fix: add optional score property to Domain type for TSV export

feat: expanded Domain & Motif Analysis with all features and cross-project links

fix: UniProt link shows invalid URL when accession is NCBI

feat: show PDB structures, GO terms, and expanded features in UniProt panel

fix: Ramachandran tab hidden for proteins without PDB IDs + AI interpretation error

fix: StructureComparison re-fetches on every render due to audit dep

fix: add 'running' to isActive and STATUS_ORDER to prevent false 'no results' flash; show bit_score in ScoreBars

Phase 0a: SSRF protection + auth on docking/sequencing, worker design doc

Fix color scheme switching, vina log parsing, icon dedup, dead code

Redesign Vina log panel + fix z-index overlay in docking viewer

DockingViewer: use correct pdbe-molstar viewerInstance API for representation switching

DockingViewer: full toolbar with representation/color switching, screenshot, camera controls

Fix Molstar drag: remove overflow-hidden, use direct container without absolute positioning

Fix loading overlay: detect Molstar via canvas element, add event listener, remove blocking z-index

Fix Molstar viewer: prevent double-init, fix container sizing, separate interaction updates

Fix DockingViewer: use pdbe-molstar web component instead of broken JS API

Docking viewer upgrade: Molstar GPU rendering, proper interaction geometry, 3D dashed-line rendering

fix: add missing /api prefix to audit fetch URLs so rewrite proxy reaches backend router at /api/audit/event

feat: add interaction fingerprinting and 3Dmol.js viewer to molecular docking page

feat: add query coverage, organism, and query accession to BLAST results

fix: stabilize useAuditTrail return reference with useMemo, remove setLoading(true) from effect re-fetches

fix: remove opacity:0 flicker from all pages

feat: add DNA sequence output across BLAST, UniProt, sequencing, primers, and SequenceRetrieval

feat: implement 8 tool bridges (F1-F8) + audit child components

fix: prevent page scroll when zooming phylo tree (non-passive wheel listener)

feat: interactive phylo tree — pan/zoom, hover highlight, collapse/expand, node selection

feat: improve phylo tree viz — branch length labels, bigger nodes, hub labels, tooltips, ML recommendation

feat: 4-layer audit/observability system

fix: replace iframe structure viewer with PDBe Molstar web component

feat: molecular docking (AutoDock Vina) + docs site + Sentry + cache stats + Phase 2 docs update

fix: default import PhyloTreeViewer in alignment, report, and PipelineResults

feat: dedicated phylo router (NJ/UPGMA/ML), local PhyML binary, standalone phylo page, PhyloTreeViewer redesign

fix: accurate phylogenetic tree visualization — proportional branch lengths, scale bar, bootstrap labels, circular layout mode

feat: in-memory pipeline v2 with MSA, phylo tree, domains; PipelineResults component; standalone phylo page; report page; wizard step checkboxes

fix: convert AlignmentView.tsx light-theme classes to dark void theme tokens

feat: add PNG/TSV/JSON/CSV/FASTA export to all 8 tool components

fix: use STRING-DB image API for accurate PPI diagram, add PNG/TSV/copy export buttons

fix: primer error handling, interactions scores, structure comparison API

fix: forward backend error detail in 4 components

fix: handle non-200 responses in domains, interactions, ramachandran, SS components

feat: domains, interactions, primers, structure analysis, wizard, phylo tree, conservation

Fix invisible fonts in Reactome DiagramJs: isolate widget from dark-theme CSS overrides

Add Reactome diagrams, KEGG search, pathway enrichment (pipeline + standalone)

Security, crash fixes, demo prep, dead code removal

Polish: restyle blast/dashboard/jobs/history/results pages to dark theme, fix Loader2 icons, update result components

Guest upgrade, DB migration, settings functional, full Phase 1 feature set

fix: animate='visible' -> animate='show' to match fadeUp variant

full dark migration: CSS overrides for all legacy classes, framer-motion animations across every page/component, rebrand to Bio Nexus

redesign: BioFlow AI void-dark theme — new landing page, dashboard, Three.js DNA helix, Lenis smooth scroll

named exports, any->unknown, theme toggle (light/dark), dark mode fixes, error extractor, deleted pipline/ typo dir