feat: techspec additions — de novo tier-6 branch, structure export, page capture + final synthesis

fix: NGS fallback to Python aligner when native tools missing; add missing re import in sequence_utils

chore: increase daily rate limits for testing (50 global, 20 NGS)

feat: add full 6-step NGS pipeline + fix sequencing WinError 193

feat(pipeline): multi-database UniProt identifier resolution

feat(primers): add NCBI gene search + sequence retrieval, oligo QC and in-silico PCR verification with recharts graphs

fix(pathways): read enrichment results from projection response, add p-value and gene ratio

fix(blast): honor program/db/max_hits params, accept DNA queries, poll cap 65 min

fix: PDB IDs like 1TIM rejected as NCBI accessions causing 400 error

fix: case-insensitive accession lookup - normalize to uppercase at entry points

fix: UniProt mapping resilience - skip gracefully instead of failing pipeline

fix: prevent GROQ restricted-key hang in interpret and audit steps

fix: rewrite map_refseq_to_uniprot to use two-step ID mapping API

fix: BLAST pipeline crash — accession misclassification + missing error handling

Phase 1: harden rate limits — JWT-aware keys, per-endpoint caps, daily limits on all job types

Phase 0c: offload large artifacts to Supabase Storage (docking, pipeline, sequencing)

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

Fix docking: add pdb_to_pdbqt_receptor() for protein PDBQT conversion

feat: 4-layer audit/observability system

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

feat: complete Phase 2 — API keys, share links, export, pipeline steps, guest upgrade

fix: add logging to init_redis() so Redis failures are visible in server logs

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

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

Security, crash fixes, demo prep, dead code removal

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

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

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

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

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)