Polished Example CRISPR notebook

pydna-group · Oct 4, 2024 · deccbc5 · deccbc5
1 parent 0b7c4a5
commit deccbc5
Showing 1 changed file with 27 additions and 8 deletions.
diff --git a/docs/notebooks/Example_CRISPR.ipynb b/docs/notebooks/Example_CRISPR.ipynb
@@ -4,11 +4,14 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# CRISPR-Cas9 Implementation with Oligonucleotide-based CRISPR-Cas9 toolbox for efficient engineering of Komagataella phaffii \n",
+    "# Implementation of Oligonucleotide-based CRISPR-Cas9 toolbox for efficient engineering of Komagataella phaffii \n",
     "\n",
     "\n",
     "In this example we wanted to give a real life intuition on how to use the module in practice. \n",
-    "For this purpose we have chosen to use the oligonucleotide-based CRISPR-Cas9 toolbox that i described here: \n",
+    "\n",
+    "For this purpose we have chosen to use the oligonucleotide-based CRISPR-Cas9 toolbox that i described \n",
+    "here by Strucko et al 2024, in the industrially relevant K. phaffi production organism: \n",
+    "\n",
     "https://academic.oup.com/femsyr/article/doi/10.1093/femsyr/foae026/7740463?login=false "
    ]
   },
@@ -33,19 +36,28 @@
    ],
    "source": [
     "from IPython.display import Image\n",
-    "Image(url=\"https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/femsyr/24/10.1093_femsyr_foae026/1/m_foae026fig3.jpeg?Expires=1730974846&Signature=iBKvkhkUn1823IljQ~1uFEnKO0VqWrwiXADvCwQLz6Yv8yDEAFkgt~tsLrXKFTmGYIq3ZINcj5a5yNgs4cP4NeCvRcQh7Ad~1ZejIwNrjqw51CJhGcZWPzz~NDr93QVLZZd2Re41cJNFKFmEu756KxrHQxwKTQe2QPMPfiKBvhvo8J28PERj3vNjZ3LQRsFp9qUPpdsZEyWIiNY92jsuy448YyuaGCgaC2ExGDLeuArTEJmq8gtb0QnTPV0dEdtoxIfZpgavdvO~QyqikjCLj6hebUYU1lH7StuS8oqCQE82CXO0IUcjYF6m2Lb0evXhqdLDQe90M-NrKjzNRmBA0A__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA\")\n"
+    "Image(url=\"https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/femsyr/24/10.1093_femsyr_foae026/1/m_foae026fig3.jpeg?Expires=1730974846&Signature=iBKvkhkUn1823IljQ~1uFEnKO0VqWrwiXADvCwQLz6Yv8yDEAFkgt~tsLrXKFTmGYIq3ZINcj5a5yNgs4cP4NeCvRcQh7Ad~1ZejIwNrjqw51CJhGcZWPzz~NDr93QVLZZd2Re41cJNFKFmEu756KxrHQxwKTQe2QPMPfiKBvhvo8J28PERj3vNjZ3LQRsFp9qUPpdsZEyWIiNY92jsuy448YyuaGCgaC2ExGDLeuArTEJmq8gtb0QnTPV0dEdtoxIfZpgavdvO~QyqikjCLj6hebUYU1lH7StuS8oqCQE82CXO0IUcjYF6m2Lb0evXhqdLDQe90M-NrKjzNRmBA0A__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Figure 1. oligo assisted repair in K. phaffi. "
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "\n",
-    "Basically we can make two cuts in the genome, and repair it with an oligo.\n",
+    "- Basically we can make two cuts in the genome, and repair it with an oligo (Figure 1A, 1B).\n",
     "\n",
-    "Let's see how this can be implemented in pydna\n",
     "\n",
-    "We can start by loading in our target. Here we have integrated LAC12 in our K. phaffi strain but want to knock it out. "
+    "- We can start by loading in our target. Here we have integrated LAC12 in our K. phaffi strain but want to knock it out. \n",
+    "\n",
+    "\n",
+    "- Let's see how this can be implemented in pydna\n"
    ]
   },
   {
@@ -65,7 +77,14 @@
    "source": [
     "#Install pydna for colab.\n",
     "%%capture\n",
-    "!pip install pydna"
+    "!pip install git+https://github.com/BjornFJohansson/pydna.git@dev_bjorn"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Import the gene we are going to work with"
    ]
   },
   {
@@ -188,7 +207,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The final gene would look like this\n"
+    "The final edit gene would look like this in a case of homologous recombination. \n"
    ]
   },
   {