wetSpring — Life Science & Analytical Chemistry
16S metagenomics, LC-MS, PFAS screening — 5,707+ checks across 376 experiments, 63/63 papers reproduced in sovereign Rust
Domain
16S metagenomics, LC-MS feature extraction, PFAS screening, microbial ecology.
Repository: syntheticChemistry/wetSpring
The Science Story
wetSpring proves barraCuda can replace the Galaxy/QIIME2/Python bioinformatics stack with sovereign Rust. The complete 16S pipeline — FASTQ → quality → merge → dereplicate → DADA2 → chimera → taxonomy → diversity → UniFrac — runs in Rust with 1 runtime dependency (flate2 for gzip). The sovereign XML parser eliminates quick-xml; the sovereign FASTQ parser eliminates needletail.
63/63 papers reproduced across 4 research tracks: Waters c-di-GMP/QS, Liu comparative genomics, deep-sea metagenomics, Jones PFAS. 50/50 three-tier eligible papers have full CPU + GPU + metalForge validation.
Headline Results
- 5,707+ checks across 376 experiments — all passing
- 1,077× GPU speedup for spectral cosine matching
- 30 sovereign bio modules, 1 runtime dependency
- Public benchmark against 4 BioProjects (22 samples) — all match paper ground truth
Validation Phases
| Phase | Key Result |
|---|---|
| 1-2 (Galaxy→Rust) | 30 sovereign bio modules, 135/135 checks |
| 3-7 (GPU pipeline) | Complete 16S on GPU. 1,077× spectral cosine speedup |
| V53+ (Anderson QS) | 52/52 papers, Anderson localization applied to biology |
| V86 (Cross-spring) | 23/23 across 5 springs. -4,753 net lines (deep debt elimination) |
Researchers Reproduced
| Researcher | Department | Domain |
|---|---|---|
| Christopher Waters | MMG, MSU | Quorum sensing, c-di-GMP |
| Kevin Liu | CMSE, MSU | Comparative genomics, phylogenetics |
| Jesse Cahill & Chuck Smallwood | Bioscience, Sandia | Biosurveillance |
| A. Daniel Jones | BMB/Chemistry, MSU | Mass spectrometry, PFAS |
| Rika Anderson | Biology, Carleton | Vent metagenomics, pangenomics |
What the Constraint Revealed
Zero local WGSL — every GPU operation delegates to barraCuda via ToadStool. wetSpring consumes 79 barraCuda primitives without duplicating any math. The three-tier validation pattern (CPU → GPU → metalForge) was pioneered here and adopted across all springs.
wetSpring found and fixed the log_f64 bug in ToadStool (coefficients halved, causing 1e-3 instead of 1e-15 precision) during Shannon entropy validation — the spring improved the infrastructure it depends on. Also resolved 4 barraCuda gaps: ODE solver, Gillespie stochastic sim, HMM Viterbi, Smith-Waterman alignment.
Cross-Spring Connections
- → ToadStool: log_f64 bug found and fixed; 79 primitives consumed; three-tier validated
- → airSpring: kriging spatial interpolation; dynamic Anderson W(t) models soil moisture coupling
- → hotSpring: Anderson localization applied to biology — shared spectral primitives
- → neuralSpring: ESN/LSTM anomaly detection for sentinel microbes; NPU int8 quantization validated
- → healthSpring: diversity indices, Anderson lattice → gut colonization resistance, 16S pipeline
- → groundSpring: sequencing noise calibrates rarefaction; 86 named tolerances with provenance
Public Notebooks
Interactive Jupyter notebooks that visualize wetSpring’s frozen experiment data:
- 01 — 16S Pipeline Validation: Galaxy bootstrap, Track 2 LC-MS, R/vegan diversity parity, NCBI real data
- 02 — Python vs Rust vs GPU: Benchmark timings, speedup charts, energy consumption
- 03 — Paper Reproductions: 63/63 papers across 5 researchers and 6 tracks
- 04 — Cross-Spring Connections: 79 barraCuda primitives, constraint-driven discoveries
- 05 — Soil Anderson Deep Dive: Track 4 domain exemplar, QS-pore geometry, chemotaxis
Clone the repository, cd notebooks/, jupyter lab. Or access via JupyterHub.
baseCamp Papers
Papers 01, 03, 04, 05, 06 — see baseCamp Science for full list.