MPUSP · finstermeier · Apr 28, 2026 · Apr 27, 2026 · Apr 27, 2026 · Apr 27, 2026
diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,13 @@
+# generic ignores
+*.Rhistory
+*.RData
+*.Rproj.user
+.ipynb_checkpoints
 .vscode
 exercises/*
 templates/*.html
 templates/*_files
+
 # pixi environments
 .pixi/*
 !.pixi/config.toml
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Max Planck Unit for the Science of Pathogens
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/README.md b/README.md
@@ -6,19 +6,45 @@ This Github repository contains all course materials. Issues can be reported [he
 
 For comments, criticism, and general feedback please contact the [authors](#authors) at bioinformatics@mpusp.mpg.de
 
-## Course materials and structure
+## Course materials
+
+### Sources and license
+
+The course materials are a blend of own works and code examples from Justin Bois' [Introduction to Programming in the Biological Sciences Bootcamp](https://justinbois.github.io/bootcamp/2024/). The code examples from the Bootcamp course are released with the [MIT License](https://opensource.org/license/mit).
+
+All other code examples and documentation added by the [authors](#authors) is also released under the [MIT License](https://opensource.org/license/mit), except where explicitly noted.
+
+All example datasets are taken from published sources which are referenced in [Data sources](#data-sources).
+These datasets are **not covered by the MIT License**, but are licensed under their respective terms.
 
 ### Dependencies
 
 In order to work with the course materials, you need to have [Python](https://www.python.org/downloads/), [R](https://cran.r-project.org/mirrors.html), and optionally [Quarto](https://quarto.org/docs/get-started/) (a notebook framework) installed.
 
+With [`pixi`](https://pixi.prefix.dev) as package manager (recommended), you can create an environment with the required dependencies by running:
+
+```bash
+pixi init
+pixi add python pandas matplotlib jupyter r-tidyverse r-irkernel
+```
+
+Or simply use the provided `pixi.toml` file to activate the environment:
+
+```bash
+pixi shell
+```
+
 With conda/mamba, you can create an environment with all dependencies by running:
 
 ```bash
-mamba create -p <dirname>/python-course python pandas matplotlib jupyter quarto r-recommended r-tidyverse r-reticulate
+mamba create -p <dirname>/python-course python pandas matplotlib jupyter r-tidyverse r-irkernel
 mamba activate python-course
 ```
 
+When using Jupyter Notebooks (in VSCode), make sure to select the correct kernel (Python or R) for each notebook.
+
+The R kernel for Jupyter is installed with the `r-irkernel` package, a detailed setup for VSCode can be found [here](https://davidzhao1015.github.io/blog/2024/R-kernel-jupyter/).
+
 When running a Quarto notebook, make sure that the R package `reticulate` is installed and configured to use the correct Python environment. You can specify the path to the Python binary by running the following command in the terminal:
 
 ```bash
@@ -35,21 +61,23 @@ export RETICULATE_PYTHON="/path/to/your/env/bin/python"
 
 - `data/`: Contains datasets used in the course
 - `lessons/`: Contains the lesson notebooks, e.g. in Jupyter format (`.ipynb`)
+- `solutions/`: Contains solutions to the exercises provided in the lessons
 - `templates`: Contains templates for creating new lessons or exercises
 - `README.md`: Instructions and information about the course
 - `.gitignore`: Specifies files and directories to be ignored by Git
 
-## Data origins / citations:
-- gfmt_sleep*: Beattie, L., Walsh, D., McLaren, J., Biello, S.M. and White, D., 2016. Perceptual impairment in face identification with poor sleep. Royal Society Open Science, 3(10).
-- iris.data: Anderson, E., 1935. The irises of the Gaspe Peninsula. Bulletin of American Iris Society, 59, pp.2-5.
-- ls_orchids.*: Cox, A.V., Pridgeon, A.M., Albert, V.A. and Chase, M.W., 1997. Phylogenetics of the slipper orchids (Cypripedioideae, Orchidaceae): nuclear rDNA ITS sequences. Plant Systematics and Evolution, 208(3), pp.197-223.
-- NC_005816.gb: Zhou, D., Tong, Z., Song, Y., Han, Y., Pei, D., Pang, X., Zhai, J., Li, M., Cui, B., Qi, Z. and Jin, L., 2004. Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus. Journal of bacteriology, 186(15), pp.5147-5152.
-- reeves_gradient_width_various_methods.cvs: Reeves, G.T., Trisnadi, N., Truong, T.V., Nahmad, M., Katz, S. and Stathopoulos, A., 2012. Dorsal-ventral gene expression in the Drosophila embryo reflects the dynamics and precision of the dorsal nuclear gradient. Developmental cell, 22(3), pp.544-557.
-- towels.txt: Douglas Adams, The Hitch Hiker's Guide to the Galaxy, ISBN: 0345391802
+## Data sources
+
+- `gfmt_sleep\*`: Beattie, L., Walsh, D., McLaren, J., Biello, S.M. and White, D., 2016. Perceptual impairment in face identification with poor sleep. Royal Society Open Science, 3(10). Released to [Public domain, CC0](https://datadryad.org/dataset/doi:10.5061/dryad.r620r).
+- `iris.data`: Anderson, E., 1935. The irises of the Gaspe Peninsula. Bulletin of American Iris Society, 59, pp.2-5. [CC-BY-4.0 License](https://doi.org/10.1111/j.1469-1809.1936.tb02137.x).
+- `ls_orchids.\*`: Cox, A.V., Pridgeon, A.M., Albert, V.A. and Chase, M.W., 1997. Phylogenetics of the slipper orchids (Cypripedioideae, Orchidaceae): nuclear rDNA ITS sequences. Plant Systematics and Evolution, 208(3), pp.197-223. [Freely available on NCBI](https://www.ncbi.nlm.nih.gov/nuccore/?term=Phylogenetics%20of%20the%20slipper%20orchids).
+- `NC_005816.gb`: Zhou, D., Tong, Z., Song, Y., Han, Y., Pei, D., Pang, X., Zhai, J., Li, M., Cui, B., Qi, Z. and Jin, L., 2004. Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus. Journal of bacteriology, 186(15), pp.5147-5152.  [Freely available on NCBI](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000007885.1/).
+- `Jahn_eLife_2021.csv`: Jahn, M., Crang, N., Janasch, M., Hober, A., Forsström, B., Kimler, K., Mattausch, A., Chen, Q., Asplund-Samuelsson, J., & Hudson, E. P. (2021). Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator. eLife, 10(e69019), 1–26. [Freely available on Github, GPL v3](https://github.com/m-jahn/R-notebook-ralstonia-proteome).
 
-## Adding and changing contents
+## Contributions
 
-To be added.
+**Contributions to the course materials are very welcome!**
+If you have suggestions for improvements, or want to report issues, please feel free to [open an issue](https://github.com/MPUSP/coding-for-biologists/issues) or submit a pull request on GitHub.
 
 ## Authors
 

diff --git a/data/Jahn_eLife_2021.csv b/data/Jahn_eLife_2021.csv
@@ -0,0 +1,21 @@
+uniprot,substrate,growthrate,R1,R2,R3,R4
+Q0K1H0,formate,0.05,900578172,441270170,3122542832,680060600
+Q0K1H0,formate,0.1,614552208,2398450248,366775320,1015804992
+Q0K1H0,formate,0.15,705491384,367461526,803938584,782118008
+Q0K1H0,formate,0.2,438389228,580611700,938426916,464743138
+Q0K1H0,formate,0.25,522893276,1364078846,1373663968,942002356
+Q0K1H0,fructose,0.05,305158214,332735058,1400748272,877117100
+Q0K1H0,fructose,0.1,78090540,NA,396061392,778370782
+Q0K1H0,fructose,0.15,15727490,464742468,398025584,260101530
+Q0K1H0,fructose,0.2,79098500,590114016,133964096,296108304
+Q0K1H0,fructose,0.25,32359600,257136500,201190480,89447700
+Q0K1H0,ammonium,0.05,72514300,378991192,1095938008,641173112
+Q0K1H0,ammonium,0.1,8652209052,1020382916,682807584,388322042
+Q0K1H0,ammonium,0.15,292831192,728197400,691936776,243449700
+Q0K1H0,ammonium,0.2,181858100,260700392,5612858216,6030139888
+Q0K1H0,ammonium,0.25,7295757960,284956160,658380400,259553392
+Q0K1H0,succinate,0.05,607908460,418218000,463238600,692957484
+Q0K1H0,succinate,0.1,460987046,385657000,469888616,310468790
+Q0K1H0,succinate,0.15,450655732,408609784,1087130084,333188100
+Q0K1H0,succinate,0.2,299384900,656712030,591076116,691310308
+Q0K1H0,succinate,0.25,427697608,289053748,562829796,211568150
diff --git a/data/reeves_gradient_width_various_methods.csv b/data/reeves_gradient_width_various_methods.csv
diff --git a/data/towels.txt b/data/towels.txt
diff --git a/lessons/lesson_01.ipynb b/lessons/lesson_01.ipynb
@@ -36,9 +36,10 @@
     "## Course materials and structure\n",
     "\n",
     "- all course participants can be contacted via the mailing list `python_2026@mpusp.mpg.de`\n",
-    "- all materials are available at our Github repository: https://github.com/MPUSP/python_course/ (currently private)\n",
+    "- all materials are available at our Github repository: https://github.com/MPUSP/python_course/\n",
     "- each lesson is provided as a Jupyter notebook (`.ipynb`), or alternatively a Quarto (`.qmd`) or R markdown (`.Rmd`) notebook\n",
-    "- the course material is a blend of own works examples from Justin Bois from Caltech (http://bois.caltech.edu/)\n",
+    "- the course materials are a blend of own works and code examples from Justin Bois' [Introduction to Programming in the Biological Sciences Bootcamp](https://justinbois.github.io/bootcamp/2024/). The code examples from the Bootcamp course are released with the [MIT License](https://opensource.org/license/mit).\n",
+    "- all other content that was added is also released under the [MIT License](https://opensource.org/license/mit), except where explicitly noted\n",
     "- each lesson is supposed to be worked through in about 90 minutes\n",
     "- the course is **interactive (!)**: we will mix small introductory lectures with hands-on exercises\n",
     "- participants are expected to actively work through the notebooks, run code cells, and try to understand/solve the given tasks\n",