diff --git a/.gitpod.yml b/.gitpod.yml
index db47294..fff417a 100644
--- a/.gitpod.yml
+++ b/.gitpod.yml
@@ -11,7 +11,7 @@ tasks:
     init: |
       echo "Building development environment..."
       mamba env create -f environment.yml --prefix ./.warlock
-      bash prepare-environments.sh
+      bash -c 'CONDA_PREFIX="/workspace/warlock/.warlock" ./prepare-environments.sh'
       echo "Development environment ready!"
     # adjust PS1 + activate dev. env. + compile demon
     command: |
diff --git a/notebook.ipynb b/notebook.ipynb
deleted file mode 100644
index d6f9d88..0000000
--- a/notebook.ipynb
+++ /dev/null
@@ -1,292 +0,0 @@
-{
- "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": [
-    "%%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": "code",
-   "execution_count": null,
-   "id": "ecdd65e6",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%load_ext rpy2.ipython"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b02b223b",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%R\n",
-    "\n",
-    "library('demonanalysis')\n",
-    "\n",
-    "plot_all_images(\n",
-    "    path=\"tests/binder/output/simulations/00000000\",\n",
-    "    output_filename=\"summary\",\n",
-    "    output_dir=\"tests/binder/output/simulations/00000000\"\n",
-    ")\n",
-    "\n",
-    "plot_all_images(\n",
-    "    path=\"tests/binder/output/simulations/00000001\",\n",
-    "    output_filename=\"summary\",\n",
-    "    output_dir=\"tests/binder/output/simulations/00000001\"\n",
-    ")\n",
-    "\n",
-    "plot_all_images(\n",
-    "    path=\"tests/binder/output/simulations/00000002\",\n",
-    "    output_filename=\"summary\",\n",
-    "    output_dir=\"tests/binder/output/simulations/00000002\"\n",
-    ")"
-   ]
-  },
-  {
-   "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": {
-   "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": 5
-}