2026 edition - update materials

_solved/00-jupyter_introduction.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "<p><font size=\"6\"><b>Jupyter notebook INTRODUCTION </b></font></p>\n",
     "\n",
-    "> *© 2025, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
+    "> *© 2026, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
     "\n",
     "---"
    ]
@@ -577,6 +577,7 @@
  ],
  "metadata": {
   "jupytext": {
+   "default_lexer": "ipython3",
    "formats": "ipynb,md:myst"
   },
   "kernelspec": {
@@ -594,7 +595,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.11"
   },
   "nav_menu": {},
   "toc": {

_solved/case1_bike_count.ipynb

@@ -8,7 +8,7 @@
    "source": [
     "<p><font size=\"6\"><b> CASE - Bike count data</b></font></p>\n",
     "\n",
-    "> *© 2025, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
+    "> *© 2026, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
     "\n",
     "---"
    ]
@@ -1322,6 +1322,7 @@
  "metadata": {
   "celltoolbar": "Nbtutor - export exercises",
   "jupytext": {
+   "default_lexer": "ipython3",
    "formats": "ipynb,md:myst"
   },
   "kernelspec": {
@@ -1339,7 +1340,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.11"
   },
   "nav_menu": {},
   "toc": {

_solved/case2_observations.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "<p><font size=\"6\"><b>CASE - Observation data</b></font></p>\n",
     "\n",
-    "> *© 2025, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
+    "> *© 2026, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
     "\n",
     "---"
    ]
@@ -1661,6 +1661,7 @@
  "metadata": {
   "celltoolbar": "Nbtutor - export exercises",
   "jupytext": {
+   "default_lexer": "ipython3",
    "formats": "ipynb,md:myst"
   },
   "kernelspec": {
@@ -1678,7 +1679,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.11"
   },
   "nav_menu": {},
   "toc": {

_solved/case3_bacterial_resistance_lab_experiment.ipynb

@@ -8,7 +8,7 @@
    "source": [
     "<p><font size=\"6\"><b>CASE - Bacterial resistance experiment</b></font></p>\n",
     "\n",
-    "> *© 2025, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
+    "> *© 2026, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
     "\n",
     "---"
    ]
@@ -17,7 +17,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In this case study, we will make use of the open data, affiliated to the following [journal article](http://rsbl.royalsocietypublishing.org/content/12/5/20160064):\n",
+    "In this case study, we will make use of the open data, affiliated to the following [journal article](https://royalsocietypublishing.org/rsbl/article/12/5/20160064/50398/Effects-of-antibiotic-resistance-alleles-on):\n",
     "\n",
     ">Arias-Sánchez FI, Hall A (2016) Effects of antibiotic resistance alleles on bacterial evolutionary responses to viral parasites. Biology Letters 12(5): 20160064. https://doi.org/10.1098/rsbl.2016.0064"
    ]
@@ -33,7 +33,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Check the full paper on the [web version](http://rsbl.royalsocietypublishing.org/content/12/5/20160064). The study handles:\n",
+    "Check the full paper on the [web version](https://royalsocietypublishing.org/rsbl/article/12/5/20160064/50398/Effects-of-antibiotic-resistance-alleles-on). The study handles:\n",
     "> Antibiotic resistance has wide-ranging effects on bacterial phenotypes and evolution. However, the influence of antibiotic resistance on bacterial responses to parasitic viruses remains unclear, despite the ubiquity of such viruses in nature and current interest in therapeutic applications. We experimentally investigated this by exposing various Escherichia coli genotypes, including eight antibiotic-resistant genotypes and a mutator, to different viruses (lytic bacteriophages). Across 960 populations, we measured changes in population density and sensitivity to viruses, and tested whether variation among bacterial genotypes was explained by their relative growth in the absence of parasites, or mutation rate towards phage resistance measured by fluctuation tests for each phage"
    ]
   },
@@ -540,9 +540,9 @@
     "tags": []
    },
    "source": [
-    "Check Figure 2 of the original journal paper in the 'correction' part of the <a href=\"http://rsbl.royalsocietypublishing.org/content/roybiolett/12/5/20160064.full.pdf\">pdf</a>:\n",
+    "Check Figure 2 in the results section of the original <a href=\"https://royalsocietypublishing.org/rsbl/article/12/5/20160064/50398/Effects-of-antibiotic-resistance-alleles-on#16147318\">paper</a>:\n",
     "\n",
-    "<img src=\"https://royalsocietypublishing.org/cms/attachment/eb511c57-4167-4575-b8b3-93fbcf728572/rsbl20160064f02.jpg\" width=\"500\">"
+    "<img src=\"../img/rsbl20160064f02.jpeg\" width=\"500\">"
    ]
   },
   {
@@ -710,6 +710,7 @@
  "metadata": {
   "celltoolbar": "Nbtutor - export exercises",
   "jupytext": {
+   "default_lexer": "ipython3",
    "formats": "ipynb,md:myst"
   },
   "kernelspec": {
@@ -727,7 +728,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.11"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

_solved/case4_air_quality_analysis.ipynb

@@ -8,7 +8,7 @@
    "source": [
     "<p><font size=\"6\"><b> CASE - air quality data of European monitoring stations (AirBase)</b></font></p>\n",
     "\n",
-    "> *© 2025, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
+    "> *© 2026, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
     "\n",
     "---"
    ]
@@ -39,7 +39,7 @@
     "- BETR802: urban traffic site in Antwerp, Belgium\n",
     "- BETN029: rural background site in Houtem, Belgium\n",
     "\n",
-    "See http://www.eea.europa.eu/themes/air/interactive/no2"
+    "See https://www.eea.europa.eu/en/topics/in-depth/air-pollution"
    ]
   },
   {
@@ -1416,6 +1416,7 @@
  "metadata": {
   "celltoolbar": "Nbtutor - export exercises",
   "jupytext": {
+   "default_lexer": "ipython3",
    "formats": "ipynb,md:myst"
   },
   "kernelspec": {
@@ -1433,7 +1434,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.11"
   },
   "nav_menu": {},
   "toc": {

_solved/case4_air_quality_processing.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "<p><font size=\"6\"><b> CASE - air quality data of European monitoring stations (AirBase)</b></font></p>\n",
     "\n",
-    "> *© 2025, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
+    "> *© 2026, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
     "\n",
     "---"
    ]
@@ -29,7 +29,7 @@
     "- BETR802: urban traffic site in Antwerp, Belgium\n",
     "- BETN029: rural background site in Houtem, Belgium\n",
     "\n",
-    "See http://www.eea.europa.eu/themes/air/interactive/no2"
+    "See https://www.eea.europa.eu/en/topics/in-depth/air-pollution"
    ]
   },
   {
@@ -754,6 +754,7 @@
  ],
  "metadata": {
   "jupytext": {
+   "default_lexer": "ipython3",
    "formats": "ipynb,md:myst"
   },
   "kernelspec": {
@@ -771,7 +772,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.11"
   },
   "nav_menu": {},
   "toc": {

_solved/pandas_01_data_structures.ipynb

@@ -7,7 +7,7 @@
    "source": [
     "<p><font size=\"6\"><b>01 - Pandas: Data Structures </b></font></p>\n",
     "\n",
-    "> *© 2025, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
+    "> *© 2026, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
     "\n",
     "---"
    ]
@@ -754,6 +754,7 @@
  ],
  "metadata": {
   "jupytext": {
+   "default_lexer": "ipython3",
    "formats": "ipynb,md:myst"
   },
   "kernelspec": {
@@ -771,7 +772,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.11"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

_solved/pandas_02_basic_operations.ipynb

@@ -8,7 +8,7 @@
     "<p><font size=\"6\"><b> 02 - Pandas: Basic operations on Series and DataFrames</b></font></p>\n",
     "\n",
     "\n",
-    "> *© 2025, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
+    "> *© 2026, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
     "\n",
     "---"
    ]
@@ -777,6 +777,7 @@
  ],
  "metadata": {
   "jupytext": {
+   "default_lexer": "ipython3",
    "formats": "ipynb,md:myst"
   },
   "kernelspec": {
@@ -794,7 +795,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.11"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

_solved/pandas_03a_selecting_data.ipynb

@@ -8,7 +8,7 @@
     "<p><font size=\"6\"><b>03 - Pandas: Indexing and selecting data - part I</b></font></p>\n",
     "\n",
     "\n",
-    "> *© 2025, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
+    "> *© 2026, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
     "\n",
     "---"
    ]
@@ -1024,6 +1024,7 @@
  ],
  "metadata": {
   "jupytext": {
+   "default_lexer": "ipython3",
    "formats": "ipynb,md:myst"
   },
   "kernelspec": {
@@ -1041,7 +1042,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.11"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

_solved/pandas_03b_indexing.ipynb

@@ -7,7 +7,7 @@
    "source": [
     "<p><font size=\"6\"><b>03 - Pandas: Indexing and selecting data - part II</b></font></p>\n",
     "\n",
-    "> *© 2025, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
+    "> *© 2026, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
     "\n",
     "---"
    ]
@@ -693,6 +693,7 @@
  ],
  "metadata": {
   "jupytext": {
+   "default_lexer": "ipython3",
    "formats": "ipynb,md:myst"
   },
   "kernelspec": {
@@ -710,7 +711,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.11"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

_solved/pandas_04_time_series_data.ipynb

@@ -9,7 +9,7 @@
    "source": [
     "<p><font size=\"6\"><b>04 - Pandas: Working with time series data</b></font></p>\n",
     "\n",
-    "> *© 2025, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
+    "> *© 2026, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
     "\n",
     "---"
    ]
@@ -1045,6 +1045,7 @@
  ],
  "metadata": {
   "jupytext": {
+   "default_lexer": "ipython3",
    "formats": "ipynb,md:myst"
   },
   "kernelspec": {
@@ -1062,7 +1063,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.11"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

_solved/pandas_05_groupby_operations.ipynb

@@ -8,7 +8,7 @@
     "<p><font size=\"6\"><b>05 - Pandas: \"Group by\" operations</b></font></p>\n",
     "\n",
     "\n",
-    "> *© 2025, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
+    "> *© 2026, Joris Van den Bossche and Stijn Van Hoey  (<mailto:jorisvandenbossche@gmail.com>, <mailto:stijnvanhoey@gmail.com>). Licensed under [CC BY 4.0 Creative Commons](http://creativecommons.org/licenses/by/4.0/)*\n",
     "\n",
     "---"
    ]
@@ -1228,6 +1228,7 @@
  ],
  "metadata": {
   "jupytext": {
+   "default_lexer": "ipython3",
    "formats": "ipynb,md:myst"
   },
   "kernelspec": {
@@ -1245,7 +1246,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.8"
+   "version": "3.13.11"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {