Metaboverse-v0.11.4

• Add build workflows (#164)
• Flexible file reading in case of bytes characters in user's input (#159)
• Update toggle switches for clarity (#163)

Full Changelog: v0.11.3...v0.11.4

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NOTE

The auto-build of the macOS distributions failed. A manually compiled version has been replaced. Users should use the x64 version on arm64 systems for now, which should operate fine, just slower as it needs to translate the code between architectures.

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Metaboverse-v0.11.3

Addresses:

• Fixes issues accessing pre-built files on Sourceforge and changing to Reactome database file keys (issue #159)
• Removes unnecessary warning on app load/exit (issue #160)
• And other minor formatting and stability changes

Note:
I am having issues compiling x64 MacOS on an arm64 Mac, so for now I can only compile and deliver arm64 (M1/2/3) distributions. If anyone needs x64 (Intel Macbook chips), reach out and we can discuss further. I will keep looking for a viable workaround.

Full Changelog: v0.11.2...v0.11.3

Metaboverse-v0.11.2

What's Changed

• Entity mapping improvements so user can select between standard display names and user-provided names for metabolites (by @j-berg in #153)
• Fixes to error on window close (by @j-berg in c3f153a)

Full Changelog: v0.11.1...v0.11.2

Metaboverse-v0.11.1

• Fixes issues with HMDB ID mapping in back-end (#144, #146)
• Prints note about using HMDB IDs with MetaboAnalyst API (#144)
• Updates MetaboAnalyst API address for metabolite name conversion (#144)
• Reverts to using Reactome metabolite names for visualization (will give the option in the future - #151, but need to handle cases where HMDB IDs are used as these are not very useful for visualization)
• Updated documentation specifying that Ensembl transcript IDs or names should be used as Ensembl gene IDs do not work well. (#146)

What's Changed

• V0.11.1 by @j-berg in #152

Full Changelog: v0.11.0...v0.11.1

Metaboverse-v0.11.0

What's Changed

• Include scripts to automatically build release across platforms by @j-berg in #136
• FDR fix & electron compatibility bumps by @j-berg in #143
• Add more data checking for errors (see issues #128, #129, #130, #131)

We are trying to get a better sense of how we can best continue to develop Metaboverse for the community. If you are using Metaboverse, we would appreciate it if you took a few moments to fill out this survey: https://forms.gle/YdM1caZ7NhLAjxCGA. Thank you!

Full Changelog: v0.10.1...v0.11.0

Metaboverse-v0.10.1

• Updated license to MIT
• Fixed version check when launching GUI to make sure it sorts version numbers correctly
• Updated documentation (expanded walkthrough, added dev notes)
• Added more test datasets distributed with each release
• Added sample distribution display for Data Formatting tool
• Fixes issue where collapsed reactions in other timepoints were not being highlighted

Full Changelog: v0.10.0...v0.10.1

Metaboverse-v0.10.0

What's Changed

• Introduces Co-factor Selection, a drop-down menu available in Pattern Analysis. Selected a specific factor will limit the Pattern Analysis results to only the reactions containing the selected entity.
• Implements a Pattern Analysis Table Export utility, whereby the user can export the Reaction Patterns of a given type.
• Fixes an issue where some non-collapsed reactions were not showing up in Pattern results.

Full Changelog: v0.9.0...v0.10.0

Metaboverse-v0.9.0

Note: Files curated and analyzed using Metaboverse v0.9.0 will not be backward compatible with files generated using earlier versions of Metaboverse.

Major

• Integration of confidence values during data formatting, curation, and analysis.
• Fixed issues during curation arising from updates to the formatting of Reactome source files.

Minor

• Streamlined option buttons available during Pattern Analysis.
• Force directed networks now have sticky nodes once a user a dragged them to a new position.
• Added statistical thresholding visualization to Pattern Analysis module.
• Output session file with each successful build - will have experiment name appended to file.
• Sort Average reaction pattern by best statistic on each side of reaction
• Fix reaction filtering to more strictly and flexibly remove transport reactions from reaction pattern categories, and to only display transport reactions in the TransReg reaction pattern category.
• Node labels will default to the user-provided names if not the same as the curated default name.

Full Changelog: v0.8.0...v0.9.0 , Metaboverse/metaboverse-cli@v0.7.1...v0.9.0

Metaboverse-v0.8.0

UPDATE (07 Feb 22): Previous issues with Reactome network building have been fixed for the upcoming release of Metaboverse! The Reactome annotation has changed, thus older versions of Metaboverse will no longer be able to create a fresh organism reaction network. However, by default, Metaboverse will always rely on a pre-existing, stable curation unless otherwise specified - this is so that if a change in the Reactome codebase does occur, it should not affect current or previous versions of Metaboverse as long as an already-curated network file is used.

Major

• Added data formatting aid page (see issue #86).
• Added ability to cross-reference metabolite names with MetaboAnalyst and find more compatible names (see issue #74).

Minor

• Fixed issue where Metaboverse would not populate selected organism from drop-down if previously selected and the user returns to the page (see commit).
• Fixed issue where Metaboverse would not show the Continue button on the Curation page if necessary inputs were previously selected and the user returns to the page (see commit).

Note:

This version of Metaboverse only makes changes to the user interface and its backend. Thus, Metaboverse v0.8.0 continues to use metaboverse-cli 0.7.1.

Metaboverse-v0.7.1

Important Notes

• After curating your data on the metabolic model, you may receive an alert saying it cannot load the file, but the progress bar will show 100%. If you close the alert box and you see the button for the different analytical modules appear, you can ignore this warning. I am still working on diagnosing why this occasionally occurs and will hopefully have a solution soon.
• Many of the changes introduced in v0.7.0 to session and intermediate file metadata will likely be incompatible with previous versions of Metaboverse.

Minor

• Fix Session Data page to format variables, file paths better (see commit)
• More flexible blocklist to capture all components with the same name, even if they have different species IDs (see commit1 ; commit2)
• Find largest change possible for modifier regulation patterns (see commit)
• Sort by best p-value (previously had taken a more conservative approach by using the worst p-value on each side of the reaction) (see commit)
• Add button and capabilities to switch between inferred complex values or to compare each complex component individually within the reaction pattern (see commit1 ; commit2)
  • Will still display the complex as inferred value, but evaluated as each individual component during reaction pattern search
• Protein complex inference/aggregation
  • mean -> median for generating aggregate magnitude value for protein complex from component parts (see commit)
  • Aggregate statistic calculated using e * gmean(p-array) (see commit)
  • Max aggregate p-value set to 1 (see commit)
• Allow exporting line plots for time-course and multi-condition datasets (see issue #89)
• Use user-provided names in labeling (see issue #87)
• Toggle analyte labels on by default (see commit)
• Allow flexibility for input data where commas are used in place of decimals (see issue #92)
• Remove duplicate rows from input data (interactive input will warn about these) (see commit)
• Fix Sustained reaction pattern to not identify is input and output value being compared are identical (see commit)
• Fix issue with parseComponents() function where usage of modifiers in pattern determination was pushing all modifiers (catalysts and inhibitors) to reactants list (see commit)
• For upregulated sustained reactions, get max of inputs and outputs (previously was getting min) (see commit)
• Fixed global motif searching for pathway and perturbation visualization to search non-collapsed reaction dictionary too. (see commit)
• Added reaction pattern tooltips on button to show a graphical example of each (see commit)
• Move some shared utilities to the motif-utils.js file (see commit)