.0-alpha.8
Release v2.0.0-alpha.8 of the Unipept Desktop application provides a solution for a few bug fixes.
Bug fixes: * Fixed an issue where saving the functional annotations summary as a file was not possible (#255). * Fixed an issue where saving the SVG-version of a heatmap resulted in the application doing nothing (#255). * Fixed an issue where too many proteomes are marked as redundant by the app (#256).
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 2.0.0-alpha.7
Release v2.0.0-alpha.7 of the Unipept Desktop application provides a long list of fixes for small bugs and issues that were discovered while working with the application.
New features / enhancements: * A warning is now shown when the user tries to add and process a reference proteome that's marked as redundant (#242).
Bug fixes: * Pressing enter in the "add reference proteome" textfield now also adds the proteome to the selection (#239). * Set a max width on the "sources" column in the custom database overview table (#238). * The message "something changed about this assay" was shown much too frequent (#240). * If too many taxa were selected for filtering, the list with all selected taxa overflowed (#244). * Duplicating assays works again now (#246). * No margin was present between the icon and text for the "add assay placeholder" in the ProjectExplorer (#248). * Fixed an error that was thrown when no assays were selected (#249). * Experiment summary dialog that shows the list of all unmatched peptides is no longer broken (#251).
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 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)
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 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).
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 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).
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 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).
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 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)
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 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
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 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
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 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)
- Pep8
Published by pverscha over 3 years ago
unipept-desktop - 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)
- Pep8
Published by pverscha almost 4 years ago
unipept-desktop - 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 unipept@ugent.be 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)
- Pep8
Published by pverscha almost 4 years ago
unipept-desktop - 1.2.3
This release provides a fix for some issues that were reported since the previous version of the Unipept Desktop app.
Bug fixes: * Fixed a bug that made it impossible to export results from an analysis (#159) * Fixed a bug where linking to a single peptide from the peptide summary table did not work (#160)
- Pep8
Published by pverscha almost 4 years ago
unipept-desktop - 1.2.2
This release is mostly a maintenance release of the Unipept Desktop application.
New features / enhancements: * Completely redesigned the sample progress viewer. It is now much clearer what the application is exactly doing during the analysis of a sample. * We redesigned the assay creation wizard, already preparing it for new functionality that's coming in future versions of Unipept.
Bug fixes: * Fixed a bug that caused the analysis results to be recovered incorrectly in specific cases. * Improved overall stability of the application.
- Pep8
Published by pverscha almost 4 years ago
unipept-desktop - 1.2.1
This is a maintenance release of the Unipept Desktop application.
Bug fixes: * Fixed a bug that caused the application to crash when trying to save a large project.
- Pep8
Published by pverscha over 4 years ago
unipept-desktop - 1.2.0
This release provides support for the new NCBI "strain" rank that's been added to the UniProt database some time ago. A new release of the Unipept database will soon follow, which will then also provide access to a lot of new taxa that are annotated with the "strain" rank.
New features / enhancements: * Official support for the new NCBI strain rank. The ranks "parvorder" and "infraclass" are no longer shown since only very few taxa exist that are annotated with these ranks (< 10) (#136).
Bug fixes: * Fixed bug that caused the demo project to fail on Linux-based operating systems (#135).
- Pep8
Published by pverscha almost 5 years ago
unipept-desktop - 1.1.2
Version 1.1.2 of the Unipept Desktop app improves upon some issues that were recently reported. Upgrading to this version is highly recommended.
Bug fixes: * A check that detects if a name has been specified when manually creating an assay has been added (#129) * A check that detects if the user tries to process binary files has been added (#128) * Electron has been updated to v11.1.0 (#132) * Marked has been updated to v2.0.3 (#131)
- Pep8
Published by pverscha almost 5 years ago
unipept-desktop - 1.1.1
Version 1.1.1 of the Unipept Desktop application is a hotfix release, fixing the "save image" button for all visualizations that broke in the previous version.
Bug fixes: * Fix "save image" button for all visualizations (#127).
- Pep8
Published by pverscha almost 5 years ago
unipept-desktop - 1.1.0
Version 1.1.0 of the Unipept Desktop application focuses on improving the performance of the visualizations. Warnings for datasets that are too large and might produce visualizations that take too long to render are removed (since the speed of rendering the visualization has increased enough that this no longer proves to be an issue).
New features / enhancements: * Drastically improved rendering performance of Sunburst (#126) * Dendrogram that displays clustering order for the heatmaps has been added (#126)
- Pep8
Published by pverscha almost 5 years ago
unipept-desktop - 1.0.0
This is the long awaited 1.0.0 release of Unipept Desktop! 🎉 This release provides some new features as well as some bug fixes. This release mainly focuses on improvements of the user experience. Our application new supports bulk import of multiple assays and a fullscreen mode for all visualizations. See the list below for the complete changelog.
🎉 Thank you all for the interest in this application! We have some more things to come in the (near) future, and we will keep you posted!
New features / enhancements: * Bulk import assays from files. Select multiple files when trying to import assays. The import dialog has been redesigned to conveniently configure the newly created assays and easily import them. (#117) * Fullscreen mode for the heatmap visualization has been added. (#120) * Add automatic crash reporting. If (part of) the application crashes, a detailed crash report will automatically be uploaded. This allows us to respond to problems as soon as possible and get a more detailed crash report, without manual intervention. (#122)
Bug fixes: * Fixed fullscreen mode for all other visualizations. (#120) * Fixed padding around the TreeView visualization in the functional annotations table. (#120) * Fixed wrong layout of cancelled assay in project explorer. (#118)
- Pep8
Published by pverscha about 5 years ago
unipept-desktop - 0.7.1
Version 0.7.1 of the Unipept Desktop application fixes an issue that could lead to inconsistent storage of analysis results. Upgrading as soon as possible to this version is highly recommended.
Bug fixes: * Fixed an issue where wrong search configuration settings could have been associated with previously stored analysis results. The issue only occurs if the analysis process of an assay is unexpectedly interrupted (e.g. force quit of the application, crash or similar). (#115)
- Pep8
Published by pverscha about 5 years ago
unipept-desktop - 0.7.0
Version 0.7.0 of the Unipept Desktop application mainly improves upon the rendering and export functionality of the visualizations. The heatmap is completely redesigned and now allows to be dragged and zoomed. It's also possible to render much larger heatmaps than before thanks to a lot of performance optimizations under the hood. This release is mainly a feature release.
New features / enhancements: * Export heatmap to SVG and PNG (UWC#159) * Completely redesigned the "export visualization" modal (UWC#159) * Resolution of PNG export for visualizations can now be configured (scaling factors between 50% and 1000%) (UWC#159) * Inter-assay comparative heatmap can now be transposed (UWC#157) * Implemented zoom and drag functionality for heatmap (UWC#155)
- Pep8
Published by pverscha about 5 years ago
unipept-desktop - 0.6.4
Version 0.6.4 of the Unipept Desktop application fixes a few minor bugs. No major changes or new features are introduced with this update.
Changes: * Add cancel button to "create assay" dialog (#102)
Bug fixes: * Fix crash when external network requests are blocked (#108) * Fix peptide list is not reset when creating multiple assays, one after another (#104)
- Pep8
Published by pverscha about 5 years ago
unipept-desktop - 0.6.3
This release is mainly a maintenance release, fixing quite a lot of different bugs and improving performance of the application. A few improvements to the UI and functionality of the app were made.
Version 0.6.3 of the application also includes a new "What's new" popup, that can be used to see the changelog of the currently installed version. If a new update is available, the application will notify the user about this and displays a list of all changes between the current version and the most recent version.
New features / enhancements: * "What's new" button that shows the changelog of the currently installed version of the application (#89) * A warning will be shown on the homepage when an update for the application is available (#91) * Assays and studies can now also be created when performing a comparative analysis (#95) * Snake can now also be started from the comparative analysis page (#95) * More uniform error messages for the comparative analysis and single assay analysis (#95) * Checkboxes for adding assays to the comparison moved to the left of the assay's name in the project explorer (#95)
Bug fixes: * Also show "new folder" button in the "open file dialog" on macOS 11 and above (#90) * Remember previously used directory when creating a new assay on Linux (#92) * Improve performance when resizing the project explorer (no more laggy resize) (#93) * Fix positioning of "create study" button when project is empty (#94) * Assays that were added to the comparison from a previous project were still visible when loading a new project (#96) * Currently active assay was not reset when switching to a new project (#97) * Exit application button that was shown when an updated is completed did not do anything (#88)
- Pep8
Published by pverscha about 5 years ago
unipept-desktop - 0.6.2
This release contains a few very important bug fixes. Upgrading to version 0.6.2 is highly recommended.
Bug fixes: * Fixed a critical bug that broke the demo project * Fixed a critical bug that could make it impossible to start a new project in specific situations
- Pep8
Published by pverscha over 5 years ago
unipept-desktop - 0.6.1
This release improves the security of Unipept Desktop by signing both the application and installer on Windows (this was already the case on macOS). Our code signing certificate was issued by SSL.com. Note that Windows will still show a warning when starting the application, since we have not yet built up enough trust on the platform. The more users start to use this application, the faster Windows will start to trust our certificate.
Improvements: * Also sign application and installer on Windows, using a valid code signing certificate
- Pep8
Published by pverscha over 5 years ago
unipept-desktop - 0.1.2
Another test for Unipept Desktop auto-updating
- Pep8
Published by pverscha almost 6 years ago
unipept-desktop - 0.1.1
Test release for the Unipept Desktop auto-updater.
- Pep8
Published by pverscha almost 6 years ago