From eed063f16c8dd9248529a864840c30171feacdc2 Mon Sep 17 00:00:00 2001
From: ltadeu6 <ltadeu6@protonmail.com>
Date: Sun, 24 May 2026 18:26:19 -0300
Subject: [PATCH] =?UTF-8?q?Remove=20c=C3=B3digo=20morto,=20eliminar=20cons?=
 =?UTF-8?q?ole.log=20e=20deduplicate=20cat=C3=A1logo=20de=20par=C3=A2metro?=
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- 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>
---
 CLAUDE.md         |  85 ++++++++++++++++++++++++++++++++++
 www/index.html    | 113 +---------------------------------------------
 www/src/PSO.js    |   5 --
 www/src/search.js |   6 +--
 www/src/solve.js  |  45 ------------------
 5 files changed, 89 insertions(+), 165 deletions(-)
 create mode 100644 CLAUDE.md
 delete mode 100644 www/src/solve.js

diff --git a/CLAUDE.md b/CLAUDE.md
new file mode 100644
index 0000000..151da5c
--- /dev/null
+++ b/CLAUDE.md
@@ -0,0 +1,85 @@
+# 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.
diff --git a/www/index.html b/www/index.html
index c124531..2780064 100644
--- a/www/index.html
+++ b/www/index.html
@@ -253,7 +253,7 @@
         </div>
 
         <script type="module">
-          import { main } from "./src/search.js";
+          import { main, parameterCatalog, modelParameters, getParamDisplayInfo } from "./src/search.js";
 
           const measurementUnits = {
             time: "h",
@@ -267,117 +267,6 @@
             `cells (${measurementUnits.cells})`,
           ];
 
-          const parameterCatalog = {
-            K_S: {
-              latex: "K_S",
-              unitText: "g/L",
-              unitLatex: "\\mathrm{g\\,L^{-1}}",
-              overrides: {
-                contois: {
-                  unitText: "g_S/g_X",
-                  unitLatex: "\\frac{\\mathrm{g}_{S}}{\\mathrm{g}_{X}}",
-                },
-              },
-            },
-            mu_max: {
-              latex: "\\mu_{max}",
-              unitText: "h⁻¹",
-              unitLatex: "\\mathrm{h^{-1}}",
-            },
-            K_I: {
-              latex: "K_I",
-              unitText: "g/L",
-              unitLatex: "\\mathrm{g\\,L^{-1}}",
-              overrides: {
-                aiba: {
-                  unitText: "L/g",
-                  unitLatex: "\\mathrm{L\\,g^{-1}}",
-                },
-              },
-            },
-            m_S: {
-              latex: "m_S",
-              unitText: "g_S/(g_X·h)",
-              unitLatex: "\\frac{\\mathrm{g}_{S}}{\\mathrm{g}_{X}\\,\\mathrm{h}}",
-            },
-            Y_XS: {
-              latex: "Y_{XS}",
-              unitText: "g_X/g_S",
-              unitLatex: "\\frac{\\mathrm{g}_{X}}{\\mathrm{g}_{S}}",
-            },
-            T: {
-              latex: "T",
-              unitText: "h",
-              unitLatex: "\\mathrm{h}",
-            },
-            n: {
-              latex: "n",
-              unitText: null,
-              unitLatex: null,
-            },
-          };
-
-          const modelParameters = {
-            aiba: [
-              { key: "K_S", bounds: [0.005, 2] },
-              { key: "mu_max", bounds: [0.05, 0.9] },
-              { key: "K_I", bounds: [0.01, 1] },
-              { key: "m_S", bounds: [0.0015, 0.05] },
-              { key: "Y_XS", bounds: [0.3, 0.7] },
-            ],
-            andrews: [
-              { key: "K_S", bounds: [0.005, 2] },
-              { key: "mu_max", bounds: [0.05, 0.9] },
-              { key: "K_I", bounds: [5, 150] },
-              { key: "m_S", bounds: [0.0015, 0.05] },
-              { key: "Y_XS", bounds: [0.3, 0.7] },
-            ],
-            bergter: [
-              { key: "K_S", bounds: [0.005, 2] },
-              { key: "mu_max", bounds: [0.05, 0.9] },
-              { key: "T", bounds: [5, 80] },
-              { key: "m_S", bounds: [0.0015, 0.05] },
-              { key: "Y_XS", bounds: [0.3, 0.7] },
-            ],
-            contois: [
-              { key: "K_S", bounds: [0.005, 2] },
-              { key: "mu_max", bounds: [0.05, 0.9] },
-              { key: "m_S", bounds: [0.0015, 0.05] },
-              { key: "Y_XS", bounds: [0.3, 0.7] },
-            ],
-            monod: [
-              { key: "K_S", bounds: [0.005, 2] },
-              { key: "mu_max", bounds: [0.05, 0.9] },
-              { key: "m_S", bounds: [0.0015, 0.05] },
-              { key: "Y_XS", bounds: [0.3, 0.7] },
-            ],
-            moser: [
-              { key: "K_S", bounds: [0.005, 2] },
-              { key: "mu_max", bounds: [0.05, 0.9] },
-              { key: "n", bounds: [0.8, 2.5] },
-              { key: "m_S", bounds: [0.0015, 0.05] },
-              { key: "Y_XS", bounds: [0.3, 0.7] },
-            ],
-            tessier: [
-              { key: "K_S", bounds: [0.005, 2] },
-              { key: "mu_max", bounds: [0.2, 0.9] },
-              { key: "m_S", bounds: [0.005, 0.05] },
-              { key: "Y_XS", bounds: [0.3, 0.7] },
-            ],
-          };
-
-          function getParamDisplayInfo(paramKey, modelKey) {
-            const baseInfo = parameterCatalog[paramKey];
-            if (!baseInfo) {
-              throw new Error(`Unknown parameter: ${paramKey}`);
-            }
-            const override = baseInfo.overrides?.[modelKey];
-            if (!override) {
-              return baseInfo;
-            }
-            return { ...baseInfo, ...override };
-          }
-
           const demoData = [
             dataHeader,
             [0, 3.0, 0.05],
diff --git a/www/src/PSO.js b/www/src/PSO.js
index a81ce14..0d79d07 100644
--- a/www/src/PSO.js
+++ b/www/src/PSO.js
@@ -44,12 +44,7 @@ export class PSO {
   run(c1, c2, w, iteration) {
     for (let i = 0; i < iteration; i++) {
       this.update(c1, c2, w);
-      // console.log(i, "/", iteration, "\t", this.err_best_g);
     }
-
-    console.log(this.pos_best_g);
-    // console.log(this.err_best_g)
-    // console.table(this.pos)
   }
 
   update(c1, c2, w) {
diff --git a/www/src/search.js b/www/src/search.js
index d57c1ad..5c1fd5e 100644
--- a/www/src/search.js
+++ b/www/src/search.js
@@ -13,7 +13,7 @@ import {
 } from "./conhecidos.js";
 import "https://cdn.plot.ly/plotly-2.29.1.min.js";
 
-const parameterCatalog = {
+export const parameterCatalog = {
   K_S: {
     latex: "K_S",
     unitText: "g/L",
@@ -63,7 +63,7 @@ const parameterCatalog = {
   },
 };
 
-const modelParameters = {
+export const modelParameters = {
   aiba: [
     { key: "K_S", bounds: [0.005, 2] },
     { key: "mu_max", bounds: [0.05, 0.9] },
@@ -112,7 +112,7 @@ const modelParameters = {
   ],
 };
 
-function getParamDisplayInfo(paramKey, modelKey) {
+export function getParamDisplayInfo(paramKey, modelKey) {
   const baseInfo = parameterCatalog[paramKey];
   if (!baseInfo) {
     throw new Error(`Unknown parameter: ${paramKey}`);
diff --git a/www/src/solve.js b/www/src/solve.js
deleted file mode 100644
index 2b49f7d..0000000
--- a/www/src/solve.js
+++ /dev/null
@@ -1,45 +0,0 @@
-function solve(tf, Ks, mu_max, m_S, Y_XS, X0, S0) {
-  let res = 5000;
-  let timeArray = [];
-  for (let i = 0; i <= res; i++) {
-    timeArray[i] = (i * tf) / res;
-  }
-
-  let sol = RK4(model, timeArray, [X0, S0], [Ks, mu_max, m_S, Y_XS]);
-  let cels = [];
-  let subs = [];
-  for (let i = 0; i < sol.length; i++) {
-    cels[i] = sol[i][0];
-    subs[i] = sol[i][1];
-  }
-
-  TESTER = document.getElementById("tester");
-  Plotly.newPlot(
-    TESTER,
-    [
-      {
-        x: timeArray,
-        y: subs,
-        name: "Calculated substrate",
-        line: { color: "#4a90e2" },
-      },
-      {
-        x: timeArray,
-        y: cels,
-        name: "Calculated cells",
-        line: { color: "#50e3c2" },
-      },
-    ],
-    {
-      margin: { t: 10, b: 30 },
-      paper_bgcolor: "#f0f4f8",
-      plot_bgcolor: "#f0f4f8",
-      legend: {
-        orientation: "h",
-        yanchor: "top",
-        y: -0.2,
-        font: { size: 10 },
-      },
-    },
-  );
-}