RohanMehta/ OpenChemicalSystems

Model, stochastically simulate, and visualize arbitrary open chemical systems using a Petri Net framework

Contributed by: Rohan Mehta

Installation Instructions

To install this paclet in your Wolfram Language environment, evaluate this code:
PacletInstall["RohanMehta/OpenChemicalSystems"]

To load the code after installation, evaluate this code:
Needs["RohanMehta`OpenChemicalSystems`"]

Examples

Basic Examples

Generate a Petri Net for the Beaverator.

In[1]:=

$beaverator = InterpretationBox[FrameBox[TagBox[TooltipBox[PaneBox[GridBox[List[List[GraphicsBox[List[Thickness[0.0025`], List[FaceForm[List[RGBColor[0.9607843137254902`, 0.5058823529411764`, 0.19607843137254902`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3]]], List[List[List[205.`, 22.863691329956055`], List[205.`, 212.31669425964355`], List[246.01799774169922`, 235.99870109558105`], List[369.0710144042969`, 307.0436840057373`], List[369.0710144042969`, 117.59068870544434`], List[205.`, 22.863691329956055`]], List[List[30.928985595703125`, 307.0436840057373`], List[153.98200225830078`, 235.99870109558105`], List[195.`, 212.31669425964355`], List[195.`, 22.863691329956055`], List[30.928985595703125`, 117.59068870544434`], List[30.928985595703125`, 307.0436840057373`]], List[List[200.`, 410.42970085144043`], List[364.0710144042969`, 315.7036876678467`], List[241.01799774169922`, 244.65868949890137`], List[200.`, 220.97669792175293`], List[158.98200225830078`, 244.65868949890137`], List[35.928985595703125`, 315.7036876678467`], List[200.`, 410.42970085144043`]], List[List[376.5710144042969`, 320.03370475769043`], List[202.5`, 420.53370475769043`], List[200.95300006866455`, 421.42667961120605`], List[199.04699993133545`, 421.42667961120605`], List[197.5`, 420.53370475769043`], List[23.428985595703125`, 320.03370475769043`], List[21.882003784179688`, 319.1406993865967`], List[20.928985595703125`, 317.4896984100342`], List[20.928985595703125`, 315.7036876678467`], List[20.928985595703125`, 114.70369529724121`], List[20.928985595703125`, 112.91769218444824`], List[21.882003784179688`, 111.26669120788574`], List[23.428985595703125`, 110.37369346618652`], List[197.5`, 9.87369155883789`], List[198.27300024032593`, 9.426692008972168`], List[199.13700008392334`, 9.203690528869629`], List[200.`, 9.203690528869629`], List[200.86299991607666`, 9.203690528869629`], List[201.72699999809265`, 9.426692008972168`], List[202.5`, 9.87369155883789`], List[376.5710144042969`, 110.37369346618652`], List[378.1179962158203`, 111.26669120788574`], List[379.0710144042969`, 112.91769218444824`], List[379.0710144042969`, 114.70369529724121`], List[379.0710144042969`, 315.7036876678467`], List[379.0710144042969`, 317.4896984100342`], List[378.1179962158203`, 319.1406993865967`], List[376.5710144042969`, 320.03370475769043`]]]]], List[FaceForm[List[RGBColor[0.5529411764705883`, 0.6745098039215687`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[44.92900085449219`, 282.59088134765625`], List[181.00001525878906`, 204.0298843383789`], List[181.00001525878906`, 46.90887451171875`], List[44.92900085449219`, 125.46986389160156`], List[44.92900085449219`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6627450980392157`, 0.803921568627451`, 0.5686274509803921`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[355.0710144042969`, 282.59088134765625`], List[355.0710144042969`, 125.46986389160156`], List[219.`, 46.90887451171875`], List[219.`, 204.0298843383789`], List[355.0710144042969`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6901960784313725`, 0.5882352941176471`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[200.`, 394.0606994628906`], List[336.0710144042969`, 315.4997024536133`], List[200.`, 236.93968200683594`], List[63.928985595703125`, 315.4997024536133`], List[200.`, 394.0606994628906`]]]]]], List[Rule[BaselinePosition, Scaled[0.15`]], Rule[ImageSize, 10], Rule[ImageSize, 15]]], StyleBox[RowBox[List["generatePetriNet", " "]], Rule[ShowAutoStyles, False], Rule[ShowStringCharacters, False], Rule[FontSize, Times[0.9`, Inherited]], Rule[FontColor, GrayLevel[0.1`]]]]], Rule[GridBoxSpacings, List[Rule["Columns", List[List[0.25`]]]]]], Rule[Alignment, List[Left, Baseline]], Rule[BaselinePosition, Baseline], Rule[FrameMargins, List[List[3, 0], List[0, 0]]], Rule[BaseStyle, List[Rule[LineSpacing, List[0, 0]], Rule[LineBreakWithin, False]]]], RowBox[List["PacletSymbol", "[", RowBox[List["\"RohanMehta/OpenChemicalSystems\"", ",", "\"generatePetriNet\""]], "]"]], Rule[TooltipStyle, List[Rule[ShowAutoStyles, True], Rule[ShowStringCharacters, True]]]], Function[Annotation[Slot[1], Style[Defer[PacletSymbol["RohanMehta/OpenChemicalSystems", "generatePetriNet"]], Rule[ShowStringCharacters, True]], "Tooltip"]]], Rule[Background, RGBColor[0.968`, 0.976`, 0.984`]], Rule[BaselinePosition, Baseline], Rule[DefaultBaseStyle, List[]], Rule[FrameMargins, List[List[0, 0], List[1, 1]]], Rule[FrameStyle, RGBColor[0.831`, 0.847`, 0.85`]], Rule[RoundingRadius, 4]], PacletSymbol["RohanMehta/OpenChemicalSystems", "generatePetriNet"], Rule[Selectable, False], Rule[SelectWithContents, True], Rule[BoxID, "PacletSymbolBox"]][<| rxn1 -> {{X, X, Y}, {X, X, X}}, rxn2 -> {{X}, {Y}}, rxn3 -> {{X}, {}}, rxn4 -> {{}, {X}}|>]$

Out[1]=

Initialize it with certain initial conditions (i.e., concentrations and rate constants).

In[2]:=

$beaverator = InterpretationBox[FrameBox[TagBox[TooltipBox[PaneBox[GridBox[List[List[GraphicsBox[List[Thickness[0.0025`], List[FaceForm[List[RGBColor[0.9607843137254902`, 0.5058823529411764`, 0.19607843137254902`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3]]], List[List[List[205.`, 22.863691329956055`], List[205.`, 212.31669425964355`], List[246.01799774169922`, 235.99870109558105`], List[369.0710144042969`, 307.0436840057373`], List[369.0710144042969`, 117.59068870544434`], List[205.`, 22.863691329956055`]], List[List[30.928985595703125`, 307.0436840057373`], List[153.98200225830078`, 235.99870109558105`], List[195.`, 212.31669425964355`], List[195.`, 22.863691329956055`], List[30.928985595703125`, 117.59068870544434`], List[30.928985595703125`, 307.0436840057373`]], List[List[200.`, 410.42970085144043`], List[364.0710144042969`, 315.7036876678467`], List[241.01799774169922`, 244.65868949890137`], List[200.`, 220.97669792175293`], List[158.98200225830078`, 244.65868949890137`], List[35.928985595703125`, 315.7036876678467`], List[200.`, 410.42970085144043`]], List[List[376.5710144042969`, 320.03370475769043`], List[202.5`, 420.53370475769043`], List[200.95300006866455`, 421.42667961120605`], List[199.04699993133545`, 421.42667961120605`], List[197.5`, 420.53370475769043`], List[23.428985595703125`, 320.03370475769043`], List[21.882003784179688`, 319.1406993865967`], List[20.928985595703125`, 317.4896984100342`], List[20.928985595703125`, 315.7036876678467`], List[20.928985595703125`, 114.70369529724121`], List[20.928985595703125`, 112.91769218444824`], List[21.882003784179688`, 111.26669120788574`], List[23.428985595703125`, 110.37369346618652`], List[197.5`, 9.87369155883789`], List[198.27300024032593`, 9.426692008972168`], List[199.13700008392334`, 9.203690528869629`], List[200.`, 9.203690528869629`], List[200.86299991607666`, 9.203690528869629`], List[201.72699999809265`, 9.426692008972168`], List[202.5`, 9.87369155883789`], List[376.5710144042969`, 110.37369346618652`], List[378.1179962158203`, 111.26669120788574`], List[379.0710144042969`, 112.91769218444824`], List[379.0710144042969`, 114.70369529724121`], List[379.0710144042969`, 315.7036876678467`], List[379.0710144042969`, 317.4896984100342`], List[378.1179962158203`, 319.1406993865967`], List[376.5710144042969`, 320.03370475769043`]]]]], List[FaceForm[List[RGBColor[0.5529411764705883`, 0.6745098039215687`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[44.92900085449219`, 282.59088134765625`], List[181.00001525878906`, 204.0298843383789`], List[181.00001525878906`, 46.90887451171875`], List[44.92900085449219`, 125.46986389160156`], List[44.92900085449219`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6627450980392157`, 0.803921568627451`, 0.5686274509803921`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[355.0710144042969`, 282.59088134765625`], List[355.0710144042969`, 125.46986389160156`], List[219.`, 46.90887451171875`], List[219.`, 204.0298843383789`], List[355.0710144042969`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6901960784313725`, 0.5882352941176471`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[200.`, 394.0606994628906`], List[336.0710144042969`, 315.4997024536133`], List[200.`, 236.93968200683594`], List[63.928985595703125`, 315.4997024536133`], List[200.`, 394.0606994628906`]]]]]], List[Rule[BaselinePosition, Scaled[0.15`]], Rule[ImageSize, 10], Rule[ImageSize, 15]]], StyleBox[RowBox[List["initPetriNet", " "]], Rule[ShowAutoStyles, False], Rule[ShowStringCharacters, False], Rule[FontSize, Times[0.9`, Inherited]], Rule[FontColor, GrayLevel[0.1`]]]]], Rule[GridBoxSpacings, List[Rule["Columns", List[List[0.25`]]]]]], Rule[Alignment, List[Left, Baseline]], Rule[BaselinePosition, Baseline], Rule[FrameMargins, List[List[3, 0], List[0, 0]]], Rule[BaseStyle, List[Rule[LineSpacing, List[0, 0]], Rule[LineBreakWithin, False]]]], RowBox[List["PacletSymbol", "[", RowBox[List["\"RohanMehta/OpenChemicalSystems\"", ",", "\"initPetriNet\""]], "]"]], Rule[TooltipStyle, List[Rule[ShowAutoStyles, True], Rule[ShowStringCharacters, True]]]], Function[Annotation[Slot[1], Style[Defer[PacletSymbol["RohanMehta/OpenChemicalSystems", "initPetriNet"]], Rule[ShowStringCharacters, True]], "Tooltip"]]], Rule[Background, RGBColor[0.968`, 0.976`, 0.984`]], Rule[BaselinePosition, Baseline], Rule[DefaultBaseStyle, List[]], Rule[FrameMargins, List[List[0, 0], List[1, 1]]], Rule[FrameStyle, RGBColor[0.831`, 0.847`, 0.85`]], Rule[RoundingRadius, 4]], PacletSymbol["RohanMehta/OpenChemicalSystems", "initPetriNet"], Rule[Selectable, False], Rule[SelectWithContents, True], Rule[BoxID, "PacletSymbolBox"]][ beaverator, {X -> 1, Y -> 1}, {rxn1 -> 1, rxn2 -> 5, rxn3 -> 1, rxn4 -> 1}]$

Out[2]=

Stochastically evolve the Beaverator for 10 seconds.

In[3]:=

$nets = InterpretationBox[FrameBox[TagBox[TooltipBox[PaneBox[GridBox[List[List[GraphicsBox[List[Thickness[0.0025`], List[FaceForm[List[RGBColor[0.9607843137254902`, 0.5058823529411764`, 0.19607843137254902`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]], List[List[0, 2, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3], List[0, 1, 0], List[1, 3, 3]]], List[List[List[205.`, 22.863691329956055`], List[205.`, 212.31669425964355`], List[246.01799774169922`, 235.99870109558105`], List[369.0710144042969`, 307.0436840057373`], List[369.0710144042969`, 117.59068870544434`], List[205.`, 22.863691329956055`]], List[List[30.928985595703125`, 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0]]], List[List[List[44.92900085449219`, 282.59088134765625`], List[181.00001525878906`, 204.0298843383789`], List[181.00001525878906`, 46.90887451171875`], List[44.92900085449219`, 125.46986389160156`], List[44.92900085449219`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6627450980392157`, 0.803921568627451`, 0.5686274509803921`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[355.0710144042969`, 282.59088134765625`], List[355.0710144042969`, 125.46986389160156`], List[219.`, 46.90887451171875`], List[219.`, 204.0298843383789`], List[355.0710144042969`, 282.59088134765625`]]]]], List[FaceForm[List[RGBColor[0.6901960784313725`, 0.5882352941176471`, 0.8117647058823529`], Opacity[1.`]]], FilledCurveBox[List[List[List[0, 2, 0], List[0, 1, 0], List[0, 1, 0], List[0, 1, 0]]], List[List[List[200.`, 394.0606994628906`], List[336.0710144042969`, 315.4997024536133`], List[200.`, 236.93968200683594`], List[63.928985595703125`, 315.4997024536133`], List[200.`, 394.0606994628906`]]]]]], List[Rule[BaselinePosition, Scaled[0.15`]], Rule[ImageSize, 10], Rule[ImageSize, 15]]], StyleBox[RowBox[List["spnUpdate", " "]], Rule[ShowAutoStyles, False], Rule[ShowStringCharacters, False], Rule[FontSize, Times[0.9`, Inherited]], Rule[FontColor, GrayLevel[0.1`]]]]], Rule[GridBoxSpacings, List[Rule["Columns", List[List[0.25`]]]]]], Rule[Alignment, List[Left, Baseline]], Rule[BaselinePosition, Baseline], Rule[FrameMargins, List[List[3, 0], List[0, 0]]], Rule[BaseStyle, List[Rule[LineSpacing, List[0, 0]], Rule[LineBreakWithin, False]]]], RowBox[List["PacletSymbol", "[", RowBox[List["\"RohanMehta/OpenChemicalSystems\"", ",", "\"spnUpdate\""]], "]"]], Rule[TooltipStyle, List[Rule[ShowAutoStyles, True], Rule[ShowStringCharacters, True]]]], Function[Annotation[Slot[1], Style[Defer[PacletSymbol["RohanMehta/OpenChemicalSystems", "spnUpdate"]], Rule[ShowStringCharacters, True]], "Tooltip"]]], Rule[Background, RGBColor[0.968`, 0.976`, 0.984`]], Rule[BaselinePosition, Baseline], Rule[DefaultBaseStyle, List[]], Rule[FrameMargins, List[List[0, 0], List[1, 1]]], Rule[FrameStyle, RGBColor[0.831`, 0.847`, 0.85`]], Rule[RoundingRadius, 4]], PacletSymbol["RohanMehta/OpenChemicalSystems", "spnUpdate"], Rule[Selectable, False], Rule[SelectWithContents, True], Rule[BoxID, "PacletSymbolBox"]][beaverator, 100];$

Visualize the corresponding kinetics.

In[4]:=

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Out[4]=

As well as phase space.

In[5]:=

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Out[5]=

Scope

You can generate complex phase space plots, too, like the following which highlights elementary reactions.

In[6]:=

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Out[6]=

And also plot the smaller oscillatory motifs within these phase spaces.

In[7]:=

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Out[7]=

Check out the rest of the functions for lower-level control of the Petri Net, as well as more visualizations!

Publisher

Rohan Mehta

Compatibility

Wolfram Language Version 13.1

Version History

1.0.0 – 16 February 2023

License Information

MIT License

Paclet Source

Definition Notebook »