eed063f16c
- Remove solve.js (código morto que referenciava globais inexistentes) - Remove console.log de PSO.run() e comentários de debug - Exporta parameterCatalog, modelParameters e getParamDisplayInfo de search.js - index.html passa a importar esses símbolos em vez de redefiní-los Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
85 lines
4.1 KiB
Markdown
85 lines
4.1 KiB
Markdown
# CLAUDE.md
|
||
|
||
This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
|
||
|
||
## What is BioLab
|
||
|
||
BioLab Parameter Explorer is a scientific web application that estimates kinetic parameters for microbial growth and substrate consumption models. Given time-series measurements of biomass (cells, g/L) and residual substrate (g/L), it runs Particle Swarm Optimization (PSO) over seven built-in kinetic models and ranks them by the Akaike Information Criterion (AIC).
|
||
|
||
The app is packaged with Apache Cordova and targets Electron (desktop), Android, and Browser.
|
||
|
||
## Commands
|
||
|
||
### Tests (run from `www/`)
|
||
|
||
```sh
|
||
cd www && node tests/demo.mjs
|
||
cd www && node tests/synthetic-search.mjs
|
||
# or both at once:
|
||
cd www && npm test
|
||
```
|
||
|
||
Tests use Node.js directly — no test runner or build step needed.
|
||
|
||
### Run / build (Electron)
|
||
|
||
```sh
|
||
cordova run electron # dev run
|
||
cordova build electron --release --verbose # release build
|
||
```
|
||
|
||
### Run on Android
|
||
|
||
```sh
|
||
# Set up environment first (or source env.sh):
|
||
source env.sh
|
||
# env.sh sets ANDROID_HOME, ANDROID_SDK_ROOT, PATH entries for the SDK,
|
||
# and isolates Gradle cache to ./.gradle, then calls `cordova run android`.
|
||
```
|
||
|
||
### Serve in browser
|
||
|
||
```sh
|
||
cordova run browser
|
||
# or just open www/index.html via any static file server
|
||
```
|
||
|
||
## Architecture
|
||
|
||
```
|
||
www/
|
||
index.html — single-page app; all UI logic is an inline <script type="module">
|
||
src/
|
||
conhecidos.js — pure functions: the seven kinetic µ(S) equations + Pirt
|
||
runge-kutta.js — RK4 solver (RK4) and point interpolator (RK4getvalue)
|
||
Objective.js — Objective class: wraps experimental data + ODE, computes normalized SSR
|
||
PSO.js — PSO class: initializes swarm, runs iterations, exposes pos_best_g / err_best_g
|
||
search.js — orchestrates everything: builds ODE functions (model × Pirt coupling),
|
||
runs PSO per model, renders Plotly charts, computes AIC, sorts results
|
||
rrandom.js — Math.random wrapper used by PSO
|
||
solve.js — standalone legacy helper (not imported by search.js)
|
||
tests/
|
||
demo.mjs — smoke test: PSO converges to a finite error
|
||
synthetic-search.mjs — accuracy test: PSO recovers known Monod params from synthetic data
|
||
assets/
|
||
dados.json — default experimental dataset loaded on page start
|
||
```
|
||
|
||
### Data flow
|
||
|
||
1. `index.html` collects experimental data, PSO hyperparameters, and per-model parameter bounds from the form.
|
||
2. It calls `main(data, { alg, bounds, onProgress })` exported from `search.js`.
|
||
3. For each of the seven models, `search.js` constructs an ODE function (`<model>Pirt`) that couples a growth-rate formula from `conhecidos.js` with the Pirt substrate consumption equation.
|
||
4. An `Objective` instance wraps the ODE and experimental data. It normalizes residuals by column mean before summing squared errors — this makes SSR dimensionless and comparable across variables with different scales.
|
||
5. `PSO` minimizes the objective over the parameter bounds, producing `pos_best_g` (best parameter vector).
|
||
6. RK4 integrates the ODE at 500 internal steps; `RK4getvalue` interpolates from that solution to exact experimental time points.
|
||
7. After all models complete, results are sorted by AIC and a comparison table is rendered.
|
||
|
||
### Key design constraints
|
||
|
||
- The frontend is **no-build**: ES modules loaded directly in the browser; no bundler.
|
||
- `www/package.json` has `"type": "module"` so Node can run the tests with native ESM imports.
|
||
- External CDN dependencies: KaTeX (math rendering), Plotly (charts). Both are loaded in `index.html`; `search.js` assumes `Plotly` and `katex` are globals.
|
||
- The `Objective` constructor detects column order from header keywords (Portuguese and English), so column order in the data table matters only when headers are absent or unrecognized.
|
||
- `PSO` uses `Math.random` directly — `synthetic-search.mjs` patches it with a deterministic LCG for reproducible test results.
|
||
- `solve.js` is a legacy standalone function that references globals (`RK4`, `Plotly`, `document`) and is not imported anywhere in the current codebase.
|