Feature/3rd module by meganrm · Pull Request #208 · simularium/binding-sim-edu

meganrm · 2025-11-22T02:28:26Z

Problem

Estimated review size: Medium

closes #207 and #204

Solution

Added the written content for the 3rd module and updated the simulation to handle a new Agent, D

Type of change

Please delete options that are not relevant.

New feature (non-breaking change which adds functionality)

Steps to Verify:

bun dev
click on Competitive Binding on the progress bar to go to that section
follow the instructions

there are still more things to do to finish this module

Co-authored-by: Peyton Lee <peytonalee@gmail.com>

…nding-sim-edu into feature/navigation

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

…nding-sim-edu into feature/navigation

…into feature/3rd-module

Copilot

Pull request overview

This PR adds support for a third module on competitive binding by introducing Agent D and updating the simulation system to handle multiple complex formations. The changes extend the existing two-agent binding system to support a competitive inhibitor that can bind to the same target as Agent B.

Key changes:

Added Agent D as a competitive inhibitor with its own binding characteristics
Refactored the simulation to track multiple complex types (AB, AC, AD) separately
Updated the UI and content to guide users through the competitive binding experiment

Reviewed changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
src/types/index.ts	Added new agent types (D, Adjustable_2, Complex_3), product name (AD), and ViewType enum
src/simulation/context.tsx	Added viewport type state and setter to simulation context
src/simulation/PreComputedSimulationData.ts	Renamed AgentFunction to AgentType, updated method names
src/simulation/LiveSimulationData.ts	Added Agent D configuration, restructured concentrations by module, added competitive binding logic
src/simulation/ISimulationData.ts	Updated interface to reflect AgentType rename and method signature changes
src/simulation/BindingSimulator2D.ts	Refactored to track multiple complex types with individual colors, removed unused productColor parameter
src/simulation/BindingInstance.ts	Modified unbinding to return the released child instance
src/content/LowAffinity.tsx	Fixed typo in completion message
src/content/Competitive.tsx	Added complete content flow for competitive binding module
src/components/main-layout/LeftPanel.tsx	Hidden events over time plot for competitive binding module
src/components/concentration-display/LiveConcentrationDisplay.tsx	Fixed Math.min to Math.max for step calculation
src/components/concentration-display/ConcentrationSlider.tsx	Added decimal number formatting for slider marks
src/components/ViewSwitch.tsx	Refactored to use context-based view state instead of local state
src/App.tsx	Added experiment initialization, view state management, and module-specific concentration handling

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src/content/Competitive.tsx

src/components/concentration-display/ConcentrationSlider.tsx

src/components/concentration-display/LiveConcentrationDisplay.tsx

src/simulation/BindingSimulator2D.ts

src/App.tsx

src/components/concentration-display/LiveConcentrationDisplay.tsx

src/content/Competitive.tsx

src/simulation/BindingSimulator2D.ts

Co-authored-by: toloudis <toloudis@users.noreply.github.com>

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

Copilot

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 3 comments.

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src/content/Competitive.tsx

src/simulation/BindingSimulator2D.ts

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

…nding-sim-edu into feature/3rd-module

Copilot

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 2 comments.

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src/simulation/BindingSimulator2D.ts

src/App.tsx

Copilot

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 3 comments.

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src/simulation/BindingSimulator2D.ts

Copilot · 2025-12-05T01:49:05Z

src/components/concentration-display/ConcentrationSlider.tsx

+                        index={
+                            index < 1 && index > 0
+                                ? Number(index.toFixed(1))
+                                : index
+                        }


[nitpick] The conditional formatting logic for decimal marks is unclear and fragile. Consider extracting this to a named function with a descriptive name like formatSliderMark to improve readability and make the intent explicit.

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

Copilot

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated 1 comment.

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Copilot · 2025-12-05T02:02:19Z

src/content/Competitive.tsx

+        title: "Start the experiment",
+        content: (
+            <>
+                We cannot directly measure the formation of <AD /> (which is why
+                it's shown in grey). To figure out how strongly <D /> binds to{" "}
+                <A /> we're going to keep track of how adding more <D /> affects
+                the amount of <AB /> formed.
+            </>
+        ),
+        layout: LayoutType.LiveSimulation,
+        section: Section.Introduction,
+        actionButton: <StartExperiment />,
+        progressionElement: PLAY_BUTTON_ID,
+        callToAction: (
+            <>
+                Click the <strong>Start experiment</strong> button to reset the
+                simulation and begin by pressing <strong>play</strong>!
+            </>
+        ),
    },

+    {


Two consecutive page entries have identical title, content, layout, section, and actionButton. The only difference is progressionElement (START_EXPERIMENT_ID vs PLAY_BUTTON_ID). This duplication should be eliminated by either combining into one entry or extracting common content.

Suggested change

title: "Start the experiment",

content: (

<>

We cannot directly measure the formation of <AD /> (which is why

it's shown in grey). To figure out how strongly <D /> binds to{" "}

<A /> we're going to keep track of how adding more <D /> affects

the amount of <AB /> formed.

</>

),

layout: LayoutType.LiveSimulation,

section: Section.Introduction,

actionButton: <StartExperiment />,

progressionElement: PLAY_BUTTON_ID,

callToAction: (

<>

Click the <strong>Start experiment</strong> button to reset the

simulation and begin by pressing <strong>play</strong>!

</>

),

},

{

meganrm and others added 26 commits August 28, 2025 12:31

make indicator clickable

4753a11

switch module and save which have been completed

c5f2deb

add pop confirm

fe0c926

Update src/components/PageIndicator.tsx

e54b3e1

Co-authored-by: Peyton Lee <peytonalee@gmail.com>

type index as number

ad535ef

Merge branch 'feature/navigation' of https://github.com/simularium/bi…

2d25fe0

…nding-sim-edu into feature/navigation

add key

9a87d17

make sure index is a number

57a2de7

use a set for completed modules

59cdf1f

show cursor

21dab42

Merge branch 'main' into feature/navigation

13a1254

fix merge conflict

16e1b16

fix merge conflict

e425c5e

Update src/components/PageIndicator.tsx

a25115d

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

clean up css

b9f55f1

Merge branch 'feature/navigation' of https://github.com/simularium/bi…

b22c34d

…nding-sim-edu into feature/navigation

display adjustments

ee64742

add competitive content

a2e517a

remove unused imports

57dada6

change data structure

d6b35c8

use type id

e4c3d4a

content adjustments

a85f67b

Merge branch 'main' of https://github.com/simularium/binding-sim-edu …

4c17e56

…into feature/3rd-module

change vis control

8064b34

remove log

b1a4989

lift state up

060b30e

meganrm requested a review from a team as a code owner November 22, 2025 02:28

meganrm requested review from toloudis and tyler-foster and removed request for a team November 22, 2025 02:28

meganrm requested a review from Copilot November 22, 2025 02:29

Copilot AI reviewed Nov 22, 2025

View reviewed changes

toloudis approved these changes Nov 24, 2025

View reviewed changes

meganrm and others added 7 commits November 25, 2025 09:46

Update src/content/Competitive.tsx

b270d35

Co-authored-by: toloudis <toloudis@users.noreply.github.com>

Update src/App.tsx

c39141d

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

changes based on comments

52a6650

changes based on comments

800f22f

write logic consistently

4806e87

add comment

1fd19ae

fix error

e02a457

meganrm requested a review from Copilot December 5, 2025 01:38

Copilot AI reviewed Dec 5, 2025

View reviewed changes

src/content/Competitive.tsx Outdated Show resolved Hide resolved

src/simulation/BindingSimulator2D.ts Show resolved Hide resolved

src/simulation/BindingSimulator2D.ts Outdated Show resolved Hide resolved

meganrm and others added 3 commits December 4, 2025 17:41

fix ic50

7fe65d5

Update src/simulation/BindingSimulator2D.ts

59193e7

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

Merge branch 'feature/3rd-module' of https://github.com/simularium/bi…

07698c9

…nding-sim-edu into feature/3rd-module

meganrm requested a review from Copilot December 5, 2025 01:44

Copilot AI reviewed Dec 5, 2025

View reviewed changes

src/simulation/BindingSimulator2D.ts Show resolved Hide resolved

src/App.tsx Outdated Show resolved Hide resolved

meganrm added 2 commits December 4, 2025 17:46

remove duplicate call

abe6556

add comment and error check

3e0de31

meganrm requested a review from Copilot December 5, 2025 01:47

Copilot AI reviewed Dec 5, 2025

View reviewed changes

meganrm and others added 2 commits December 4, 2025 17:50

Update src/simulation/BindingSimulator2D.ts

142f897

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

more explicit checks

ec81d10

meganrm requested a review from Copilot December 5, 2025 02:01

Copilot AI reviewed Dec 5, 2025

View reviewed changes

meganrm merged commit 0030d55 into main Dec 5, 2025
3 checks passed

meganrm deleted the feature/3rd-module branch December 5, 2025 02:02

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meganrm commented Nov 22, 2025

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