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TREND v0.1.0

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@SyntheticImmunity SyntheticImmunity released this 23 Apr 22:48
· 55 commits to main since this release
v0.1.0
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Changelog

v0.1.0 — 2026-04-23

Initial release. Three artifacts in one repository:

pipeline/ — trend-pipeline CLI

  • trend init — scaffold a project from ovarian_cancer or T_cell_activation templates
  • trend run — execute the 9-step pipeline locally or via Snakemake on SLURM (--profile slurm)
  • trend run --example {smoke,step9,pipeline} — three reviewer-facing reproducibility tiers
  • trend dashboard — launch the web UI pointed at any runs directory
  • trend status — one-screen run summary
  • trend preflight — environment check with per-OS install hints
  • Bundled Snakemake workflow with conda env definitions and SLURM profile
  • Bioconda recipe at pipeline/conda-recipe/meta.yaml ready for submission

dashboard/ — interactive web dashboard

  • Library composition view faithful to manuscript Figure 1 (panels A, B, C, D, E, F)
    • Library target composition pyramid (1,068 → 729 / 91 / 248 decomposition)
    • DBD family composition bar chart (49 Lambert families; 28 named bars + Other)
    • Sensors per DBD family bar chart
    • TREND coverage of CaCTS cancer master TFs across 34 TCGA tumor types
    • TREND coverage of D'Alessio cell identity TFs across 15 anatomical systems
    • Cancer-selectivity scatter for the OvCa project
  • Enhancer table with sortable columns, free-text search, Lambert taxonomy badges, and click-to-filter from any panel
  • Pipeline runner with 9-step state machine visualization
  • Three-tier reproducibility check with green/red oracle badges
  • Published-results browser with column-by-column tooltips
  • System status page with FR-2 environment preflight
  • Lovable-inspired warm cream / charcoal visual system (shadcn/ui + Tailwind)

tools/

  • build_fixtures.py — deterministic fixture generator for the three reviewer tiers (subsamples real OvCa data + simulates FASTQs with planted activity profiles)

Reproducibility tiers

  • Tier 1 — Quick check (1 s, no external tools): comparator validates against bundled published outputs
  • Tier 2 — Activity reproduction (~30 s, requires R + tidyverse + Rsamtools): unchanged Step 9 R script reproduces published activity from a 1,000-promoter slice of real OvCa data
  • Tier 3 — Full pipeline (~3 min, requires conda env): Steps 1-9 end-to-end on simulated FASTQs (50 promoters x 5 barcodes x 8 samples) with analytically-correct expected count matrix

Tests

  • 18 passing tests under tests/ (pytest tests/ -v)
    • 7 csv-comparator unit tests (the C2 equivalence predicate)
    • 2 oracle E2E tests (OvCa + T-cell)
    • 9 trend CLI tests

Documentation

  • README.md — short overview, install summary
  • MANUAL.md — comprehensive user + reviewer manual (install, three-tier verification, dashboard tour, adopter walkthrough, troubleshooting, glossary)
  • DASHBOARD_PRD.md — product requirements
  • DESIGN.md — visual system specification
  • references/TREND_library_TF_breakdown.md — TF composition reconciliation against Lambert / Reddy / D'Alessio

Data hosting

  • Code + bundled fixtures: GitHub
  • Full data (~3 GB: published alignment count tables + Lib4 reference + per-construct metadata): Dropbox, fetched by scripts/download_data.{sh,ps1}
  • Post-acceptance: planned migration of full data to Zenodo with citable DOI
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