remove experimental parameters from simulations nb

notebooks/simulation_validation.ipynb

@@ -176,31 +176,6 @@
     "    os.makedirs(csv_output_dir)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "035de633",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "\n",
-    "# libs = [\"lib_1\", \"lib_2\"]  # distinct libraries of gene\n",
-    "\n",
-    "# variants_per_lib = variants_per_lib_genelength_scalar * genelength\n",
-    "\n",
-    "# bottlenecks = {\n",
-    "#     name : variants_per_lib * scalar\n",
-    "#     for name, scalar in bottleneck_variants_per_lib_scalar.items()\n",
-    "# }\n",
-    "\n",
-    "# fitting_params = {\n",
-    "#     \"iterations_per_step\": [iterations_per_step], # default 20000\n",
-    "#     \"scale_coeff_lasso_shift\": scale_coeff_lasso_shift, # the sweep of lasso coefficient params\n",
-    "#     \"init_beta_naught\" : [init_beta_naught], # We've found that we need to start with a higher beta_naught to get the model to converge correctly,\n",
-    "#     \"scale_coeff_ridge_beta\" : [scale_coeff_ridge_beta], # the sweep of ridge coefficient params\n",
-    "# }\n"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "cbc66da4",