STRIDES · zbyosufzai · May 2, 2025 · Apr 29, 2025 · Apr 29, 2025 · Apr 29, 2025
diff --git a/docs/compute-engine-idle-shutdown.md b/docs/compute-engine-idle-shutdown.md
@@ -2,7 +2,9 @@
 This guide walks you through how to automatically configure auto-shutdown capabilities on any GCP virtual machine. Put simply, you only need to add a startup script that shuts down the VM after a specified period of inactivity. This safeguard helps ensure you don't forget to shut off your VM over the weekend, and accidentally burn through a big chunk of your budget.
 
 ## 1. Configure auto-shutdown on Vertex AI Notebook Instance
-When starting a new VertexAI notebook, you can enable idle shutdown by simply clicking a box and specifying the amount of time you want your machine idle before it shuts down. See our [VertexAI startup guide](/docs/vertexai.md) to see how to enable this important feature. 
+When starting a new VertexAI notebook, you can enable idle shutdown by navigating to **Advanced options** and checking the box for enabling auto-shutdown. You must specify the amount of time you want your machine idle before it shuts down. See our [VertexAI startup guide](/docs/vertexai.md) to see how to enable this important feature. 
+
+![image showing idle shutdown selection](/images/images_for_creating_GCP_instances/6_instance_idle_shutdown.png) 
 
 For additional details on the other settings for user managed notebooks, see [this VertexAI Quickstart](https://cloud.google.com/vertex-ai/docs/workbench/user-managed/create-user-managed-notebooks-instance-console-quickstart).
 

diff --git a/docs/idle-shutdown.sh b/docs/idle-shutdown.sh
@@ -4,7 +4,7 @@
 # NOTE: requires `bc`, eg, sudo apt-get install bc
 # Modified from https://stackoverflow.com/questions/30556920/how-can-i-automatically-kill-idle-gce-instances-based-on-cpu-usage
 
-sudo apt-get install bc 
+sudo apt-get install bc -y
 
 # This is the CPU usage threshold. If activity falls below 10% for the specified time below, the VM shutsdown.
 # If you want the shutdown to be more sensitive, you can set this higher, so that a smaller drop in CPU activity will cause shutdown.

diff --git a/docs/protein_setup.md b/docs/protein_setup.md
@@ -1,7 +1,21 @@
-!curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh
+# Setting Up the Environment to Run AlphaFold on Vertex AI
 
-!bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge
+## 1. Install Mamba (via Mambaforge)
+Use the following commands to install Mambaforge:
 
-!../../mambaforge/bin/mamba install -y -c conda-forge pandas-gbq pandas
+```bash
+# Download the Mambaforge installer
+curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh
 
+# Install Mambaforge to your home directory
+bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge
+
+# Use mamba to install required Python packages
+$HOME/mambaforge/bin/mamba install -y -c conda-forge pandas-gbq pandas
+```
+## 2. Install Google Colab Package
+Use the following command to install google-colab: 
+
+```bash
 pip install google-colab
+```
diff --git a/docs/vertexai.md b/docs/vertexai.md
@@ -1,9 +1,9 @@
 # Using VertexAI Notebooks
 
 ### 1. Spin up an Instance
-1. Start by clicking the `hamburger menu` (the three horizontal lines in the top left of your console). Go to `Artificial Intelligence > Vertex AI > Workbench`. 
+1. Start by clicking the `hamburger menu` (the three horizontal lines in the top left of your console). Go to `Vertex AI > Workbench`. 
 
-![screenshot showing how to select Vertex AI workbench](/images/images_for_creating_GCP_instances/1_select_vertexAI.png)
+![screenshot showing how to select Vertex AI workbench](../images/1_select_vertexAI.jpeg)
 
 2. If not already selected, click **Instances**, then **Instances**
 3. Click **+ Create New**

diff --git a/images/10_chatbot_grounding.jpeg b/images/10_chatbot_grounding.jpeg
diff --git a/images/12_chatbot_grounding.jpeg b/images/12_chatbot_grounding.jpeg
diff --git a/images/13_chatbot_grounding.jpeg b/images/13_chatbot_grounding.jpeg
diff --git a/images/14_chatbot_grounding.jpeg b/images/14_chatbot_grounding.jpeg
diff --git a/images/1_select_vertexAI.jpeg b/images/1_select_vertexAI.jpeg
diff --git a/images/7_chatbot_grounding.jpeg b/images/7_chatbot_grounding.jpeg
diff --git a/images/8_chatbot_grounding.jpeg b/images/8_chatbot_grounding.jpeg
diff --git a/images/9_chatbot_grounding.jpeg b/images/9_chatbot_grounding.jpeg
diff --git a/images/agent_builder1.jpeg b/images/agent_builder1.jpeg
diff --git a/images/agent_builder2.jpeg b/images/agent_builder2.jpeg
diff --git a/images/create-prompt.jpeg b/images/create-prompt.jpeg
diff --git a/images/vertex-ai-create-prompt.jpeg b/images/vertex-ai-create-prompt.jpeg
diff --git a/notebooks/DL-gwas-gcp-example/1-d10-run-first.ipynb b/notebooks/DL-gwas-gcp-example/1-d10-run-first.ipynb
@@ -34,7 +34,7 @@
    "metadata": {},
    "source": [
     "## Prerequisites\n",
-    "See the [README](/notebooks/DL-gwas-gcp-example/README.md) in this directory. "
+    "See the [README](./README.md) in this directory. "
    ]
   },
   {

diff --git a/notebooks/GWASCoatColor/GWAS_coat_color.ipynb b/notebooks/GWASCoatColor/GWAS_coat_color.ipynb
@@ -81,7 +81,16 @@
    "metadata": {},
    "source": [
     "#### Install dependencies\n",
-    "Here we install mamba, which is faster than conda, but it can be tricky to add to path in a Sagemaker notebook so we just call the whole path. You could also skip this install and just use conda since that is preinstalled in the kernel."
+    "\n",
+    "The dependencies required to run this tutorial are `plink` and `vcftools`. A few different installation methods are given below. \n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "aa39cb82-ad03-4427-8173-2d5738e3eff5",
+   "metadata": {},
+   "source": [
+    "##### Method 1: Install with Mamba "
    ]
   },
   {
@@ -91,6 +100,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "#If you don't have mamba installed, you can install it with the following command: \n",
     "! curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh\n",
     "! bash Mambaforge-$(uname)-$(uname -m).sh -b -p $HOME/mambaforge"
    ]
@@ -102,7 +112,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#add to your path\n",
+    "#add mamba to your path\n",
     "import os\n",
     "os.environ[\"PATH\"] += os.pathsep + os.environ[\"HOME\"]+\"/mambaforge/bin\""
    ]
@@ -114,9 +124,52 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "#Install dependencies with mamba\n",
     "! mamba install -y -c bioconda plink vcftools"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "720c6daa-4ee0-4db1-a94f-1f2b01e2f9f3",
+   "metadata": {},
+   "source": [
+    "##### Method 2: Install manually"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1718f0a0-00b8-4d8b-8049-1bf705d1a8da",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#Plink installation \n",
+    "\n",
+    "# Please run these steps in the terminal\n",
+    "# 1. Download the PLINK 1.9 binary (Linux 64-bit)\n",
+    "! wget http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20210606.zip\n",
+    "\n",
+    "# 2. Unzip the archive\n",
+    "! unzip plink_linux_x86_64_20210606.zip\n",
+    "\n",
+    "# 5. Move it to /usr/local/bin for global access (requires sudo)\n",
+    "! sudo mv plink /usr/local/bin/\n",
+    "\n",
+    "# 6. Check that it's installed correctly\n",
+    "! plink --version"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "891ccfbd-472d-4ebc-b326-6a81e19c2e6c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# VCFTools Installation\n",
+    "! sudo apt-get -y install vcftools"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "3de2fc4c",

diff --git a/notebooks/GenAI/GCP_AI_Applications.ipynb b/notebooks/GenAI/GCP_AI_Applications.ipynb
@@ -79,7 +79,7 @@
    "metadata": {},
    "source": [
     "This tutorial will cost up to ~$6, pricing is based on the cost of AI Applications and Jupyter notebooks.\n",
-    "For this tutorial we used a n2-standard-2 instance to run the python commands and created a App [Google Cloud Pricing Calculator](https://cloud.google.com/products/calculator?hl=en)."
+    "For this tutorial we used a n2-standard-2 instance to run the python commands and create an App. For more detailed information on how to calculate the price of various services on GCP, please access the [Google Cloud Pricing Calculator](https://cloud.google.com/products/calculator?hl=en)."
    ]
   },
   {
@@ -200,7 +200,7 @@
     "    doc_name=i.split(r'/')[-1]\n",
     "    x = requests.get(i)\n",
     "    doc = x.text\n",
-    "    upload_blob_from_memory(bucket, doc, {doc_name})"
+    "    upload_blob_from_memory(bucket, doc, doc_name)"
    ]
   },
   {
@@ -220,7 +220,7 @@
     "- Chatbots\n",
     "- Search engine\n",
     "- Recommendations bot\n",
-    "- Agent development\n",
+    "- Conversational Agents\n",
     "\n",
     "For this tutorial we are creating a GenAI agent to help guide our chatbot in certain situations. Start by searching up **'AI Applications'** on the console. Then once you are on the page shown below click **'CREATE APP'**."
    ]
@@ -238,31 +238,31 @@
    "id": "e6906e34-31a0-4e88-85e9-62abee5ed6cd",
    "metadata": {},
    "source": [
-    "Click **'SELECT'** for the app named **Agent**."
+    "Click **'SELECT'** for the app named **Conversational Agent**."
    ]
   },
   {
    "cell_type": "markdown",
    "id": "39beb2ac-c377-4201-9973-5fdb738159d8",
    "metadata": {},
    "source": [
-    "![agent_builder1](../../images/agent_builder1.png)"
+    "![agent_builder1](../../images/agent_builder1.jepg)"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "8d32f806-cef5-401b-be7b-b60ff2686a76",
    "metadata": {},
    "source": [
-    "Give your agent a name, select your region, then click **'CREATE'**."
+    "Select **Build your own**. Give your agent a name, select your region, select **Playbook** and the conversation start method, then click **'CREATE'**."
    ]
   },
   {
    "cell_type": "markdown",
    "id": "0b59fa7c-b082-4372-9d9d-c299565f67dd",
    "metadata": {},
    "source": [
-    "![agent_builder2](../../images/agent_builder2.png)"
+    "![agent_builder2](../../images/agent_builder2.jpeg)"
    ]
   },
   {