Removed class model - user now only interacts with cobra models v0.2.0

segrelab · Mar 13, 2019 · d47ca85 · d47ca85
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diff --git a/.ipynb_checkpoints/colony-checkpoint.ipynb b/.ipynb_checkpoints/colony-checkpoint.ipynb
diff --git a/.ipynb_checkpoints/evolution-checkpoint.ipynb b/.ipynb_checkpoints/evolution-checkpoint.ipynb
diff --git a/.ipynb_checkpoints/model_testing-checkpoint.ipynb b/.ipynb_checkpoints/model_testing-checkpoint.ipynb
diff --git a/.ipynb_checkpoints/serial_transfers-checkpoint.ipynb b/.ipynb_checkpoints/serial_transfers-checkpoint.ipynb
diff --git a/backup/comets (copy).py b/backup/comets (copy).py
diff --git a/src/comets.py → backup/comets.py b/src/comets.py → backup/comets.py
diff --git a/backup/comets_BACKUP.py b/backup/comets_BACKUP.py
diff --git a/batch.ipynb b/batch.ipynb
diff --git a/colony.ipynb b/colony.ipynb
@@ -0,0 +1,196 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Simulating the growth of a colony\n",
+    "\n",
+    "We demonstrate here a simple `COMETS` simulation with space, the growth of an *E. coli* colony using a 2D spatial lattice."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import comets as c\n",
+    "import os\n",
+    "import pandas as pd\n",
+    "pd.options.display.max_rows = 10"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "As usual, we first create a parameters object using the `params` class."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "my_params = c.params()\n",
+    "my_params.all_params['maxCycles'] = 300\n",
+    "my_params.all_params['writeBiomassLog'] = True"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We next load a layout for our simulation "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Academic license - for non-commercial use only\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "[[10.0, 10.0, 1e-07]]"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "my_layout = c.layout('test_colony/colony_layout')\n",
+    "my_layout.initial_pop"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "Running COMETS simulation ...\n",
+      "Done!\n"
+     ]
+    }
+   ],
+   "source": [
+    "# create comets object from the loaded parameters and layout \n",
+    "my_comets = c.comets(my_layout, my_params)\n",
+    "\n",
+    "# run comets simulation\n",
+    "my_comets.run()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can print the stderr and stdout, which are stored in the `run_errors` and `run_output` fields:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "STDERR empty.\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(my_comets.run_errors)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "And here is how our incipient *E. coli* colony looks like: "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "\n",
+    "biomass_END = np.zeros((my_layout.grid[0], my_layout.grid[1]))\n",
+    "\n",
+    "aux = my_comets.biomass.loc[my_comets.biomass['Cycle'] == 300]\n",
+    "for index, row in aux.iterrows():\n",
+    "    biomass_END[row['x'], row['y']] = row['biomass']"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<matplotlib.image.AxesImage at 0x7f201a255518>"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.cm, matplotlib.colors\n",
+    "import copy\n",
+    "\n",
+    "my_cmap = copy.copy(matplotlib.cm.get_cmap('PuBu')) # copy the default cmap\n",
+    "my_cmap.set_bad((0,0,0))\n",
+    "\n",
+    "plt.imshow(biomass_END, interpolation='nearest', \n",
+    "           norm=matplotlib.colors.LogNorm(), cmap=my_cmap)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.5.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}