Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased] - TBD

Known Issues

• RAST MS FBA not working
• PATRIC-only model submission
• Workspace write operations limited

Expected Behaviors

• Models/Media differ between RAST and PATRIC (intentional system design)

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[3.0.1] - 2026-05-12

Added

• Find-in-page style search replacing the legacy search bar across the application
• Multiple filter rows with AND/OR logic in the DataControlHeader toolbar
• Case-insensitive Solr matching via case-variant filter clauses
• Hover tooltips and popup dialog for pathway visualization in the reactions table
• Reaction comments API route with modal UI integration
• PlantSEED copy functionality with editing restrictions for reconstructed models
• Branch name and upstream repository link displayed on the /about/version screen
• Compound synonym formatting with chemistry-aware scripts and improved list layout
• Gene reactions rendered as linked chips on model detail pages
• Production-quality polish applied to 8 secondary pages

Changed

• Compound detail and reaction detail pages stabilized with improved metadata presentation
• Reaction structure cards fixed and compound detail refined

Fixed

• Compounds Solr quick search repaired (was using invalid ontology field)
• DataControlHeader hardened across all grid consumers to prevent filter state loss
• Dual-backend filtering in search hardened
• Grid state preserved when using onApplyFilterModel for server-side pagination
• Toolbar filter intent preserved correctly across community grid constraint changes
• FBA detail data now loaded by fba_id instead of incorrect reference
• Model detail pages now use canonical model ref for both FBA and gapfill data
• Gapfill page fixed to properly parse solution data and handle incorrect API refs
• Explicit unavailable-image placeholders added to prevent broken image UI
• Filtered row count now used in CustomPagination for accurate display
• JSON parse error handling in the comments route returns 400 on malformed input
• Boolean parsing in the comments route fixed with explicit typeof check
• React key uniqueness enforced in ChemicalEquation token rendering
• Next.js upgraded to patched 16.2.6 to resolve high-severity advisories

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[3.0.0] - 2026-04-06

Added

• Compound structure images on reaction pages with click-through to compound detail pages
• Comprehensive troubleshooting documentation and enhanced README with SSH tunnel setup instructions

Changed

• Version display updated to show v3.0.0 from environment

Fixed

• Invalid gapfill URL handling to gracefully return empty results instead of 404 errors
• Improved Reaction/Compound detail drawer with better typography and monospace formatting

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[3] - 2026-03-27

Fixed

• Plant build maintenance dialog display
• Model landing page biomass tab display
• User data navigation tab persistence

[0.1.3] - 2026-03-25

Added

• Build Model page description

Changed

• PlantSEED banner formatting and clarity
• Biomass tab with auto-discovery fallback

Fixed

• Genome ID prefixing in reconstruction jobs

[0.1.2] - 2026-03-25

Added

• PlantSEED v2/v3 maintenance banner

Changed

• Reaction/Compound detail drawer formatting

[0.1.1] - 2026-03-24

Changed

• PlantSEED banner and download options link alignment

Fixed

• Version page changelog loading from project root

[0.1.0] - 2026-03-24

Added

• Build Model pages with FASTA upload, PATRIC, and RAST options
• Model detail pages (Reactions, Compounds, Genes, Compartments, Biomass, Pathways)
• FBA and Gapfilling job submission
• Model download options (SBML, JSON, TSV)
• Biochemistry reference pages (Compounds, Reactions, Media)
• Authentication and authorization

Changed

• Migrated from Angular/Flask to Next.js 14 with Material-UI

Legacy Changelog

Below contains a summary of notable changes and deploy dates for each release from the legacy ModelSEED UI.

[2.6.1] - 2020-07-31

• Addition of status and notes columns, with tooltips, for greater transparency

[2.6.0] - 2020-06-10

• Rather significant release, making the entire reference data area as accessible as possible by not requiring a login

[2.5.1] - 2019-07-02

• Several bug fixes related to biochemistry visualization and search

[2.5.0] - 2019-06-06

• Major upgrade to biochemistry data and visualization

[2.4.0] - 2018-11-12

• Fixed visualization of gapfilling results, they now can be seen in the Model reactions table

[2.3.0] - 2018-09-23

• Fixed and restyled media choices when building a microbial model from file

[2.2.0] - 2018-08-15

• Revamped Biochemistry tables including aliases and synonyms to search
• Improved "Reconstruct Model" behaviour for plant models
• Stylistic modifications and visual/search bugfixes for FBA and Gene tables

[2.1.0] - 2018-01-02

• Minor stylistic modifications for major release
• Moved "Build Model" to main toolbar
• Improved media selection for Model Construction

[2.0.0] - 2017-11-03

• Major refactor of ModelSEED.org interface and functionality

[1.5.0-beta] - 2016-08-04

• Plants: tFBA, annotation, genome view, etc.

[1.3.3-beta] - 2016-07-15

• Enable plants portion of app (pending service updates).
• Enable plant upload (pending service updates).

[1.3.1-beta] - 2016-03-03

• Add permalink compound and reaction pages
• Add Fusions project
• Stylistic fixes

[1.3.0-beta] - 2016-02-02

• Beta (early preview) version announced via email

[1.2.1-alpha] - 2015-11-30

• Allow reconstruction from previously annotated genomes

[1.2.0-alpha] - 2015-10-26

• Start public portion of site (researchers, publications, etc)
• Force login

[1.1.4-alpha] - 2015-10-08

• URLs no longer require hashes

[1.1.3-alpha]

• Temp fix for queries with spaces against public genome table
• Change columns in public genome table

[1.1.2-alpha]

• Don't allow table for old model objects to avoid confusion in comparison of gapfilled data
• Fix |flux| button (default for heatmap)

[1.1.1-alpha]

• Update model list after reconstruct
• Add gapfill data to model

[1.1.0-alpha]

• Add media editor
• Add 'create new media' option
• Add delete, rename, 'can not overwrite' error message on media section
• Add ability to select custom media for reconstruct/fba/gapfilling
• Preserve last selected tab state on main pages
• Add gapfill page

[1.0.0-alpha] - 2015-09-01

• Add comparison tools
• Remove sidebar
• Add hover-over main toolbar dropdown menus
• Add "About ModelSEED" page