Process tutorial notebooks

neuromatch · Jul 1, 2024 · 25eec7c · 25eec7c
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diff --git a/tutorials/README.md b/tutorials/README.md
@@ -50,7 +50,7 @@ Slides: [Intro](https://mfr.ca-1.osf.io/render?url=https://osf.io/gsuhq/?direct%
 
 [YouTube Playlist](https://www.youtube.com/playlist?list=PLkBQOLLbi18O2wSDMRLrZNyKBuRwvoE6K)
 
-Slides: [Intro](https://mfr.ca-1.osf.io/render?url=https://osf.io/g8jzu/?direct%26mode=render%26action=download%26mode=render) | [Tutorials](https://mfr.ca-1.osf.io/render?url=https://osf.io/uwn2g/?direct%26mode=render%26action=download%26mode=render)
+Slides: [Intro](https://mfr.ca-1.osf.io/render?url=https://osf.io/g8jzu/?direct%26mode=render%26action=download%26mode=render) | [Tutorials](https://mfr.ca-1.osf.io/render?url=https://osf.io/uwn2g/?direct%26mode=render%26action=download%26mode=render) | [Bonus](https://mfr.ca-1.osf.io/render?url=https://osf.io/8fx23/?direct%26mode=render%26action=download%26mode=render)
 
 |   | Run | Run | View |
 | - | --- | --- | ---- |
@@ -59,6 +59,7 @@ Slides: [Intro](https://mfr.ca-1.osf.io/render?url=https://osf.io/g8jzu/?direct%
 | Tutorial 2 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial2.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial2.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial2.ipynb?flush_cache=true) |
 | Tutorial 3 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial3.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial3.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial3.ipynb?flush_cache=true) |
 | Tutorial 4 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial4.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial4.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial4.ipynb?flush_cache=true) |
+| Tutorial 5 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial5.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial5.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial5.ipynb?flush_cache=true) |
 | Outro | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb?flush_cache=true) |
 
 

diff --git a/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/README.md b/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/README.md
@@ -9,6 +9,7 @@
 | Tutorial 2 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial2.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial2.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial2.ipynb?flush_cache=true) |
 | Tutorial 3 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial3.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial3.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial3.ipynb?flush_cache=true) |
 | Tutorial 4 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial4.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial4.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial4.ipynb?flush_cache=true) |
+| Tutorial 5 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial5.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial5.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/instructor/W1D3_Tutorial5.ipynb?flush_cache=true) |
 | Outro | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb?flush_cache=true) |
 
 
@@ -21,5 +22,6 @@
 | Tutorial 2 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial2.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial2.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial2.ipynb?flush_cache=true) |
 | Tutorial 3 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial3.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial3.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial3.ipynb?flush_cache=true) |
 | Tutorial 4 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial4.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial4.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial4.ipynb?flush_cache=true) |
+| Tutorial 5 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial5.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial5.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/student/W1D3_Tutorial5.ipynb?flush_cache=true) |
 | Outro | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/NeuroAI_Course/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/NeuroAI_Course/blob/main/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Outro.ipynb?flush_cache=true) |
 
diff --git a/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Tutorial1.ipynb b/tutorials/W1D3_ComparingArtificialAndBiologicalNetworks/W1D3_Tutorial1.ipynb
@@ -60,7 +60,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -103,7 +104,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -131,7 +133,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -158,7 +161,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -207,7 +211,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -224,7 +229,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -308,7 +314,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -671,7 +678,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -712,7 +720,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -741,7 +750,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -775,7 +785,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -828,7 +839,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -884,7 +896,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -936,7 +949,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -962,7 +976,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -998,7 +1013,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1029,7 +1045,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1064,7 +1081,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1080,7 +1098,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1094,7 +1113,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1129,7 +1149,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1166,7 +1187,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1184,7 +1206,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1238,7 +1261,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1272,7 +1296,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1285,7 +1310,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1308,7 +1334,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "execution": {}
+   },
    "outputs": [],
    "source": [
     "#to_remove explanation\n",
@@ -1342,7 +1370,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1355,7 +1384,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1378,7 +1408,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "execution": {}
+   },
    "outputs": [],
    "source": [
     "#to_remove explanation\n",
@@ -1405,7 +1437,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "execution": {}
+   },
    "outputs": [],
    "source": [
     "#to_remove explanation\n",
@@ -1421,7 +1455,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1471,7 +1506,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "execution": {}
+   },
    "outputs": [],
    "source": [
     "# Enable the custom widget manager in Colab.\n",
@@ -1486,7 +1523,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1610,7 +1648,8 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "cellView": "form"
+    "cellView": "form",
+    "execution": {}
    },
    "outputs": [],
    "source": [
@@ -1666,7 +1705,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.9.19"
   }
  },
  "nbformat": 4,