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

feat: structure preparation pipeline — broken chains → SWISS-MODEL repair → PyMOL cleanup → fpocket + CASTp

feat: add CASTp pockets, SWISS-MODEL, ESMFold + fix Dockerfiles

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

feat(seq-tools): add sequence utilities, motif scanner and dot plot tools with frontend pages

feat(md): verified force field/solvent menu (ff14SB/ff15ipq/ff19SB/amberfb15/CHARMM36 x OBC1/OBC2/GBN2) with alanine-dipeptide createSystem startup probe; explicit errors for invalid combos; dynamic frontend menu

fix(md): reflect OXT across C-CA axis so GBSA stops NaNing on Linux CPU

debug: add OpenMM verification steps + startup check so we can see what fails

fix: always start in-process worker, remove ENABLE_INPROCESS_WORKER gate

Phase 3a/4/5: ADMET descriptors (RDKit), MD simulation (OpenMM), function prediction (DeepFRI-inspired) — backend + frontend

Phase 2: structured JSON logging, request ID middleware, enhanced health endpoint, Sentry breadcrumbs

Phase 0b: durable worker with FOR UPDATE SKIP LOCKED, per-type concurrency, separate container

Docking: minimal INSERT (only id/status/smiles), startup table check, migration SQL

fix: encode grace_cutoff with strftime to avoid + in URL query param

fix: migrate docking/sequencing job store from file-backed dict to Supabase

feat: 4-layer audit/observability system

fix: resolve 10 bugs in sequencing/docking pipelines

Phase 3: Sequencing pipeline (FASTQ -> QC -> alignment -> variant calling -> report)

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

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

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

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

Security, crash fixes, demo prep, dead code removal

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 startup resume hook for stuck jobs + persist NCBI RID

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

debug: expose real error in 500 response

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

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