About lab
Microbiology Hello World Growth Lab
This beginner lab shows how Biosimulant can connect several simple models into one friendly story. You choose a starting plate, viable cells grow while food is available, and the final node explains why the colony declines after starvation begins.
What You'll See
The canvas has three steps:
starter_setup: choose the starting plate.microbial_growth: watch viable cells eat, multiply, run out of food, and decline.story_reporter: read the result and try a next experiment.
With the bundled defaults, the run produces viable-cell and food charts plus simple tables for the setup and story. The screenshots below show the same lab run for 50 hours so the post-food starvation decline is visible.
The first view shows the three-model canvas next to the Results panel. starter_setup records the starting plate, while microbial_growth plots viable cells rising to a peak and then declining after food is exhausted.
The second view shows the food curve reaching zero, the plain-language "What Happened" table, and the story reporter explaining that starvation is now the main limit.
The third view shows the editable parameters alongside the results, so a new user can connect each simple control to the final story.
How to Read the Visualizations
The viable-cell chart shows how many living cells are present over time. A steep upward line means the colony is multiplying quickly. A downward line after food reaches zero represents starvation death in this teaching model.
The food chart shows food units left over time. When it reaches zero, the colony cannot add new cells, and viable cells begin to decline at the built-in starvation rate.
The setup and story tables restate the starting plate, the main bottleneck, and simple changes to try next.
What This Lab Contains
| Path | Purpose |
|---|---|
lab.yaml | Public lab controls, outputs, model list, and wiring. |
wiring-layout.json | Three-node canvas layout. |
models/starter-culture/ | Setup model that turns four controls into a starting plate. |
models/microbial-growth/ | Middle model that simulates viable-cell growth and starvation decline. |
models/growth-story/ | Story model that explains the growth results. |
tests/ | Integration tests for the three-model lab. |
assets/ | Screenshots for the lab README. |
Inputs
| Input | Meaning |
|---|---|
initial_cells | How many cells are on the plate at the start. |
available_food | How much food is available. |
growth_rate | How quickly the cells can multiply when food and space are available. |
space_limit | Approximate maximum colony size the space can hold. |
Outputs
| Output | Meaning |
|---|---|
colony_state | Current viable cell count, food remaining, starvation loss, and main limit. |
lesson_summary | Short explanation from the growth model. |
hello_world_story | Plain-language story that combines setup and growth. |
next_steps | Simple ideas for changing the next run. |
Running in Biosimulant Desktop
Import the lab from the repository root:
biosimulant labs import labs/microbiology-hello-world-growth
Notes
This is an educational model, not a publication-grade microbiology model. It is intentionally small so new users can see how inputs, wiring, model outputs, and visual summaries fit together.
The growth math is a simple resource-limited teaching simulation. It includes a default starvation-death term so the post-food phase is easier to understand, but it is not calibrated to a real organism and should not be used to make organism-specific or clinical decisions.
Beginner-friendly multi-model tutorial lab where users choose a starting plate, watch viable cells grow, and read why starvation changes the curve.
Runtime
Duration12
Comms Step0.25
Runs
Total6
Completed6
Failed0
Metadata
Packagemicrobiology-hello-world-growth-lab
Created2026-05-01
Updated2026-05-23
microbiologytutorialhello-worldsetuppopulation-growthexplanationother
Manifest
{
"io": {
"inputs": [
{
"name": "initial_cells",
"maps_to": "starter_setup.initial_cells"
},
{
"name": "available_food",
"maps_to": "starter_setup.available_food"
},
{
"name": "growth_rate",
"maps_to": "starter_setup.growth_rate"
},
{
"name": "space_limit",
"maps_to": "starter_setup.space_limit"
}
],
"outputs": [
{
"name": "colony_state",
"maps_to": "microbial_growth.colony_state"
},
{
"name": "lesson_summary",
"maps_to": "microbial_growth.lesson_summary"
},
{
"name": "hello_world_story",
"maps_to": "story_reporter.hello_world_story"
},
{
"name": "next_steps",
"maps_to": "story_reporter.next_steps"
}
]
},
"title": "Microbiology Hello World Growth Lab",
"models": [
{
"path": "owned/models/starter_setup",
"alias": "starter_setup",
"parameters": {
"growth_rate": 0.8,
"space_limit": 200,
"initial_cells": 10,
"available_food": 80,
"integration_step": 0.25
},
"provenance": {
"owned_path": "owned/models/starter_setup"
}
},
{
"path": "owned/models/microbial_growth",
"alias": "microbial_growth",
"parameters": {
"growth_rate": 0.8,
"space_limit": 200,
"initial_cells": 10,
"available_food": 80,
"integration_step": 0.05,
"food_per_new_cell": 1,
"starvation_death_rate": 0.04
},
"provenance": {
"owned_path": "owned/models/microbial_growth"
}
},
{
"path": "owned/models/story_reporter",
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"parameters": {
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},
"provenance": {
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}
}
],
"wiring": [
{
"to": [
"microbial_growth.growth_setup",
"story_reporter.growth_setup"
],
"from": "starter_setup.growth_setup"
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{
"to": [
"story_reporter.colony_state"
],
"from": "microbial_growth.colony_state"
},
{
"to": [
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],
"from": "microbial_growth.lesson_summary"
}
],
"runtime": {
"duration": 12,
"initial_inputs": {},
"communication_step": 0.25
},
"description": "Beginner-friendly multi-model tutorial lab where users choose a starting plate, watch viable cells grow, and read why starvation changes the curve.",
"schema_version": "2.0"
}Sign in to start your own run. Public-lab history stays visible here.
Logs
No logs yet.
JSON
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"result": "After 11.8 hours, the colony peaked at 90.0 viable cells and ended at 77.9.",
"title": "Microbiology Hello World",
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"title": "Viable Colony Cells",
"x_unit": "hour",
"y_unit": "cells"
},
"description": "Viable cell count over time.",
"render": "timeseries"
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],
[
10.150000000000002,
9.75556490730016e-10
],
[
10.200000000000005,
9.75556490730016e-10
],
[
10.25,
9.75556490730016e-10
],
[
10.3,
9.75556490730016e-10
],
[
10.35,
9.75556490730016e-10
],
[
10.400000000000002,
9.75556490730016e-10
],
[
10.450000000000005,
9.75556490730016e-10
],
[
10.5,
9.75556490730016e-10
],
[
10.55,
9.75556490730016e-10
],
[
10.6,
9.75556490730016e-10
],
[
10.650000000000002,
9.75556490730016e-10
],
[
10.700000000000005,
9.75556490730016e-10
],
[
10.75,
9.75556490730016e-10
],
[
10.8,
9.75556490730016e-10
],
[
10.85,
9.75556490730016e-10
],
[
10.900000000000002,
9.75556490730016e-10
],
[
10.950000000000005,
9.75556490730016e-10
],
[
11,
9.75556490730016e-10
],
[
11.05,
9.75556490730016e-10
],
[
11.1,
9.75556490730016e-10
],
[
11.150000000000002,
9.75556490730016e-10
],
[
11.200000000000005,
9.75556490730016e-10
],
[
11.25,
9.75556490730016e-10
],
[
11.3,
9.75556490730016e-10
],
[
11.35,
9.75556490730016e-10
],
[
11.400000000000002,
9.75556490730016e-10
],
[
11.450000000000005,
9.75556490730016e-10
],
[
11.5,
9.75556490730016e-10
],
[
11.55,
9.75556490730016e-10
],
[
11.6,
9.75556490730016e-10
],
[
11.650000000000002,
9.75556490730016e-10
],
[
11.700000000000005,
9.75556490730016e-10
],
[
11.75,
9.75556490730016e-10
],
[
11.8,
9.75556490730016e-10
],
[
11.85,
9.75556490730016e-10
],
[
11.900000000000002,
9.75556490730016e-10
],
[
11.950000000000005,
9.75556490730016e-10
],
[
12,
9.75556490730016e-10
]
]
}
],
"title": "Food Supply",
"x_unit": "hour",
"y_unit": "food_unit"
},
"description": "Food remaining over time.",
"render": "timeseries"
},
{
"data": {
"columns": [
"Question",
"Answer"
],
"rows": [
[
"What changed?",
"The colony grew from 10.0 to a peak of 90.0 viable cells, then ended at 77.2."
],
[
"Why did it change?",
"Cells multiplied until food ran out; after that, the viable population declined from starvation."
],
[
"Main limit",
"starvation"
],
[
"Food used",
"80.00 food units"
],
[
"Space used",
"38.6%"
]
],
"title": "What Happened"
},
"description": "Plain-language explanation of the run.",
"render": "table"
}
]
},
{
"module": "story_reporter",
"module_class": "GrowthStoryReporter",
"visuals": [
{
"data": {
"columns": [
"Part",
"Meaning"
],
"rows": [
[
"Start",
"You started with 10.0 cells, 80.0 food units, and room for 200.0 cells."
],
[
"Result",
"After 11.8 hours, the colony peaked at 90.0 viable cells and ended at 77.9."
],
[
"Why it matters",
"Food ran out, so viable cells declined under starvation. This shows how Biosimulant can pass a setup through growth, resource use, and explanation."
]
],
"title": "Hello World Story"
},
"description": "Plain-language story for the run.",
"render": "table"
},
{
"data": {
"columns": [
"Idea"
],
"rows": [
[
"Increase food to see whether the colony grows longer."
],
[
"Lower the space limit to see crowding happen sooner."
],
[
"Set growth rate to zero to see a no-growth control."
]
],
"title": "Try Next"
},
"description": "Simple ideas for the next run.",
"render": "table"
}
]
}
]
}