chore: remove dangling cells

wilhelm-lab · Oct 15, 2024 · 4cb9d88 · 4cb9d88
1 parent 5c9f5d7
commit 4cb9d88
Showing 1 changed file with 1 addition and 67 deletions.
diff --git a/tutorials/Oktoberfest Tutorial Using Local Intensity Prediction.ipynb b/tutorials/Oktoberfest Tutorial Using Local Intensity Prediction.ipynb
@@ -114,72 +114,6 @@
     "## 3 - Running Oktoberfest"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "{\n",
-    "    \"type\": \"Rescoring\",\n",
-    "    \"tag\": \"\",\n",
-    "    \"output\": \"./out\",\n",
-    "    \"inputs\": {\n",
-    "        \"search_results\": \"./msms.txt\",\n",
-    "        \"search_results_type\": \"Maxquant\",\n",
-    "        \"spectra\": \"./\",\n",
-    "        \"spectra_type\": \"raw\",\n",
-    "        \"instrument_type\": \"QE\"\n",
-    "    },\n",
-    "    \"models\": {\n",
-    "        \"intensity\": \"baseline\",\n",
-    "        \"irt\": \"Prosit_2019_irt\"\n",
-    "    },\n",
-    "    \"prediction_server\": \"koina.wilhelmlab.org:443\",\n",
-    "    \"numThreads\": 1,\n",
-    "    \"dlomixInferenceBatchSize\": 1024,\n",
-    "    \"refinementLearningOptions\": {\n",
-    "        \"batchSize\": 1024,\n",
-    "        \"includeOriginalSequences\": false,\n",
-    "        \"improveFurther\": false,\n",
-    "        \"datasetFilteringOptions\": {\n",
-    "            \"searchEngineScoreThreshold\": 0,\n",
-    "            \"numDuplicates\": 100\n",
-    "        }\n",
-    "    },\n",
-    "    \"fdr_estimation_method\": \"mokapot\",\n",
-    "    \"allFeatures\": false,\n",
-    "    \"regressionMethod\": \"spline\",\n",
-    "    \"ssl\": true,\n",
-    "    \"thermoExe\": \"ThermoRawFileParser.exe\",\n",
-    "    \"massTolerance\": 20,\n",
-    "    \"unitMassTolerance\": \"ppm\",\n",
-    "    \"ce_alignment_options\": {\n",
-    "        \"ce_range\": [19,50],\n",
-    "        \"use_ransac_model\": false\n",
-    "    }\n",
-    "}"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "with open(\"./rescoring_config.json\", 'w') as f:\n",
-    "    json.dump(rescoring_config, f)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "run_job(\"./rescoring_config.json\")"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -223,7 +157,7 @@
     "    },\n",
     "    \"prediction_server\": \"koina.wilhelmlab.org:443\",\n",
     "    \"ssl\": True,\n",
-    "    \"thermoExe\": \"/opt/compomics/ThermoRawFileParser.exe\",  # ensure you point to the right location of the executable here!\n",
+    "    \"thermoExe\": \"ThermoRawFileParser.exe\",\n",
     "    \"massTolerance\": 20,\n",
     "    \"unitMassTolerance\": \"ppm\",\n",
     "    \"numThreads\": 1\n",