Updated submodule notebooks with titles and learning objectives

ncgr · Sep 6, 2024 · d953cf0 · d953cf0
1 parent dbd7b26
commit d953cf0
Show file tree

Hide file tree

Showing 5 changed files with 71 additions and 40 deletions.
diff --git a/module_notebooks/01-intro-to-pangenomics.ipynb b/module_notebooks/01-intro-to-pangenomics.ipynb
@@ -4,15 +4,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Typical Notebook Section Structure\n",
+    "# Pangenomics\n",
     "--------------------------------------------"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# [Title of Module]"
+    "# Intro to Graphical Pangenomics"
    ]
   },
   {
@@ -29,11 +29,14 @@
    "metadata": {},
    "source": [
     "## Learning Objectives\n",
-    "+ Learning Objective 1\n",
-    "+ Learning Objective 2\n",
-    "    - Learning Objective 2.1\n",
-    "    - Learning Objective 2.2\n",
-    "+ Learning Objective 3"
+    "+ Understand what pangenomic data is\n",
+    "+ Understand what pangenome graphs are\n",
+    "+ Overview of different types of pangenome graphs and discussion of their pros/cons\n",
+    "+ Overview of pipeline that will be used in module\n",
+    "    - Build graphs\n",
+    "    - Map reads\n",
+    "    - Call variants\n",
+    "    - Visualize graphs and mapped reads3"
    ]
   },
   {
@@ -713,7 +716,15 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "kernelspec": {
+   "display_name": "",
+   "name": ""
+  },
+  "language_info": {
+   "name": ""
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 4
 }
diff --git a/module_notebooks/02-building-graphs-with-pggb.ipynb b/module_notebooks/02-building-graphs-with-pggb.ipynb
@@ -4,15 +4,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Typical Notebook Section Structure\n",
+    "# Pangenomics\n",
     "--------------------------------------------"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# [Title of Module]"
+    "# Building graphs with PGGB"
    ]
   },
   {
@@ -29,11 +29,8 @@
    "metadata": {},
    "source": [
     "## Learning Objectives\n",
-    "+ Learning Objective 1\n",
-    "+ Learning Objective 2\n",
-    "    - Learning Objective 2.1\n",
-    "    - Learning Objective 2.2\n",
-    "+ Learning Objective 3"
+    "+ Understanding what types of graphs PGGB builds and their pros/cons\n",
+    "+ Learn how to build graphs with PGGB"
    ]
   },
   {
@@ -713,7 +710,15 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "kernelspec": {
+   "display_name": "",
+   "name": ""
+  },
+  "language_info": {
+   "name": ""
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 4
 }
diff --git a/module_notebooks/03-indexing-graphs-with-vg.ipynb b/module_notebooks/03-indexing-graphs-with-vg.ipynb
@@ -4,15 +4,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Typical Notebook Section Structure\n",
+    "# Pangenomics\n",
     "--------------------------------------------"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# [Title of Module]"
+    "# Indexing graphs with vg"
    ]
   },
   {
@@ -29,11 +29,8 @@
    "metadata": {},
    "source": [
     "## Learning Objectives\n",
-    "+ Learning Objective 1\n",
-    "+ Learning Objective 2\n",
-    "    - Learning Objective 2.1\n",
-    "    - Learning Objective 2.2\n",
-    "+ Learning Objective 3"
+    "+ Understanding of vg and the different things it can be used for\n",
+    "+ Learn how to index graphs using vg "
    ]
   },
   {
@@ -713,7 +710,15 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "kernelspec": {
+   "display_name": "",
+   "name": ""
+  },
+  "language_info": {
+   "name": ""
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 4
 }
diff --git a/module_notebooks/04-read-mapping-with-vg.ipynb b/module_notebooks/04-read-mapping-with-vg.ipynb
@@ -4,15 +4,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Typical Notebook Section Structure\n",
+    "# Pangenomics\n",
     "--------------------------------------------"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# [Title of Module]"
+    "# Reading mapping with vg"
    ]
   },
   {
@@ -29,11 +29,8 @@
    "metadata": {},
    "source": [
     "## Learning Objectives\n",
-    "+ Learning Objective 1\n",
-    "+ Learning Objective 2\n",
-    "    - Learning Objective 2.1\n",
-    "    - Learning Objective 2.2\n",
-    "+ Learning Objective 3"
+    "+ Understanding the difference between read mapping with a reference versus a pangenome\n",
+    "+ Learn how to map reads to a pangenomic graph using vg"
    ]
   },
   {
@@ -713,7 +710,15 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "kernelspec": {
+   "display_name": "",
+   "name": ""
+  },
+  "language_info": {
+   "name": ""
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 4
 }
diff --git a/module_notebooks/05-variant-calling-with-vg.ipynb b/module_notebooks/05-variant-calling-with-vg.ipynb
@@ -4,15 +4,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Typical Notebook Section Structure\n",
+    "# Pangenomics\n",
     "--------------------------------------------"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# [Title of Module]"
+    "# Variant calling with vg"
    ]
   },
   {
@@ -29,11 +29,8 @@
    "metadata": {},
    "source": [
     "## Learning Objectives\n",
-    "+ Learning Objective 1\n",
-    "+ Learning Objective 2\n",
-    "    - Learning Objective 2.1\n",
-    "    - Learning Objective 2.2\n",
-    "+ Learning Objective 3"
+    "+ Understanding different types of variants and our ability to call them with different types of reads and pangenomic graphs\n",
+    "+ Learn how to call and interpret variants with vg"
    ]
   },
   {
@@ -713,7 +710,15 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "kernelspec": {
+   "display_name": "",
+   "name": ""
+  },
+  "language_info": {
+   "name": ""
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 4
 }