nb WIP

notebook.ipynb

@@ -1,18 +1,252 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "1928a2a5",
+   "metadata": {
+    "tags": []
+   },
+   "source": [
+    "### _warlock_ vignette"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4450695b",
+   "metadata": {},
+   "source": [
+    "The following notebook demonstrates workflow execution with a simple set of simulation parameters."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "89b9ced8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "from IPython.display import Image"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0a4b57d1",
+   "metadata": {},
+   "source": [
+    "## Prepare files for the workflow"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9f7ed01b",
+   "metadata": {},
+   "source": [
+    "In the example below we will prepare a configuration file varying one specific parameter: deme carrying capacity.\n",
+    "\n",
+    "All dependencies have been already installed while building a container for this notebook."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "63403efe",
+   "metadata": {},
+   "source": [
+    "Compile _demon_"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
+   "id": "90a4c46c",
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "%%bash\n",
+    "\n",
+    "g++ resources/demon_model/src/demon.cpp -o resources/demon_model/bin/demon -I/srv/conda/envs/notebook/include/ -lm"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "cb706573",
+   "metadata": {},
+   "source": [
+    "Prepare configfile for the workflow (based on a template)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3aa3277f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with open(\"tests/binder/config-template.yml\") as f:\n",
+    "    configlines = f.read().splitlines()\n",
+    "\n",
+    "configlines[17] = \"workflow_repo_path: \\\"\" + os.getcwd() + \"\\\"\"\n",
+    "\n",
+    "outdir = os.path.join(\n",
+    "    os.getcwd(),\n",
+    "    \"tests\",\n",
+    "    \"binder\",\n",
+    "    \"output\"\n",
+    ")\n",
+    "\n",
+    "configlines[22] = \"workflow_analysis_outdir: \\\"\" + outdir + \"\\\"\"\n",
+    "\n",
+    "with open(\"tests/binder/config.yml\", \"w\") as f:\n",
+    "    for line in configlines:\n",
+    "        f.write(line + os.linesep)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5298889a",
+   "metadata": {},
+   "source": [
+    "## Execute the workflow"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "59834894",
+   "metadata": {},
+   "source": [
+    "We trigger the snakemake workflow via our main bash script (~5min runtime)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6f9a1e6a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%bash\n",
+    "\n",
+    "time \\\n",
+    "bash warlock.sh \\\n",
+    "--configfile tests/binder/config.yml \\\n",
+    "--environment local \\\n",
+    "--cores 3"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b6b91cc3",
+   "metadata": {},
+   "source": [
+    "## Example post-processing"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "90a8045e",
+   "metadata": {},
+   "source": [
+    "In order to quickly glance over simulations' results we shall utilize a [previously developed package](https://github.com/robjohnnoble/demonanalysis) (which is outside the scope if this repository)."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "7317904e",
+   "metadata": {},
+   "source": [
+    "### Inspect the summary plots:"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "01c72cb9",
+   "metadata": {},
+   "source": [
+    "$\\log_2$[deme carrying capacity] = 8"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2b0f8217",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Image(filename=\"tests/binder/output/simulations/00000000/summary.png\") "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "518dde2c",
+   "metadata": {},
+   "source": [
+    "$\\log_2$[deme carrying capacity] = 9"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0e4a74b6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Image(filename=\"tests/binder/output/simulations/00000001/summary.png\") "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "123529a1",
+   "metadata": {},
+   "source": [
+    "$\\log_2$[deme carrying capacity] = 10"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "018e1056",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Image(filename=\"tests/binder/output/simulations/00000002/summary.png\") "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "dfdd7551",
+   "metadata": {},
+   "source": [
+    "**The simple example above highlights that the higher the deme carrying capacity is the sooner the tumor evolves within the population.**"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "782ed072",
+   "metadata": {},
+   "source": [
+    "---"
+   ]
   }
  ],
  "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.0"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 5
 }