2b:null 2c:["$","title",null,{"children":"Seashell patterns simulation 5 | Chris Viau | Observable"}] 31:T233e,preset = ({ // "activatorDiffusion":0,"activatorRemovalRate":0.0022,"activatorProductionRate":0.0378,"inhibitorDiffusion":0.45,"inhibitorRemovalRate":0.05,"substanceCDiffusion":0,"substanceCRemovalRate":0,"autocatalysisSaturation":0,"inhibitorConstant":0,"hormoneLife":0,"numExecutions":100,"numIterations":159,"numCells":100 // "activatorDiffusion":0,"activatorRemovalRate":0.0022,"activatorProductionRate":0.0378,"inhibitorDiffusion":0.45,"inhibitorRemovalRate":0.05,"substanceCDiffusion":0,"substanceCRemovalRate":0,"autocatalysisSaturation":0.02,"inhibitorConstant":0,"hormoneLife":0,"numExecutions":100,"numIterations":159,"numCells":100 // "activatorDiffusion":0.031,"activatorRemovalRate":0.06,"activatorProductionRate":0,"inhibitorDiffusion":0.4,"inhibitorRemovalRate":0.05,"substanceCDiffusion":0,"substanceCRemovalRate":0.0039,"autocatalysisSaturation":0.122,"inhibitorConstant":0.2822,"hormoneLife":0,"numExecutions":100,"numIterations":163,"numCells":100 // "activatorDiffusion":0.0061,"activatorRemovalRate":0.1089,"activatorProductionRate":0,"inhibitorDiffusion":0.45,"inhibitorRemovalRate":0.05,"substanceCDiffusion":0,"substanceCRemovalRate":0,"autocatalysisSaturation":0.162,"inhibitorConstant":0.2689,"hormoneLife":0,"numExecutions":100,"numIterations":101,"numCells":100 "activatorDiffusion":0.0203,"activatorRemovalRate":0.0022,"activatorProductionRate":0,"inhibitorDiffusion":0.223,"inhibitorRemovalRate":0.0003,"substanceCDiffusion":0,"substanceCRemovalRate":0,"autocatalysisSaturation":1,"inhibitorConstant":0.0289,"hormoneLife":0.349,"numExecutions":100,"numIterations":110,"numCells":100 // "activatorDiffusion":0.0048,"activatorRemovalRate":0.002,"activatorProductionRate":0,"inhibitorDiffusion":0.165,"inhibitorRemovalRate":0.001,"substanceCDiffusion":0,"substanceCRemovalRate":0,"autocatalysisSaturation":0,"inhibitorConstant":0,"hormoneLife":0.104,"numExecutions":100,"numIterations":92,"numCells":100 // activatorDiffusion: 0.0048, // activatorRemovalRate: 0.0802, // activatorProductionRate: 0, // inhibitorDiffusion: 0.0141, // inhibitorRemovalRate: 0.0198, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 1, // inhibitorConstant: 0.0061, // hormoneLife: 0.053, // numExecutions: 100, // numIterations: 13, // numCells: 100 // activatorDiffusion: 0.0084, // activatorRemovalRate: 0.0442, // activatorProductionRate: 0, // inhibitorDiffusion: 0, // inhibitorRemovalRate: 0.0102, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 1.5, // inhibitorConstant: 0.0609, // hormoneLife: 0.041, // numExecutions: 100, // numIterations: 29, // numCells: 100 // activatorDiffusion: 0.0161, // activatorRemovalRate: 0.029, // activatorProductionRate: 0, // inhibitorDiffusion: 0.0101, // inhibitorRemovalRate: 0.0069, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0, // inhibitorConstant: 0.0757, // hormoneLife: 0.086, // numExecutions: 100, // numIterations: 21, // numCells: 100 // activatorDiffusion: 0.0054, // activatorRemovalRate: 0.0113, // activatorProductionRate: 0, // inhibitorDiffusion: 0, // inhibitorRemovalRate: 0.0067, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0, // inhibitorConstant: 0.0441, // hormoneLife: 0, // numExecutions: 100, // numIterations: 21, // numCells: 100 // activatorDiffusion: 0.0012, // activatorRemovalRate: 0.0118, // activatorProductionRate: 0, // inhibitorDiffusion: 0, // inhibitorRemovalRate: 0.0033, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0, // inhibitorConstant: 0.1503, // hormoneLife: 0.021, // numExecutions: 150, // numIterations: 100, // numCells: 100 // activatorDiffusion: 0.0018, // activatorRemovalRate: 0.01112, // activatorProductionRate: 0, // inhibitorDiffusion: 0, // inhibitorRemovalRate: 0.0028, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0, // inhibitorConstant: 0.1322, // hormoneLife: 0.021, // numExecutions: 150, // numIterations: 100, // numCells: 100 // activatorDiffusion: 0.0005, // activatorRemovalRate: 0.007, // activatorProductionRate: 0, // inhibitorDiffusion: 0, // inhibitorRemovalRate: 0.0018, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0, // inhibitorConstant: 0.0405, // hormoneLife: 0.01, // numExecutions: 150, // numIterations: 140, // numCells: 50 // activatorDiffusion: 0.0315, // activatorRemovalRate: 0.0131, // activatorProductionRate: 0, // inhibitorDiffusion: 0.4059, // inhibitorRemovalRate: 0.0075, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0, // inhibitorConstant: 0, // hormoneLife: 0.17, // numExecutions: 100, // numIterations: 12, // numCells: 100 // activatorDiffusion: 0.0012, // activatorRemovalRate: 0.0048, // activatorProductionRate: 0, // inhibitorDiffusion: 0.0007, // inhibitorRemovalRate: 0.0034, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0, // inhibitorConstant: 0.15, // hormoneLife: 0.007, // numExecutions: 100, // numIterations: 170, // numCells: 50 // activatorDiffusion: 0, // activatorRemovalRate: 0.029, // activatorProductionRate: 0, // inhibitorDiffusion: 0.0015, // inhibitorRemovalRate: 0.0081, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0.023, // inhibitorConstant: 0, // hormoneLife: 0, // numExecutions: 100, // numIterations: 75, // numCells: 50 // activatorDiffusion: 0, // activatorRemovalRate: 0.0509, // activatorProductionRate: 0, // inhibitorDiffusion: 0.0073, // inhibitorRemovalRate: 0.0159, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0, // inhibitorConstant: 0, // hormoneLife: 0, // numExecutions: 100, // numIterations: 16, // numCells: 50 // activatorDiffusion: 0.01, // activatorRemovalRate: 0.02, // activatorProductionRate: 0.001, // inhibitorDiffusion: 0.4, // inhibitorRemovalRate: 0.03, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0, // inhibitorConstant: 0, // hormoneLife: 0, // numExecutions: 100, // numIterations: 20, // numCells: 100 // activatorDiffusion: 0.015, // activatorRemovalRate: 0.08, // activatorProductionRate: 0.1, // inhibitorDiffusion: 0.01, // inhibitorRemovalRate: 0.014, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0.25, // inhibitorConstant: 0.05, // hormoneLife: 0.11, // numExecutions: 100, // numIterations: 12, // numCells: 100 // activatorDiffusion: 0.04, // activatorRemovalRate: 0.1, // activatorProductionRate: 0.001, // inhibitorDiffusion: 0.4, // inhibitorRemovalRate: 0.03, // substanceCDiffusion: 0, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0, // inhibitorConstant: 0, // hormoneLife: 0, // numExecutions: 60, // numIterations: 20, // numCells: 100 // activatorDiffusion: 0.01, // Diffusion of the activator // activatorRemovalRate: 0.02, // Removal rate of the activator // activatorProductionRate: 0.001, // Activator-independent activator production rate // inhibitorDiffusion: 0.4, // Diffusion of the inhibitor // inhibitorRemovalRate: 0.03, // Removal rate of the inhibitor // substanceCRemovalRate: 0, // autocatalysisSaturation: 0, // inhibitorConstant: 0, // hormoneLife: 0, // numExecutions: 60, // Number of displays // numIterations: 20, // number of iterations between the displays // numCells: 100 // number of cells // activatorDiffusion: 0.004, // activatorRemovalRate: 0.0015, // activatorProductionRate: 0.0001, // inhibitorDiffusion: 0.4, // inhibitorRemovalRate: 0.0025, // substanceCRemovalRate: 0, // autocatalysisSaturation: 0, // inhibitorConstant: 0, // hormoneLife: 0, // numExecutions: 50, // numIterations: 200, // numCells: 12 // activatorDiffusion: 0.003, // activatorRemovalRate: 0.002, // activatorProductionRate: 0.05, // inhibitorDiffusion: 0.4, // inhibitorRemovalRate: 0.003, // substanceCDiffusion: 0.001, // substanceCRemovalRate: 0.0001, // autocatalysisSaturation: 0, // inhibitorConstant: 0, // hormoneLife: 0, // numExecutions: 100, // numIterations: 500, // numCells: 12 // activatorDiffusion: 0.005, // activatorRemovalRate: 0.004, // activatorProductionRate: 0.05, // inhibitorDiffusion: 0.4, // inhibitorRemovalRate: 0.006, // substanceCDiffusion: 0.003, // substanceCRemovalRate: 0.0002, // autocatalysisSaturation: 0, // inhibitorConstant: 0, // hormoneLife: 0, // numExecutions: 100, // numIterations: 400, // numCells: 50 })32:Tdf6,function* computeConcentrations( { numExecutions, numIterations, numCells, activatorDiffusion, activatorRemovalRate, activatorProductionRate, inhibitorDiffusion, inhibitorRemovalRate, substanceCDiffusion, substanceCRemovalRate, autocatalysisSaturation, hormoneLife, inhibitorConstant, boundary = "tight" }, { activatorX, inhibitorX, substanceCX, sourceDensity, values } ) { const dac = 1 - activatorRemovalRate - 2 * activatorDiffusion; let dbc = 1 - inhibitorRemovalRate - 2 * inhibitorDiffusion; let hormoneConcentration = 0.5; let lifeOfInhibitor = 0; for (let i = 0; i <= numExecutions; i++) { for (let j = 0; j <= numIterations; j++) { let activatorLeftCell = activatorX[numCells], inhibitorLeftCell = inhibitorX[numCells], substanceCLeftCell = substanceCX[numCells]; activatorX[numCells + 1] = activatorX[1]; inhibitorX[numCells + 1] = inhibitorX[1]; substanceCX[numCells + 1] = substanceCX[1]; let bsa = 0; for (let k = 0; k <= numCells; k++) { const activatorConcentration = activatorX[k], inhibitorConcentration = inhibitorX[k], substanceCConcentration = substanceCX[k]; const saturatingSelfReinforcement = sourceDensity[k] * ((activatorConcentration * activatorConcentration) / (1 + autocatalysisSaturation * activatorConcentration * activatorConcentration) + 0.0000001); const activatorExchangeWithNeighbor = activatorDiffusion * (activatorLeftCell + activatorX[k + 1]) + saturatingSelfReinforcement / (inhibitorConstant + inhibitorConcentration); const inhibitorExchangeWithNeighbor = inhibitorDiffusion * (inhibitorLeftCell + inhibitorX[k + 1]) + saturatingSelfReinforcement; activatorX[k] = activatorConcentration * dac + activatorExchangeWithNeighbor; inhibitorX[k] = inhibitorConcentration * dbc + inhibitorExchangeWithNeighbor; bsa = bsa + hormoneLife * activatorConcentration; if (substanceCRemovalRate > 0) { substanceCX[k] = substanceCConcentration + substanceCRemovalRate * activatorConcentration - substanceCRemovalRate * substanceCConcentration + substanceCDiffusion * (substanceCLeftCell - substanceCConcentration + (substanceCX[k + 1] - substanceCConcentration)); } activatorLeftCell = activatorConcentration; inhibitorLeftCell = inhibitorConcentration; substanceCLeftCell = substanceCConcentration; } hormoneConcentration = hormoneConcentration * (1 - hormoneLife) + bsa / numCells; lifeOfInhibitor = inhibitorRemovalRate / hormoneConcentration; dbc = 1 - 2 * inhibitorDiffusion - lifeOfInhibitor; } for (let k = 0; k <= numCells; k++) { const concentration = activatorX[k] - inhibitorX[k]; // if (concentration < extent[0]) extent[0] = concentration; // else if (concentration > extent[1]) extent[1] = concentration; const normalized = (concentration - visConfig.concentrationMin) / (visConfig.concentrationMax - visConfig.concentrationMin); const clamped = Math.min(Math.max(normalized, 0), 1); values[k] = clamped } yield { i, activatorX, inhibitorX, substanceCX, values }; } return true; }33:[] 2f:{"id":"3b139d29ff07d97d","slug":"seashell-patterns-simulation-5","title":"Seashell patterns simulation 5","thumbnail":"8eb72432f49fa0dffcaab6353dad076ea00a14c1634e45d4652608a7e2d71a0b","access_level":"public","create_time":"$D2018-11-09T11:40:40.008Z","update_time":"$D2020-10-09T03:33:30.637Z","view_time":null,"first_public_time":"$D2018-11-23T15:25:29.674Z","fork":{"id":"cc84d8a4b9cf6eb4","slug":"seashell-patterns-simulation-4","title":"Seashell patterns simulation","owner":{"id":"ec5efd42ce7e8331","login":"biovisualize","name":"Chris Viau"}},"stars":1,"starred":false,"owner":{"type":"team","id":"ec5efd42ce7e8331","login":"biovisualize","name":"Chris Viau","avatar_url":"https://avatars-next.observableusercontent.com/65bb5f5e54396fa26f909d2d00260f5710d56692cc2360f902c4d61182af1022","tier":"starter_2024"},"version":817,"publish_version":817,"role":null,"authored":false,"authors":[{"type":"individual","id":"9f1f6ac72dad100b","login":"biovisualize","name":"Chris Viau","avatar_url":"https://avatars-next.observableusercontent.com/65bb5f5e54396fa26f909d2d00260f5710d56692cc2360f902c4d61182af1022","tier":null}],"members":[{"type":"individual","id":"9f1f6ac72dad100b","login":"biovisualize","name":"Chris Viau","avatar_url":"https://avatars-next.observableusercontent.com/65bb5f5e54396fa26f909d2d00260f5710d56692cc2360f902c4d61182af1022","tier":null,"role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"subscribed":null,"forks":1,"collection":null,"type":"notebook","body":{"title":"Seashell patterns simulation 5","cells":[{"id":0,"value":"md`# Seashell patterns simulation 5`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":21,"value":"renderSimulationTexture = {\n const cellWidth = config.width / simulationConfig.numCells;\n const cellHeight = config.height / simulationConfig.numExecutions;\n\n const container = html`

`;\n\n const textureCanvas = container.querySelector(\".texture\");\n const textureCtx = textureCanvas.getContext(\"2d\");\n textureCanvas.width = config.width;\n textureCanvas.height = config.height;\n\n const simulationGenerator = simulate(simulationConfig);\n\n for (const simulationValues of simulationGenerator) {\n renderRow({\n i: simulationValues.i,\n numCells: simulationConfig.numCells,\n cellWidth,\n cellHeight,\n values: simulationValues.values,\n ctx: textureCtx\n });\n }\n\n return container;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":553,"value":"viewof simulationConfig = formFactory(preset, {\n activatorDiffusion: { min: 0, max: 0.05, step: 0.0001 },\n activatorRemovalRate: { min: 0, max: 1, step: 0.0001 },\n activatorProductionRate: { min: 0, max: 1, step: 0.0001 },\n inhibitorDiffusion: { min: 0, max: 0.45, step: 0.0001 },\n inhibitorRemovalRate: { min: 0, max: 0.05, step: 0.0001 },\n substanceCDiffusion: { min: 0, max: 0.05, step: 0.0001 },\n substanceCRemovalRate: { min: 0, max: 0.05, step: 0.0001 },\n autocatalysisSaturation: { min: 0, max: 1, step: 0.001 },\n inhibitorConstant: { min: 0, max: 1, step: 0.0001 },\n hormoneLife: { min: 0, max: 1, step: 0.001 },\n numExecutions: { min: 1, max: 150, step: 1 },\n numIterations: { min: 1, max: 1000, step: 1 },\n numCells: { min: 1, max: 150, step: 1 }\n})","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":445,"value":"serialized = JSON.stringify(simulationConfig)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":442,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":18,"value":"viewof visConfig = formFactory(\n { concentrationMin: -0.2, concentrationMax: 1.2 },\n {\n concentrationMin: { min: -10, max: 10, step: 0.01 },\n concentrationMax: { min: -10, max: 10, step: 0.01 }\n }\n)","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":4,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":10,"value":"function simulate(config) {\n const { numCells, numExecutions, activatorRemovalRate } = config;\n const activatorX = [],\n inhibitorX = [],\n substanceCX = [],\n sourceDensity = [],\n values = [];\n\n // ----------- Initial conditions --------------------------\n const rndLUT = [0, 2, 3, 5, 7, 11, 13, 16, 19, 26, 31, 34, 39, 41, 45, 47, 51, 52, 56, 57, 58, 61, 63, 65, 67, 69, 73, 79, 83, 85, 87, 94, 95, 99]\n for (let k = 0; k <= numCells; k++) {\n const isRandomlyActivated = rndLUT.indexOf(k) > -1;\n sourceDensity[k] = activatorRemovalRate * (0.99 + 0.02 * Math.random());\n activatorX[k] = isRandomlyActivated ? 1 : 0.3;\n inhibitorX[k] = 1;\n substanceCX[k] = 0;\n values[k] = 0;\n }\n\n return computeConcentrations(config, {\n activatorX,\n inhibitorX,\n substanceCX,\n sourceDensity,\n values\n });\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":49,"value":"function renderRow({\n i,\n numCells,\n cellWidth,\n cellHeight,\n values,\n ctx\n}) {\n const imageData = ctx.getImageData(\n 0,\n i * cellHeight,\n config.width,\n cellHeight\n );\n\n const buf = new ArrayBuffer(imageData.data.length);\n const buf8 = new Uint8ClampedArray(buf);\n const colorData = new Uint32Array(buf);\n for (let k = 0; k <= numCells; k++) {\n let color = values[k] * 255;\n for (let l = 0; l <= cellWidth; l++) {\n for (let m = 0; m <= cellHeight; m++) {\n colorData[m * config.width + k * cellWidth + l] =\n (color << 24) | // alpha\n (0 << 16) | // blue\n (0 << 8) | // green\n 0; // red\n }\n }\n }\n imageData.data.set(buf8);\n ctx.putImageData(imageData, 0, i * cellHeight);\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":429,"value":"formFactory = function(items, formConfig) {\n const div = html``;\n\n const inputs = [];\n for (const key in items) {\n const input = inputFactory(\n { label: key, value: items[key] },\n formConfig[key]\n );\n inputs.push(div.appendChild(input));\n }\n\n div.oninput = () => {\n div.value = {};\n inputs.forEach(input => {\n div.value[input.className] = input.value;\n });\n };\n\n div.oninput();\n\n return div;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":425,"value":"inputFactory = function(config, options) {\n const container = html`\n \n \n \n
\n `;\n\n const range = container.querySelector(\"[type=range]\");\n const number = container.querySelector(\"[type=number]\");\n const label = container.querySelector(\"label\");\n\n if (options) {\n Object.assign(range, options);\n }\n\n label.innerText = config.label;\n container.className = config.label;\n container.value = range.value = number.value = config.value;\n\n range.addEventListener(\n \"input\",\n () => (number.value = container.value = range.valueAsNumber)\n );\n number.addEventListener(\n \"input\",\n () => (range.value = container.value = number.valueAsNumber)\n );\n\n return container;\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":402,"value":"config = {\n return {\n height: 300,\n width: 300\n };\n}","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"},{"id":202,"value":"style = html`\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined"}],"files":"$W33","stdlib":"1","titling":"auto"}} 30:"$2f:body"