matlab-build-simbiology-model

Name: matlab-build-simbiology-model
Author: matlab

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How to install matlab-build-simbiology-model?

matlab/matlab-agentic-toolkit/matlab-build-simbiology-model

$npx -y skills add matlab/matlab-agentic-toolkit --skill matlab-build-simbiology-model

Installs into the current project.

Summary

Build, modify, and diagram SimBiology models — API reference, helper functions, and layout patterns. Use when constructing or editing models programmatically or visually.

Files · 1

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SKILL.md

1	# Build SimBiology Models
2
3	API reference, helper functions, and patterns for building, modifying, and
4	diagramming SimBiology models. Works in all MATLAB environments (desktop,
5	headless, batch, remote). Diagram/layout features require the Model Builder
6	app and are activated only when the user requests visual output.
7
8	## When to Use
9
10	- Building or modifying SimBiology models (compartments, species, reactions, parameters, rules, events, doses, observables, variants)
11	- Opening, saving, or loading models in the Model Builder / Analyzer apps
12	- Designing or adjusting diagram layouts
13	- Keywords: "build", "create", "modify", "add compartment/species/reaction", "diagram", "layout"
14
15	## When NOT to Use
16
17	- Simulation and analysis (use `matlab-simulate-simbiology-model`)
18	- Parameter fitting, population modeling, NCA (use `matlab-fit-simbiology-model`)
19
20	## Must-Follow Rules
21
22	### 1. Add helper scripts to the MATLAB path first
23
24	Run at the start of every session:
25	```matlab
26	addpath(fullfile('<WORKSPACE_ROOT>', '.claude', 'skills', 'matlab-build-simbiology-model', 'scripts'));
27	disp('Helper scripts added to path.')
28	```
29
30	### 2. Only open the Builder when needed
31
32	Do NOT open the Model Builder by default. Open it when:
33	- The user explicitly requests a diagram, layout, or visual
34	- The input is an `.sbproj` file — use `loadViaBuilder` to preserve
35	diagram layout/styling (`sbioloadproject` loses this data)
36
37	A model is fully functional without a diagram — it can be simulated,
38	fitted, and analyzed using only the model object on `sbioroot`.
39
40	### 3. Model construction uses standard SimBiology API
41
42	Build models using `addcompartment`, `addspecies`, `addreaction`, etc.
43	directly. This works in all environments: desktop, headless, batch, remote.
44
45	```matlab
46	model = sbiomodel('MyModel'); disp(model.uuid)
47	comp = addcompartment(model, 'Central', 1);
48	addspecies(comp, 'Drug', 100);
49	addparameter(model, 'ke', 0.1);
50	rx = addreaction(model, 'Central.Drug -> null');
51	kl = addkineticlaw(rx, 'MassAction');
52	kl.ParameterVariableNames = {'ke'};
53	```
54
55	For standard PK models (1- or 2-compartment with standard dosing and
56	elimination), use `references/pk-library-guidance.md` as the reference for
57	correct parameterization, naming, and rules. When no diagram is needed,
58	call `PKModelDesign` directly. When the user requests a diagram, construct
59	the model manually following the same PK library conventions but use
60	`addAndPositionCompartment` for layout control (see Rule 8b).
61
62	### 4. Write reactions in the biological forward direction
63
64	The diagram renders arrows on products and plain lines on reactants
65	(based on the forward direction of the reaction string). Writing a reaction
66	backwards produces incorrect arrows even if the kinetics are equivalent.
67
68	```matlab
69	% CORRECT — L and R get plain lines, C gets an arrow
70	addreaction(model, 'cell.L + cell.R <-> cell.C');
71
72	% WRONG — same kinetics but L and R get arrows (they're "products" now)
73	addreaction(model, 'cell.C <-> cell.L + cell.R');
74	```
75
76	Guidelines:
77	- Binding: write `A + B -> C` (substrates on left, complex on right)
78	- Degradation/elimination: write `Drug -> null` (not `null -> Drug`)
79	- Synthesis: write `null -> mRNA` (not `mRNA -> null`)
80	- Transport: write `Source.Drug -> Dest.Drug` (source on left)
81
82	### 5. Always use qualified names for species and reaction-scoped parameters
83
84	Always reference species and reaction-scoped parameters by their qualified name. If any of the names are not valid MATLAB variable names, surround them with square brackets before building the qualified name.
85
86	- Species: `CompartmentName.SpeciesName` (e.g., `Central.Drug`, `Peripheral.[Drug-bound]`)
87	- Reaction-scoped parameters: `ReactionName.ParameterName` (e.g., `Elimination.ke`)
88
89	Qualification is always exactly one level deep — the immediate parent
90	compartment only. Multi-level paths like `Body.Central.Drug` are invalid
91	in reaction strings. This is never ambiguous because compartment names must
92	be globally unique across the entire model (SimBiology enforces this
93	regardless of nesting depth). So `Central.Drug` is always sufficient.
94
95	Compartment naming rules:
96	- Names must be unique across the entire model — no two compartments can
97	share a name even at different nesting levels
98	- If you need hierarchical naming, use underscores: `Body_Central` (not
99	nested compartments both named `Central`)
100	- Species names must be unique within a compartment but can repeat across
101	different compartments (disambiguated by `Compartment.Species`)
102
103	### 6. Use modern property names (`Value`, `Units`, `Constant`)
104
105	SimBiology objects (species, compartments, parameters) share a unified
106	property interface. Always us

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matlab-build-simbiology-model

815stars105forks

View on GitHub

How to install matlab-build-simbiology-model?

matlab/matlab-agentic-toolkit/matlab-build-simbiology-model

$npx -y skills add matlab/matlab-agentic-toolkit --skill matlab-build-simbiology-model

Installs into the current project.

Summary

Build, modify, and diagram SimBiology models — API reference, helper functions, and layout patterns. Use when constructing or editing models programmatically or visually.

Files · 1

View on GitHub

SKILL.md

1	# Build SimBiology Models
2
3	API reference, helper functions, and patterns for building, modifying, and
4	diagramming SimBiology models. Works in all MATLAB environments (desktop,
5	headless, batch, remote). Diagram/layout features require the Model Builder
6	app and are activated only when the user requests visual output.
7
8	## When to Use
9
10	- Building or modifying SimBiology models (compartments, species, reactions, parameters, rules, events, doses, observables, variants)
11	- Opening, saving, or loading models in the Model Builder / Analyzer apps
12	- Designing or adjusting diagram layouts
13	- Keywords: "build", "create", "modify", "add compartment/species/reaction", "diagram", "layout"
14
15	## When NOT to Use
16
17	- Simulation and analysis (use `matlab-simulate-simbiology-model`)
18	- Parameter fitting, population modeling, NCA (use `matlab-fit-simbiology-model`)
19
20	## Must-Follow Rules
21
22	### 1. Add helper scripts to the MATLAB path first
23
24	Run at the start of every session:
25	```matlab
26	addpath(fullfile('<WORKSPACE_ROOT>', '.claude', 'skills', 'matlab-build-simbiology-model', 'scripts'));
27	disp('Helper scripts added to path.')
28	```
29
30	### 2. Only open the Builder when needed
31
32	Do NOT open the Model Builder by default. Open it when:
33	- The user explicitly requests a diagram, layout, or visual
34	- The input is an `.sbproj` file — use `loadViaBuilder` to preserve
35	diagram layout/styling (`sbioloadproject` loses this data)
36
37	A model is fully functional without a diagram — it can be simulated,
38	fitted, and analyzed using only the model object on `sbioroot`.
39
40	### 3. Model construction uses standard SimBiology API
41
42	Build models using `addcompartment`, `addspecies`, `addreaction`, etc.
43	directly. This works in all environments: desktop, headless, batch, remote.
44
45	```matlab
46	model = sbiomodel('MyModel'); disp(model.uuid)
47	comp = addcompartment(model, 'Central', 1);
48	addspecies(comp, 'Drug', 100);
49	addparameter(model, 'ke', 0.1);
50	rx = addreaction(model, 'Central.Drug -> null');
51	kl = addkineticlaw(rx, 'MassAction');
52	kl.ParameterVariableNames = {'ke'};
53	```
54
55	For standard PK models (1- or 2-compartment with standard dosing and
56	elimination), use `references/pk-library-guidance.md` as the reference for
57	correct parameterization, naming, and rules. When no diagram is needed,
58	call `PKModelDesign` directly. When the user requests a diagram, construct
59	the model manually following the same PK library conventions but use
60	`addAndPositionCompartment` for layout control (see Rule 8b).
61
62	### 4. Write reactions in the biological forward direction
63
64	The diagram renders arrows on products and plain lines on reactants
65	(based on the forward direction of the reaction string). Writing a reaction
66	backwards produces incorrect arrows even if the kinetics are equivalent.
67
68	```matlab
69	% CORRECT — L and R get plain lines, C gets an arrow
70	addreaction(model, 'cell.L + cell.R <-> cell.C');
71
72	% WRONG — same kinetics but L and R get arrows (they're "products" now)
73	addreaction(model, 'cell.C <-> cell.L + cell.R');
74	```
75
76	Guidelines:
77	- Binding: write `A + B -> C` (substrates on left, complex on right)
78	- Degradation/elimination: write `Drug -> null` (not `null -> Drug`)
79	- Synthesis: write `null -> mRNA` (not `mRNA -> null`)
80	- Transport: write `Source.Drug -> Dest.Drug` (source on left)
81
82	### 5. Always use qualified names for species and reaction-scoped parameters
83
84	Always reference species and reaction-scoped parameters by their qualified name. If any of the names are not valid MATLAB variable names, surround them with square brackets before building the qualified name.
85
86	- Species: `CompartmentName.SpeciesName` (e.g., `Central.Drug`, `Peripheral.[Drug-bound]`)
87	- Reaction-scoped parameters: `ReactionName.ParameterName` (e.g., `Elimination.ke`)
88
89	Qualification is always exactly one level deep — the immediate parent
90	compartment only. Multi-level paths like `Body.Central.Drug` are invalid
91	in reaction strings. This is never ambiguous because compartment names must
92	be globally unique across the entire model (SimBiology enforces this
93	regardless of nesting depth). So `Central.Drug` is always sufficient.
94
95	Compartment naming rules:
96	- Names must be unique across the entire model — no two compartments can
97	share a name even at different nesting levels
98	- If you need hierarchical naming, use underscores: `Body_Central` (not
99	nested compartments both named `Central`)
100	- Species names must be unique within a compartment but can repeat across
101	different compartments (disambiguated by `Compartment.Species`)
102
103	### 6. Use modern property names (`Value`, `Units`, `Constant`)
104
105	SimBiology objects (species, compartments, parameters) share a unified
106	property interface. Always us

People who liked this also viewed

6 picks

Type