Update GMC Proliferation Module by Jannetty · Pull Request #219 · bagherilab/ARCADE

Jannetty · 2026-04-12T02:37:30Z

Estimated time to review: Medium

Summary of changes:
In general this PR adds volume-sensitive growth and PDE-like growth for the fly GMC cells (which the Neuroblasts will also use)

Add default sigmoid volume-based growth for PottsModuleProliferationVolumeBasedDivision if growth rate is set to be volume sensitive
Add framework for simulating PDE-like growth where cell growth rate is regulated by average cell volume
Added growth rate updating function for GMCs
Added necessary parameters for volume-sensitive growth rate and PDE-like growth

How to verify changes:

run tests (PottsModuleProliferationVolumeBasedDivisionTest and PottsModuleFlyGMCDifferentiationTest)
Here is a minimal GMC setup file:

<set prefix="2024-10-25-04">
    <series name="dd" start="1" end="1"
            ds=".3" margin="0" height="1" length="302" width="302"
            dt=".083" ticks="576" interval="4">
        <potts>
            <potts.term id="volume" />
            <potts.term id="adhesion" />
            <potts.term id="surface" />
            <!-- <potts.term id="persistence" /> -->
            <!-- <potts.parameter term="adhesion" id="ADHESION" value="80" target="fly-neuron:*"/>
            <potts.parameter term="adhesion" id="ADHESION" value="80" target="fly-gmc:*"/> -->
        </potts>
        <agents>
            <populations>
                <population id="fly-gmc" class="fly-gmc" init="1">
                 <population.link id="fly-neuron" weight="1"/>
                 <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
                 <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
                </population>
                <population id="fly-neuron" class="fly-neuron" init="0">
                <population.parameter id="proliferation/CELL_GROWTH_RATE" value="0"/>
                <population.parameter id="proliferation/BASAL_APOPTOSIS_RATE" value="0"/>
                <population.parameter id="CRITICAL_VOLUME" value="11" units="um^3" conversion="DS^-3" />
                </population>
            </populations>
        </agents>
    </series>
</set>

You can add/adjust the following parameters and run simulations:

<population.parameter id="proliferation/DYNAMIC_GROWTH_RATE_VOLUME" value="1"/>
<population.parameter id="proliferation/GROWTH_RATE_VOLUME_SENSITIVITY" value="4.0"/>
<population.parameter id="proliferation/PDELIKE" value="1"/>

Dynamic growth rate volume is a boolean you can turn on and off. When on (1) small cells grow slower than big cells.
Growth rate volume sensitivity is the exponent that determines the slope of the sigmoid (essentially the hill coefficient) dictating how sensitive the growth rate is to the cell's volume.
PDELIKE is a boolean that, when on, makes the cell growth rate a function of the average GMC volume across all GMCs in the simulation.

allison-li-1016 · 2026-04-13T17:03:13Z

+
+                for (int i = 0; i < objs.numObjs; i++) {
+                    Object o = objs.objs[i];
+                    if (!(o instanceof arcade.potts.agent.cell.PottsCell)) {


To clarify, is this if statement for avoiding environmental objects (like vasculature)? Otherwise, we can't have a simulation where Patch/Potts cells both exist right?

allison-li-1016 · 2026-04-13T17:11:44Z

+     *
+     * @param sim the simulation
+     */
+    public void updateGrowthRate(Simulation sim) {


Very nitpick comments so feel free to ignore:

Consider factoring out the volume averaging logic to its own function

For readability it might be easier to do switch statements or if/else statements where the boolean is true. For example something like:

default: cellGrowthRate = cellGrowthRateBase case pdelike cellGrowthRate = averageVolume() case dynamicGrowthVolume cellGrowthRate = updateCellVolumeBasedGrowthRate()

allison-li-1016 · 2026-04-13T17:21:18Z

    <population.module module="proliferation" id="NUCLEUS_CONDENSATION_FRACTION" value="0.5" description="fraction of nuclear volume when condensed" />

+    <!-- ── Fly cell proliferation module parameters ───────────────────── -->
+    <!-- ── Dictating whether NB behavior should be the same across all NBs ──────── -->


Another very nitpick comment so feel free to ignore

Currently the comments feel more like parameter descriptions rather than categories -- consider organizing the proliferation parameters by model type?

Eg:

 ...  ...  ...

I agree that the  and  read more like descriptions than categories. I think part of it is because all the other labels end in "parameters"
I'm wondering why we need to further categorize PDELIKE, DYNAMIC_GROWTH_RATE_VOLUME, and GROWTH_RATE_VOLUME_SENSITIVITY... would it be okay to just remove the sublabels?

kristaphommatha · 2026-04-14T17:26:54Z

+                        count++;
+                    }
+                }
+                double avgVolume = volSum / count;


I think Allison touched on this in an earlier comment, but I think that finding the average volume of the Potts cells can be moved out into their own function like getAvgVolume(Simulation sim) or something.

kristaphommatha · 2026-04-14T17:46:23Z

    <population.module module="proliferation" id="NUCLEUS_CONDENSATION_FRACTION" value="0.5" description="fraction of nuclear volume when condensed" />

+    <!-- ── Fly cell proliferation module parameters ───────────────────── -->
+    <!-- ── Dictating whether NB behavior should be the same across all NBs ──────── -->


I agree that the  and  read more like descriptions than categories. I think part of it is because all the other labels end in "parameters"
I'm wondering why we need to further categorize PDELIKE, DYNAMIC_GROWTH_RATE_VOLUME, and GROWTH_RATE_VOLUME_SENSITIVITY... would it be okay to just remove the sublabels?

kristaphommatha · 2026-04-14T19:42:19Z

+        when(gmcB.getCriticalVolume()).thenReturn(100.0);
+        when(gmcC.getCriticalVolume()).thenReturn(200.0);
+
+        // Noise: different type and/or different pop → must be ignored


If you end up moving the average volume calculation into a separate function, then I think parts of this test can also be moved to test just the average volume calculation...

allison-li-1016 · 2026-04-20T23:27:42Z

+     *
+     * @param sim the simulation
+     */
+    public abstract void updateGrowthRate(Simulation sim);


Could the updateGrowthRate method look different for each type of volume-based proliferation?

I am a little confused as to why the updateGrowthRate logic is a method rather than some switch statements in the abstract class

allison-li-1016 · 2026-04-20T23:32:08Z

+    <!-- ── Fly cell proliferation module parameters ───────────────────── -->
+    <!-- ── Dictating whether NB behavior should be the same across all NBs ──────── -->
+    <population.module module="proliferation" id="PDELIKE" value="0" description="1 → all cells of a given type have same growth and division dynamics based on average metrics across the population; 0 → Cell growth and division is determined on a cell-by-cell basis, cells can differ from other cells of the same type" />
+    <!-- ── Growth rate sensitivity to cell volume dynamics ───────────────────── -->


I recall that there were non-volume based proliferation options, do you intend to have a section for that too?

After some reading I do think it would make sense to have something like:

<---- fly stem cell proliferation module params -----> <---- booleans that modulate proliferation growth rate -----> <------ volume based proliferation parameters -----> <----- time based proliferation parameters -----> <----- (other types of fly cell proliferation ----->

allison-li-1016 · 2026-04-20T23:34:16Z

+        when(parameters.getDouble("proliferation/SIZE_TARGET")).thenReturn(1.2);
+        when(parameters.getInt("proliferation/PDELIKE")).thenReturn(0);
+
+        // critVol = 150.0; sizeTarget = 1.2


is this for documentation or leftover comments?

If its for documentation its not immediately clear what these values are for

allison-li-1016 · 2026-04-20T23:38:06Z

+    }
+
+    @Test
+    public void computeEquilibriumVolume_differentSizeTarget_scalesCorrectly() {


very nitpick but for documentation might be clearer to include the multiplier in the title

e.g. computeEquilibriumVolume_doubleSizeTarget_scalesCorrectly()

allison-li-1016 · 2026-04-20T23:41:24Z

+    /**
+     * Sensitivity of growth rate to cell volume, only relevant if dynamicGrowthRateVolume is true.
+     */
+    final double growthRateVolumeSensitivity;


Ignore if this was implemented elsewhere (or if its impossible to make this error), but might be good to throw an error if growthRateVolumeSensitivity is set but dynamicGrowthRateVolume is false. If you do implement this error throw it would be good to add a test for it as well

allison-li-1016 · 2026-04-20T23:42:38Z

Finished my first pass of reviews - overall looks good but I have a couple of discussion points/questions to be resolved before approving

Jannetty added 9 commits April 11, 2026 19:33

add updateGrowthRate framework and make getUniqueIDs public

57817c1

adding dostrings

6392d9e

another docstring

488ab02

more formatting

4376f32

final formatting

731082f

adding missing parameters to potts xml. Removing unnecessary parameter

6cb465d

removing redundant section of docstring

64ce606

puppycrawler asking for some odd spacing

2ce8a27

puppycrawl now wants me to undo the odd spacing it asked for

3e8bebc

Jannetty changed the title ~~Add updateGrowthRate framework and make getUniqueIDs public~~ Update GMC Proliferation Module Apr 12, 2026

removing part of PR more relevant to neuroblasts

9238f51

Jannetty requested review from a team, afu5, allison-li-1016, cainja, jacob-evarts, jessicasyu, kristaphommatha and pohaoc2 and removed request for a team April 12, 2026 05:49

Jannetty self-assigned this Apr 12, 2026

Jannetty added type: feature Improvement or additions to the code base package: potts Related to the potts implementation category: agent Related to the agent subpackages size: medium Estimated size of issue or PR is medium labels Apr 12, 2026

Jannetty marked this pull request as ready for review April 12, 2026 05:50

This was referenced Apr 12, 2026

Add Flystem Cells #220

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Adding fly stem cells #217

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allison-li-1016 reviewed Apr 13, 2026

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kristaphommatha reviewed Apr 14, 2026

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allison-li-1016 reviewed Apr 20, 2026

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