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bio-nexus-api / bioai-platform /frontend

Commit History

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

    Samad14
    fb8c550

  1. fix: replace dead embed.rcsb.org iframe with PDBe Mol* viewer

    Samad14
    7d2b5e1

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

    Samad14
    305458b

  3. refactor: enhance dashboard with quick tools, jobs with filter tabs, settings with profile identity

    Samad14
    32dd681

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

    Samad14
    fe5ce87

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

    Samad14
    07e58f6

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

    Samad14
    9e11dca

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

    Samad14
    990c867

  2. chore: move @types /three from dependencies to devDependencies

    Samad14
    36b2c3d

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

    Samad14
    312665c

  4. fix: use embed.rcsb.org instead of www.rcsb.org for clean 3D viewer iframe

    Samad14
    567f164

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

    Samad14
    342fa92

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

    Samad14
    c1c07f1

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

    Samad14
    3030b52

  2. fix: forward backend error detail in 4 components⁠

    Samad14
    5b7a343

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

    Samad14
    9fc8479

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

    Samad14
    bac1801

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

    Samad14
    59495c0

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

    Samad14
    8ce1e37

  3. Security, crash fixes, demo prep, dead code removal⁠

    Samad14
    9a28cd0

  1. Fix structure viewer iframe: embed.rcsb.org is dead → use www.rcsb.org/3d-view/{pdbId}

    Samad14
    62d0f3d

  2. Fix: alignment sample sequences, reverse complement tool, BLAST program filtering, sample buttons on structure/pathway pages

    Samad14
    aa498ec

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

    Samad14
    13df1a1

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

    Samad14
    2a12412

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

    Samad14
    90b88af

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

    Samad14
    f0b48d6

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

    Samad14
    f8dfa58

  8. fix: remove Lenis SmoothScrollProvider - blocks native scroll in dashboard layout

    Samad14
    7bd015b

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

    Samad14
    b008d9f

  10. fix: rename lucide-react icons (LoaderCircle, CircleCheck), remove unused imports, replace Set.isSubsetOf

    Samad14
    5242ec8

  11. fix: dark input/textarea/select backgrounds and focus border override

    Samad14
    2fe4d4c

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

    Samad14
    2f67ecf

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

    Samad14
    627ac39

  14. dark mode: add missing CSS overrides (gradients, forms, badges, hover, bg-opacity, teal variants) + ThemeToggle on landing, auth, callback, shared pages

    Samad14
    076e8f2

  15. settings: mark notifications & danger zone as coming-soon, clean up unused state/imports

    Samad14
    28efc96

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

    Samad14
    973dd4c

  1. 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

    Samad14
    f42f5a6

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

    Samad14
    6c461b6

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

    Samad14
    3154548

  4. fix: use Array.from instead of Set spread for TS compatibility

    Samad14
    3bc04b9

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

    Samad14
    57fa457

  1. Simplify vercel.json — remove @-ref env vars (set via dashboard instead)

    Samad14
    8d8e1c0

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

    Samad14
    76fb273

  2. Re-enable OAuth: restore auth pages, Providers wrapper, dashboard auth guard, landing page CTA

    Samad14
    dc1f75e

  1. AlphaFold 3D viewer via 3Dmol.js — pLDDT confidence coloring, style selector, spin toggle⁠

    Samad14
    ffe46cc

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

    Samad14
    88aa370

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

    Samad14
    5a0e691