Feature/release module by meganrm · Pull Request #209 · simularium/binding-sim-edu

meganrm · 2026-03-09T23:26:18Z

Fix grammatical typo in KdQuestion.tsx helper text ("look at the where" → "look at where")
Remove unconditional console.log("NEW BINDING SIMULATOR") debug statement in App.tsx (guarded behind process.env.NODE_ENV !== "production")
Rename shadowed inner let bestFit variable to fitResult inside the bestFit useMemo in EquilibriumPlot.tsx

Full set of changes in this PR:

Rename precomputed simulation name→type map for clarity and tweak live binding parameters
Update equilibrium plot logic to support competitive binding (Ki) with exponential regression and 50%-inhibition annotation
Rename shadowed inner variable bestFit → fitResult inside EquilibriumPlot useMemo
Small UI/UX updates: enable navigation button, add quiz hint text, lock page scrolling, reset additional analysis state
Remove debug console.log (guarded behind dev-only check)
Fix grammatical typo in KdQuestion helper text

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Pull request overview

This PR updates the live-simulation equilibrium/Kd plotting and related UI flow, including adding competitive binding (Ki) support and a few UI/parameter tweaks.

Changes:

Rename the precomputed simulation name→type map for clarity and tweak live binding parameters.
Update equilibrium plot logic to support competitive binding (Ki) with different fit/annotation behavior.
Small UI/UX updates (enable navigation button, add quiz hint text, lock page scrolling, reset additional analysis state).

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
`src/simulation/PreComputedSimulationData.ts`	Renames static map used to derive agent/product types.
`src/simulation/LiveSimulationData.ts`	Adjusts binding parameter (`kOn`) and formatting.
`src/simulation/BindingSimulator2D.ts`	Formatting-only changes (trailing commas).
`src/index.css`	Enables `overflow: hidden` on `body`.
`src/content/LowAffinity.tsx`	Enables `nextButton` at end of Low Affinity content.
`src/components/quiz-questions/KdQuestion.tsx`	Adds additional hint paragraph for answering the question.
`src/components/plots/EquilibriumPlot.tsx`	Adds module-dependent regression/annotation logic (Kd vs Ki).
`src/App.tsx`	Expands analysis reset, minor navigation behavior change, and adds a debug log.

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Copilot · 2026-03-09T23:31:21Z

src/components/quiz-questions/KdQuestion.tsx

+            <p>
+                If you're not sure, look at the where the line crosses the 50%
+                mark on the <strong>Equilibrium concentration plot.</strong>
+            </p>


The new helper text has a grammatical typo: "look at the where" should be "look at where".

@copilot apply changes based on this feedback

Fixed in c8b057b — removed the extra "the" so the text now reads "look at where the line crosses the 50%".

src/App.tsx

Copilot · 2026-03-09T23:31:22Z

src/components/plots/EquilibriumPlot.tsx

+        if (module === Module.A_B_D_AB) {
+            bestFit = regression.exponential(regressionData);
+            const max = Math.max(...y);
+            const min = Math.min(...y);
+            const halfMax = (max - min) / 2 + min;
+            // for exponential, the equation is in the form y = a * e^(b*x)
+            // bestFit.equation[0] is a and bestFit.equation[1] is b, so to solve for x when y is halfMax:
+            // halfMax = a * e^(b*x)
+            // halfMax / a = e^(b*x)
+            // ln(halfMax / a) = b*x
+            // x = ln(halfMax / a) / b
+            value =
+                Math.log(halfMax / bestFit.equation[0]) / bestFit.equation[1];
+        } else {


When module === Module.A_B_D_AB and there are no recorded points yet, y can be empty here. In that case Math.max(...y)/Math.min(...y) evaluate to -Infinity/Infinity, making halfMax and the derived value become NaN. Consider guarding this branch (and skipping regression) until you have enough data points.

src/components/plots/EquilibriumPlot.tsx

Agent-Logs-Url: https://github.com/simularium/binding-sim-edu/sessions/8cd74e6d-d6f7-47e6-b8ff-ab0f707e2892 Co-authored-by: meganrm <5170636+meganrm@users.noreply.github.com>

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Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 5 comments.

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src/components/quiz-questions/KdQuestion.tsx

src/App.tsx

src/components/plots/EquilibriumPlot.tsx

Copilot · 2026-03-27T22:35:31Z

src/index.css

    background-color: var(--background-color);
    color: var(--text-color);
-    /* overflow: hidden; */
+    overflow: hidden;


Setting body { overflow: hidden; } prevents page scrolling and can clip content on smaller viewports or when text is zoomed, which is an accessibility regression. Prefer scoping overflow constraints to the simulation container/canvas, or allow vertical scrolling (overflow-y: auto) while controlling only the area that must be fixed.

Suggested change

overflow: hidden;

overflow-x: hidden;

overflow-y: auto;

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

…o to avoid variable shadowing Agent-Logs-Url: https://github.com/simularium/binding-sim-edu/sessions/25c7a586-2e66-4802-954b-ec3df06ecf12 Co-authored-by: meganrm <5170636+meganrm@users.noreply.github.com>

meganrm added 2 commits February 17, 2026 13:51

equ plot shows Ki

69c58f7

format

96023f7

meganrm requested a review from Copilot March 9, 2026 23:26

Copilot started reviewing on behalf of meganrm March 9, 2026 23:26 View session

Copilot AI reviewed Mar 9, 2026

View reviewed changes

Copilot started work on behalf of meganrm March 27, 2026 22:12 View session

fix: remove extra "the" in KdQuestion helper text

c8b057b

Agent-Logs-Url: https://github.com/simularium/binding-sim-edu/sessions/8cd74e6d-d6f7-47e6-b8ff-ab0f707e2892 Co-authored-by: meganrm <5170636+meganrm@users.noreply.github.com>

Copilot finished work on behalf of meganrm March 27, 2026 22:14

meganrm requested a review from Copilot March 27, 2026 22:30

Copilot started reviewing on behalf of meganrm March 27, 2026 22:31 View session

Copilot AI reviewed Mar 27, 2026

View reviewed changes

Copilot started work on behalf of meganrm March 27, 2026 22:48 View session

meganrm and others added 3 commits March 27, 2026 15:48

Update src/App.tsx

613ed30

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update src/components/plots/EquilibriumPlot.tsx

7129b93

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

refactor: rename inner bestFit to fitResult in EquilibriumPlot useMem…

b8eff05

…o to avoid variable shadowing Agent-Logs-Url: https://github.com/simularium/binding-sim-edu/sessions/25c7a586-2e66-4802-954b-ec3df06ecf12 Co-authored-by: meganrm <5170636+meganrm@users.noreply.github.com>

Copilot finished work on behalf of meganrm March 27, 2026 22:51

meganrm marked this pull request as ready for review March 27, 2026 22:55

meganrm requested a review from a team as a code owner March 27, 2026 22:55

meganrm requested review from ShrimpCryptid and toloudis and removed request for a team, ShrimpCryptid and toloudis March 27, 2026 22:55

meganrm merged commit cb90c6a into main Mar 27, 2026
3 checks passed

meganrm deleted the feature/release-module branch March 27, 2026 22:57

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Feature/release module#209

Feature/release module#209
meganrm merged 6 commits intomainfrom
feature/release-module

meganrm commented Mar 9, 2026 •

edited by Copilot AI

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meganrm commented Mar 9, 2026 •

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