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

Fix KEGG search: use find/hsa with symbol matching + parse get/PATHWAY section

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

Security, crash fixes, demo prep, dead code removal

Fix Reactome pathway search: correct param name and response parsing

Add Render Blueprint, GitHub Actions auto-deploy, revert to CORS fix, local startup scripts

Fix structure viewer: correct PDB API URL (+/entry/), fix RCSB UniProt search attribute + payload format

Fix MSA: use correct EBI result type 'fa' instead of 'aln-fasta' — confirmed via live API test

Fix MSA: dynamically discover EBI result types instead of hardcoding 'aln-fasta'

Fix MSA alignment: add Accept headers, result retry with delay, better error detail

Fix Phase 1 endpoints: resolve UniProt→PDB in structure viewer, use proper Reactome search, surface real backend errors in frontend

Sprint 3-7: Alignment, Structure Viewer, Pathway Analysis, Utility Tools, analyze page fully live

Sprint 1-2: JWT auth middleware + UniProt dedicated page

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

design.md + rules.md compliance: dark theme, teal palette, pulsing dot, Pydantic models, api.ts routing, config fixes, db/max_hits threading, Supabase migration 004

Fix PostgREST in() filter: quote status values in startup hook

Add RefSeq->UniProt mapping step in pipeline + demo uniprot_accession

Add startup resume hook for stuck jobs + persist NCBI RID

fix: extract user UUID from JWT for rate limiter, skip anon

fix: logger.exception instead of stderr, fail job on thread crash

fix: move first _set_step into try block + stderr fallback in run_pipeline_sync

fix: Analyze button on retrieve page + sessionStorage handoff to blast wizard

fix: UniProt API sequence key is value not sequence -- confirmed via API response

fix: UniprotTool missing sequence field — empty sequence in fetchSequence for UniProt accessions

fix: E-value underflow, AlphaFold step, steps_completed append, UniProt always runs

fix: remove current_step_label and error_message refs — columns missing from jobs table

debug: expose real error in 500 response

fix: FASTA header text bleeding into sequence validation, add IUPAC codes U O B Z X J

Deploy prep: Render config + Dockerfile, refactored backend auth flow, dashboard, landing page, error states, guest flow

Core pipeline testability: progress callback, rate limiter 429, history table

Initial commit: Bio Nexus pipeline engine — BLAST + UniProt + AlphaFold + AI interpretation (Phase 1)