📝 add links to used data for examples (download link on website)

Author: enryH

1_3_seaborn.ipynb

@@ -10,29 +10,18 @@
     "- [website](https://seaborn.pydata.org/)"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {
-    "lines_to_next_cell": 2
-   },
-   "source": [
-    "## Recreating the Figure from the sulforaphane Paper"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "## Recreating the Figure from the sulforaphane Paper\n",
     "Uses the data from [PXD04621](data/README.md) - using simulated data which looks\n",
     "similar to the original data\n",
     "([Marshall et. al. 2023)](https://www.sciencedirect.com/science/article/pii/S1756464623002451)).\n",
-    "![figure_2](https://ars.els-cdn.com/content/image/1-s2.0-S1756464623002451-gr2.jpg)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
+    "- [fake_growth_data.csv](data/growth/fake_growth_data.csv)\n",
+    "\n",
+    "![figure_2](https://ars.els-cdn.com/content/image/1-s2.0-S1756464623002451-gr2.jpg)\n",
+    "\n",
     "Take a look at this picture - do you think it is simple or complicated?\n",
     "It is not trivial to recreate it in Python - but don't worry, we will guide through all steps and tricks on making an (almost) exact copy of that picture in this notebook (at least from our knowledge). Let's get started."
    ]
@@ -63,7 +52,6 @@
     "import matplotlib as mpl\n",
     "import matplotlib.lines as mlines\n",
     "import matplotlib.pyplot as plt\n",
-    "import numpy as np\n",
     "import pandas as pd\n",
     "import seaborn as sns\n",
     "from matplotlib.ticker import MultipleLocator\n",

1_3_seaborn.py

@@ -20,15 +20,13 @@
 
 # %% [markdown]
 # ## Recreating the Figure from the sulforaphane Paper
-
-
-# %% [markdown]
 # Uses the data from [PXD04621](data/README.md) - using simulated data which looks
 # similar to the original data
 # ([Marshall et. al. 2023)](https://www.sciencedirect.com/science/article/pii/S1756464623002451)).
+# - [fake_growth_data.csv](data/growth/fake_growth_data.csv)
+#
 # ![figure_2](https://ars.els-cdn.com/content/image/1-s2.0-S1756464623002451-gr2.jpg)
-
-# %% [markdown]
+#
 # Take a look at this picture - do you think it is simple or complicated?
 # It is not trivial to recreate it in Python - but don't worry, we will guide through all steps and tricks on making an (almost) exact copy of that picture in this notebook (at least from our knowledge). Let's get started.
 
@@ -45,7 +43,6 @@
 import matplotlib as mpl
 import matplotlib.lines as mlines
 import matplotlib.pyplot as plt
-import numpy as np
 import pandas as pd
 import seaborn as sns
 from matplotlib.ticker import MultipleLocator

data/README.md

@@ -25,3 +25,9 @@ to Caroline Jachmann for the great work assembling a peptide atlas with post tra
 modifications for ecoli:
 
 - [E. coli peptide atlas with phosphosites](https://www.uniprot.org/proteomes/UP000000625)
+
+## Files used in notebooks
+
+and hosted in the repository of the course.
+
+- [data/proteins/proteins.csv](proteins/proteins.csv)

exercises/CRISPRi/README.md

@@ -9,3 +9,10 @@ Nat Commun 15, 8985 (2024). [https://doi.org/10.1038/s41467-024-53381-4](https:/
 
 Direct data link: 
 [Source data](https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-024-53381-4/MediaObjects/41467_2024_53381_MOESM6_ESM.xlsx)
+
+## Files used in notebooks
+
+- [figure_2a.csv](figure_2a.csv)
+- [figure_2b.csv](figure_2b.csv)
+- [figure_2c.csv](figure_2c.csv)
+- [figure_2d.csv](figure_2d.csv)

exercises/CRISPRi/figure_2.ipynb

@@ -17,9 +17,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "lines_to_next_cell": 2
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import os\n",
@@ -41,6 +39,22 @@
     "IN_COLAB = \"COLAB_GPU\" in os.environ"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "d848d620",
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
+   "source": [
+    "## Setup\n",
+    "Let's make use of the files\n",
+    "\n",
+    "- [figure_2a.csv](figure_2a.csv)\n",
+    "- [figure_2b.csv](figure_2b.csv)\n",
+    "- [figure_2c.csv](figure_2c.csv)\n",
+    "- [figure_2d.csv](figure_2d.csv)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

exercises/CRISPRi/figure_2.py

@@ -41,6 +41,15 @@
 
 IN_COLAB = "COLAB_GPU" in os.environ
 
+# %% [markdown]
+# ## Setup
+# Let's make use of the files
+#
+# - [figure_2a.csv](figure_2a.csv)
+# - [figure_2b.csv](figure_2b.csv)
+# - [figure_2c.csv](figure_2c.csv)
+# - [figure_2d.csv](figure_2d.csv)
+
 
 # %%
 A_DATA_FILE = "figure_2a.csv"