cacatoo

<html> <script src="../../dist/cacatoo.js"></script>  <script src="../../lib/all.js"></script>  <link rel="stylesheet" href="../../style/cacatoo.css">  <head> <title>Cacatoo examples</title> </head> <script> /*-----------------------Start user-defined code ---------------------*/ let sim; // Declare a variable named "sim" globally, so that we can access our cacatoo-simulation from wherever we need. let influx = 0.6 let init_uptake = 0.5 let upkeep = 0.4 let decay = 0.05 /** * function cacatoo() contains all the user-defined parts of a cacatoo-model. Configuration, update rules, what is displayed or plotted, etc. It's all here. */ function cacatoo() { /* 1. SETUP. First, set up a configuration-object. Here we define how large the grid is, how long will it run, what colours will the critters be, etc. */ let config = { title: "Crossfeeding (ODEs)", // The name of your cacatoo-simulation description: "", // And a description if you wish maxtime: 1000000, // How many time steps the model continues to run // (note, the onscreen FPS may drop below 60 fps when using fast mode, although many more timesteps may be handled per second) ncol: 64, // Number of columns (width of your grid) nrow: 64, // Number of rows (height of your grid) wrap: [false, false], // Wrapped boundary conditions? [COLS, ROWS] scale: 5, // Scale of the grid (nxn pixels per grid point) graph_interval: 5, graph_update: 5, statecolours: { 'species': { 1: 'yellow', 2: 'navy' } }, // Colours for each state. Background (0) defaults to black. } /* 1. SETUP. (continued) Now, let's use that configuration-object to generate a new Cacatoo simulation */ sim = new Simulation(config) // Initialise the Cacatoo simulation sim.makeGridmodel("cross") // Build a new Gridmodel within the simulation called "gol" (Game Of Life) sim.initialGrid(sim.cross, 'species', 1, 0.0, 2, 0.0) // Set half (50%) of the Gridmodel's grid points to 1 (alive) sim.createDisplay("cross", "species", "Crossfeeding cells") // Create a display so we can see our newly made gridmodel sim.createDisplay_continuous({model:"cross", property:"R", label:"Resource concentration", minval:0, maxval:100, fill:"viridis"}) sim.createDisplay_continuous({model:"cross", property:"bb1", label:"Building block 1 concentration", minval:0, maxval:100, fill:"viridis"}) sim.createDisplay_continuous({model:"cross", property:"bb2", label:"Building block 2 concentration", minval:0, maxval:100, fill:"viridis"}) // Define ODEs with some resource dynamics let resource_dynamics = function (i, u, k, d, r2b1, r2b2, bb2product) { return function (x, y) { let R = y[0] // external resources let I = y[1] // internal resources let B1 = y[2] // internal bb1 let B2 = y[3] // internal bb2 let P = y[4] // internal product let B1_e = y[5] // external bb1 let B2_e = y[6] // external bb2 return [ i - u * R - d * R, // y[0] is the external resource concentration u * R - d * I, // y[1] is the internal resource concentration 0.1 * u * B1_e + r2b1 * I - d * B1, // y[2] 0.1 * u * B2_e + r2b2 * I - d * B2, B1 * B2 * bb2product - d * P - k * P, -0.1 * u * B1_e - d * B1_e, -0.1 * u * B2_e - d * B2_e ] } } // Configuration object with initial states, parameters, and diffusion rates let ode_config = { ode_name: "resources", init_states: [1.0, 0, 0, 0, 0.5, 0, 0], // y[0] and y[1] parameters: [influx, 0.0, upkeep, decay, 0.0, 0.0, 0.1], // i,u,k diffusion_rates: [0.1, 0.0, 0.0, 0.0, 0.0, 0.05, 0.05], acceptable_error: 10 - 3 } // resources diffuse through exteral environment, but internal resources stay put // Attaches an ODE to all gridpoints with initial state = [0,0]. // If you want to access it by name, you can give a name as the final variable (here resources) sim.cross.attachODE(resource_dynamics, ode_config); for (let x = 0; x < sim.cross.nc; x++) for (let y = 0; y < sim.cross.nr; y++) if (y > sim.cross.nr / 2) { sim.cross.grid[x][y].species = 1 sim.cross.grid[x][y].resources.pars = [influx, init_uptake, upkeep, decay, 0.0, 0.1, 0.01] } else { sim.cross.grid[x][y].species = 2 sim.cross.grid[x][y].resources.pars = [influx, init_uptake, upkeep, decay, 0.1, 0.0, 0.01] } /* 2. DEFINING THE RULES. Below, the user defines the nextState function. This function will be applied for each grid point when we will update the grid later. */ sim.cross.nextState = function (x, y) { this.grid[x][y].resources.solveTimestep(1) // So, first we need to know how many cells are alive around a grid point let randomneigh = this.randomMoore8(this, x, y) // Then, let's see if this cell is dead or alive let state = this.grid[x][y].species; // Then, apply the rules of game of life shown above if (state == 0 && randomneigh.species != 0) { if (this.rng.genrand_real1() < randomneigh.resources.state[4]) { this.grid[x][y].species = randomneigh.species randomneigh.resources.state[4] = this.grid[x][y].resources.state[4] = randomneigh.resources.state[4] / 2 // divide product (e.g. "cell volume" between parent and offspring) this.grid[x][y].resources.state[1] = randomneigh.resources.state[1] // inherit internal metabolite concentration this.grid[x][y].resources.state[2] = randomneigh.resources.state[2] // inherit internal metabolite concentration this.grid[x][y].resources.state[3] = randomneigh.resources.state[3] // inherit internal metabolite concentration this.grid[x][y].resources.state[4] = randomneigh.resources.state[4] // inherit internal metabolite concentration if (this.grid[x][y].species == 1) this.grid[x][y].resources.pars = [influx, init_uptake, upkeep, decay, 0.0, 0.1, 0.1] if (this.grid[x][y].species == 2) this.grid[x][y].resources.pars = [influx, init_uptake, upkeep, decay, 0.1, 0.0, 0.1] } } else if (this.rng.genrand_real1() < 0.01 || this.grid[x][y].resources.state[4] < 0.001) { this.grid[x][y].species = 0 this.grid[x][y].resources.pars = [influx, 0.0, 0.0, decay, 0.0, 0.0, 0.0] this.grid[x][y].resources.state[0] += this.grid[x][y].resources.state[1] // Spill internal resources back into environment this.grid[x][y].resources.state[5] += this.grid[x][y].resources.state[2] // Spill internal resources back into environment this.grid[x][y].resources.state[6] += this.grid[x][y].resources.state[3] // Spill internal resources back into environment this.grid[x][y].resources.state[1] = 0.0 // no internal resources for an empty spot this.grid[x][y].resources.state[2] = 0.0 // no bbs for an empty spot this.grid[x][y].resources.state[3] = 0.0 // no bbs2 for an empty spot this.grid[x][y].resources.state[4] = 0.0 // no product for an empty spot } // Setting display colours for building block concentrations let bb1 = 5 * Math.max(0, this.grid[x][y].resources.state[5]) // Amount of resources from ODE state variable this.grid[x][y].bb1 = Math.min(Math.floor(bb1), 99) let bb2 = 5 * Math.max(0, this.grid[x][y].resources.state[6]) // Amount of resources from ODE state variable this.grid[x][y].bb2 = Math.min(Math.floor(bb2), 99) let R = 5 * Math.max(0, this.grid[x][y].resources.state[0]) // Amount of resources from ODE state variable this.grid[x][y].R = Math.min(Math.floor(R), 99) } /* 3. MAIN SIMULATION LOOP. Finally, uwe need to set the update-function, which is the mainwill be applied to the whole grid each time step. For now, all we will do is call "synchronous", which applies the next-state function shown above to each grid point. All cells are updated at the same time, rather than in turn (for this, use the function "asynchonous") */ sim.cross.update = function () { this.asynchronous() // Applied as many times as it can in 1/60th of a second this.diffuseODEstates() // Diffusion of external metabolites let sum_ext = sum_int = sum_b1 = sum_b2 = sum_product = sum_alive = sum_s1 = sum_s2 = sum_b1_e = sum_b2_e = 0 for (let x = 0; x < this.nc; x++) // x are columns for (let y = 0; y < this.nr; y++) // y are rows { sum_ext += this.grid[x][y].resources.state[0] sum_int += this.grid[x][y].resources.state[1] sum_b1 += this.grid[x][y].resources.state[2] sum_b2 += this.grid[x][y].resources.state[3] sum_b1_e += this.grid[x][y].resources.state[5] sum_b2_e += this.grid[x][y].resources.state[6] sum_product += this.grid[x][y].resources.state[4] if (this.grid[x][y].species > 0) sum_alive++ if (this.grid[x][y].species == 1) sum_s1++ if (this.grid[x][y].species == 2) sum_s2++ } sum_ext /= this.nc * this.nr sum_int /= this.nc * this.nr sum_b1 /= this.nc * this.nr sum_b2 /= this.nc * this.nr sum_b1_e /= this.nc * this.nr sum_b2_e /= this.nc * this.nr sum_product /= this.nc * this.nr this.plotArray(["Population size", "Species 1", "Species 2"], [sum_alive, sum_s1, sum_s2], ["black", "gold", "navy"], "Population sizes") this.plotArray(["Resources [external]", "Resources [internal]", "Building block 1", "Building block 2", "Product", "Building block 1 (ext)", "Building block 2 (ext)"], [sum_ext, sum_int, sum_b1, sum_b2, sum_product, sum_b1_e, sum_b2_e], ["turquoise", "gold", "blue", "#3333FF", "green"], "Metabolite concentrations") } /* OPTIONAL: Now that we have everything setup, we can also add some interactive elements (buttons or sliders). See cheater.html for more examples of this. */ sim.addButton("pause/continue", function () { sim.toggle_play() }) sim.addButton("step", function () { sim.step(); sim.display() }) sim.addButton("mix once", function () { sim.cross.perfectMix() }) // Add a button that calls function "perfectMix" in "model.cheater" sim.addButton("well-mix", function () { sim.toggle_mix() }) // Add a button that calls function "perfectMix" in "model.cheater" sim.start() } /*-------------------------End user-defined code ---------------------*/ </script> <body onload="cacatoo()"> <div class="header" id="header"> <h2>Cacatoo examples</h2> </div> <div class="content" id="canvas_holder"> </div> <div class="content" id="graph_holder"> </div> <div class="content" id="form_holder"></div> <div class="footer" id="footer"> </div> </body> </html>