ELEMENT v2.0.0 — Professional Phase-Based Structure

ELEMENT v2.0.0

Repository restructure

• matlab/ reorganized into 8 phase subdirectories: getting/, discovery/, mecate/, core/, expression/, scoring/, reporting/, orchestration/
• 44 functions renamed with descriptive, phase-prefixed names
• matlab/compat/ with 37 backward-compatibility shims — existing workflows run unchanged
• inputs/ reorganized: example data → inputs/example/, reference DBs → inputs/db/
• element_config.json rewritten as organism-agnostic v2.0.0 template
• Workflow-specific scripts archived under matlab/_archive/

Bug fix

• export_route_tsv: equation column now correctly exported (required by Phase 2 ODE)

Validation

• WF39 regression test: score_physio = 0.9347 ✅ (identical to v1.0.0)
• C2=0.872 | C4=0.976 | C5=0.993 | φ=100%

How to run

run('run_element.m')

BREAKING CHANGE: matlab/ flat layout removed. Use compat/ shims or update to new phase-prefixed names.

ELEMENT v1.0.0 — Official Release

ELEMENT v1.0.0

Organism-agnostic MATLAB platform for mechanistic metabolic route discovery.

Highlights

• Sparse MILP route discovery with stoichiometric balance guarantee (S·v=0)
• Elementary enzymatic kinetics ODE (3-step, no QSSA, Ullah 2006 framework)
• Population-level bridge fitting: D(t) = y_max·(1-exp(-H_pop(t)))
• Multi-omics coupling: RNA-seq + iBAQ proteomics + RT-qPCR
• Composite scoring C1-C10 + C_dyn
• Fully JSON-driven, organism-agnostic

Validated example

Shewanella xiamenensis LC6 — Methyl Orange decolorization:

• Score: 0.7199 ✅ [PASS ≥ 0.65]
• Bridge R² = 0.868, C_dyn = 0.814, φ = 99.7%

How to run

run('run_element.m')

See README and INSTALL for full instructions.