Initial files of analysis

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diff --git a/.gitignore b/.gitignore
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+# vscode
+.vscode
+
+# Jupyter Notebook Checkpoints
+.ipynb_checkpoints
diff --git a/LICENSE b/LICENSE
diff --git a/...lization in osteoblasts on amino group containing plasma polymer nanolayer (Python).ipynb b/...lization in osteoblasts on amino group containing plasma polymer nanolayer (Python).ipynb
diff --git a/Python/Dockerfile b/Python/Dockerfile
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+###############################################################################
+# Biomedical-Jupyter-Examples is licensed under a
+# Creative Commons Attribution 4.0 International License.
+#
+# You should have received a copy of the license along with this
+# work. If not, see <http://creativecommons.org/licenses/by/4.0/>.
+###############################################################################
+
+FROM jupyter/minimal-notebook:45f07a14b422
+
+LABEL maintainer="[email protected]"
+
+# Set user to Jupyter Notebook user
+USER $NB_USER
+
+# Change working directory to volume mount point
+WORKDIR /home/$NB_USER/work
+
+# Copy requirements file from host to temp directory
+COPY requirements.txt /tmp/requirements.txt
+
+# Install requirements
+RUN python3 -m pip install -r /tmp/requirements.txt
diff --git a/Python/EnhancedCalcium.bib b/Python/EnhancedCalcium.bib
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+% Encoding: UTF-8
+
+@Article{Staehlke2018,
+  author    = {Susanne Staehlke and Henrike Rebl and Birgit Finke and Petra Mueller and Martina Gruening and J. Barbara Nebe},
+  title     = {Enhanced calcium ion mobilization in osteoblasts on amino group containing plasma polymer nanolayer},
+  journal   = {Cell {\&} Bioscience},
+  year      = {2018},
+  volume    = {8},
+  number    = {1},
+  month     = mar,
+  doi       = {10.1186/s13578-018-0220-8},
+  publisher = {Springer Nature},
+}
+@Article{Nebe2019,
+  author    = {J. Barbara Nebe and Henrike Rebl and Michael Schlosser and Susanne Staehlke and Martina Gruening and Klaus-Dieter Weltmann and Uwe Walschus and Birgit Finke},
+  title     = {Plasma Polymerized Allylamine -- The Unique Cell-Attractive Nanolayer for Dental Implant Materials},
+  journal   = {Polymers},
+  year      = {2019},
+  volume    = {11},
+  number    = {6},
+  pages     = {1004},
+  month     = jun,
+  doi       = {10.3390/polym11061004},
+  publisher = {{MDPI} {AG}},
+}
+
+@Article{Rebl2016,
+  author    = {Henrike Rebl and Birgit Finke and Jürgen Schmidt and Heba S. Mohamad and Roland Ihrke and Christiane A. Helm and J. Barbara Nebe},
+  title     = {Accelerated cell-surface interlocking on plasma polymer-modified porous ceramics},
+  journal   = {Materials Science and Engineering: C},
+  year      = {2016},
+  volume    = {69},
+  pages     = {1116--1124},
+  month     = dec,
+  doi       = {10.1016/j.msec.2016.08.016},
+  publisher = {Elsevier {BV}},
+}
+
+@Article{Staehlke2015,
+  author    = {Susanne Staehlke and Andreas Koertge and J. Barbara Nebe},
+  title     = {Intracellular calcium dynamics dependent on defined microtopographical features of titanium},
+  journal   = {Biomaterials},
+  year      = {2015},
+  volume    = {46},
+  pages     = {48--57},
+  month     = apr,
+  doi       = {10.1016/j.biomaterials.2014.12.016},
+  publisher = {Elsevier {BV}},
+}
+
+@Article{Staehlke2018a,
+  author    = {Susanne Staehlke and Henrike Rebl and J. Barbara Nebe},
+  title     = {Phenotypic stability of the human {MG}--63 osteoblastic cell line at different passages},
+  journal   = {Cell Biology International},
+  year      = {2018},
+  volume    = {43},
+  number    = {1},
+  pages     = {22--32},
+  month     = dec,
+  doi       = {10.1002/cbin.11073},
+  publisher = {Wiley},
+}
+
+@Comment{jabref-meta: databaseType:bibtex;}
diff --git a/Python/requirements.txt b/Python/requirements.txt
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+matplotlib==3.1.1
+pandas==0.25.1
+scipy==1.3.1
+xlrd==1.2.0
+numpy==1.17.2
+watermark==2.0.1
diff --git a/Python/runtime.txt b/Python/runtime.txt
@@ -0,0 +1 @@
+python-3.7
diff --git a/... mobilization in osteoblasts on amino group containing plasma polymer nanolayer (R).ipynb b/... mobilization in osteoblasts on amino group containing plasma polymer nanolayer (R).ipynb
diff --git a/R/Dockerfile b/R/Dockerfile
@@ -0,0 +1,23 @@
+###############################################################################
+# Biomedical-Jupyter-Examples is licensed under a
+# Creative Commons Attribution 4.0 International License.
+#
+# You should have received a copy of the license along with this
+# work. If not, see <http://creativecommons.org/licenses/by/4.0/>.
+###############################################################################
+
+FROM jupyter/r-notebook:45f07a14b422
+
+LABEL maintainer="[email protected]"
+
+# Set user to Jupyter Notebook user
+USER $NB_USER
+
+# Change working directory to volume mount point
+WORKDIR /home/$NB_USER/work
+
+# Copy requirements file from host to temp directory
+COPY install.R /tmp/install.R
+
+# Install requirements
+RUN R -f /tmp/install.R
diff --git a/R/EnhancedCalcium.bib b/R/EnhancedCalcium.bib
@@ -0,0 +1,64 @@
+% Encoding: UTF-8
+
+@Article{Staehlke2018,
+  author    = {Susanne Staehlke and Henrike Rebl and Birgit Finke and Petra Mueller and Martina Gruening and J. Barbara Nebe},
+  title     = {Enhanced calcium ion mobilization in osteoblasts on amino group containing plasma polymer nanolayer},
+  journal   = {Cell {\&} Bioscience},
+  year      = {2018},
+  volume    = {8},
+  number    = {1},
+  month     = mar,
+  doi       = {10.1186/s13578-018-0220-8},
+  publisher = {Springer Nature},
+}
+@Article{Nebe2019,
+  author    = {J. Barbara Nebe and Henrike Rebl and Michael Schlosser and Susanne Staehlke and Martina Gruening and Klaus-Dieter Weltmann and Uwe Walschus and Birgit Finke},
+  title     = {Plasma Polymerized Allylamine -- The Unique Cell-Attractive Nanolayer for Dental Implant Materials},
+  journal   = {Polymers},
+  year      = {2019},
+  volume    = {11},
+  number    = {6},
+  pages     = {1004},
+  month     = jun,
+  doi       = {10.3390/polym11061004},
+  publisher = {{MDPI} {AG}},
+}
+
+@Article{Rebl2016,
+  author    = {Henrike Rebl and Birgit Finke and Jürgen Schmidt and Heba S. Mohamad and Roland Ihrke and Christiane A. Helm and J. Barbara Nebe},
+  title     = {Accelerated cell-surface interlocking on plasma polymer-modified porous ceramics},
+  journal   = {Materials Science and Engineering: C},
+  year      = {2016},
+  volume    = {69},
+  pages     = {1116--1124},
+  month     = dec,
+  doi       = {10.1016/j.msec.2016.08.016},
+  publisher = {Elsevier {BV}},
+}
+
+@Article{Staehlke2015,
+  author    = {Susanne Staehlke and Andreas Koertge and J. Barbara Nebe},
+  title     = {Intracellular calcium dynamics dependent on defined microtopographical features of titanium},
+  journal   = {Biomaterials},
+  year      = {2015},
+  volume    = {46},
+  pages     = {48--57},
+  month     = apr,
+  doi       = {10.1016/j.biomaterials.2014.12.016},
+  publisher = {Elsevier {BV}},
+}
+
+@Article{Staehlke2018a,
+  author    = {Susanne Staehlke and Henrike Rebl and J. Barbara Nebe},
+  title     = {Phenotypic stability of the human {MG}--63 osteoblastic cell line at different passages},
+  journal   = {Cell Biology International},
+  year      = {2018},
+  volume    = {43},
+  number    = {1},
+  pages     = {22--32},
+  month     = dec,
+  doi       = {10.1002/cbin.11073},
+  publisher = {Wiley},
+}
+
+@Comment{jabref-meta: databaseType:bibtex;}
diff --git a/R/install.R b/R/install.R
@@ -0,0 +1,6 @@
+install.packages(c("devtools"), repos='https://ftp.fau.de/cran/')
+
+require(devtools)
+
+install_version("tidyverse", version = "1.2.1", repos = "https://ftp.fau.de/cran/")
+install_version("readxl", version = "1.3.1", repos = "https://ftp.fau.de/cran/")
diff --git a/R/runtime.txt b/R/runtime.txt
@@ -0,0 +1 @@
+r-3.5-2019-11-20
diff --git a/README.md b/README.md
@@ -0,0 +1,100 @@
+# Biomedical Jupyter Examples
+
+This repository contains Jupyter Notebooks that resemble the following analysis as a demonstration for reproducible and executable research experiments:
+
+Susanne Staehlke, Henrike Rebl, Birgit Finke, Petra Mueller, Martina Gruening, and J. Barbara Nebe.
+“Enhanced calcium ion mobilization in osteoblasts on amino group containing plasma polymer nanolayer.”
+Cell & Bioscience, 8(1), March 2018.
+doi: 10.1186/s13578-018-0220-8
+
+## License
+
+[![Creative Commons License](https://i.creativecommons.org/l/by/4.0/88x31.png)](http://creativecommons.org/licenses/by/4.0/)
+
+This work is licensed under a [Creative Commons Attribution 4.0 International License](http://creativecommons.org/licenses/by/4.0/), please use the Zenodo reference:
+
+[![DOI](https://zenodo.org/badge/DOI/)]()
+
+In order to reference the GitHub repository, please attribute this as:
+
+Max Schröder, Susanne Staehlke, J. Barbara Nebe, and Frank Krüger. “Biomedical Jupyter Examples,” https://github.com/SFB-ELAINE/Biomedical-Jupyter-Examples
+
+## Repository Structure
+
+The repository is structured as follows:
+
+1. `_Data` contains the raw data used for the analysis in the form of Excel sheets.
+2. `EnhancedCalcium.bib` is used as central bibtex library used for references inside the Jupyter Notebooks.
+
+For each programming language a separate folder is created that contains a single Jupyter Notebook document resembling the analysis as well as the corresponding PDF export.
+
+For some programming languages additional files may be contained, e.g. for the documentation of package requirements.
+
+## Usage
+
+For each programming language a separate Docker image exists.
+There are several methods of using the Jupyter Notebooks of this repository:
+
+### Ready-to-use Docker Images
+
+The probably easiest way is to use the corresponding docker image: sfbelaine/biomedical-jupyter-notebooks:`<programming-language>` e.g. for running the Python example execute the following command in your terminal:
+
+```bash
+$ docker run --rm \
+    --name=biomedical-jupyter-python \
+    -p 127.0.0.1:8888:8888 \
+    -v "$PWD":/home/jovyan/work \
+    --user root \
+    -e NB_UID=$(id -u) \
+    -e NB_GID=$(id -g) \
+    sfbelaine/biomedical-jupyter-notebooks:python
+```
+The parameters configure the following:
+
+1. `--rm` removes the container automatically after exiting,
+2. `--name=biomedical-jupyter-python` gives the container the name `biomedical-jupyter-python` instead of a generated one,
+3. `-p 127.0.0.1:8888:8888` binds the container port `8888` (3. part) to the host ip address `127.0.0.1` and port `8888` (2. part),
+4. `-v "$PWD":/home/jovyan/work` binds the current directory `$PWD` to the container directory `/home/jovyan/work`,
+5. `--user root` is needed in order to set the UID and GID of the user running the Jupyter service inside the container,
+6. `-e NB_UID=$(id -u)` and `-e NB_GID=$(id -g)` are used to set the user and group ID to the same as the user on the host in order to enable write access to the volume mounted by `-v`.
+
+To search available docker images, use the corresponding Docker Hub repository: https://hub.docker.com/r/sfbelaine/biomedical-jupyter-notebooks
+
+### Locally Building Docker Image
+
+Despite downloading a ready-to-use Docker image, it can also be build on a local computer.
+After downloading/cloning this repository, navigate into the folder (e.g. on *nix systems use the tool `cd`) of the desired programming language and call the docker build command:
+
+```bash
+$ cd Python
+$ docker build -t biomedical-jupyter-python .
+```
+
+Afterwards, navigate into the root directory of the repository  and create a new container using this image might by e.g. using the following commands:
+
+```bash
+$ cd ../
+$ docker run --rm \
+    --name=biomedical-jupyter-python \
+    -p 127.0.0.1:8888:8888 \
+    -v "$PWD":/home/jovyan/work \
+    --user root \
+    -e NB_UID=$(id -u) \
+    -e NB_GID=$(id -g) \
+    biomedical-jupyter-python
+```
+
+For detailed information on the parameters consider the section on Ready-to-use Docker Images above.
+
+### Installing Requirements Locally
+
+Instead of using one of the provided containerization solutions, the software requirements might also be installed locally.
+For this, consider the corresponding programming language for more details.
+In many cases, a file documenting the requirements such as for the Python package manager `pip` the `requirements.txt` file is provided.
+Also consider the `Dockerfile` for an example install procedure.
+
+## Troubleshooting
+
+In case the Notebook claims about missing data you probably have started the Jupyter software inside the directory of the programming language.
+As the data is located inside the `_Data` folder in the root directory of the repository, the folder cannot be found then.
+Restart the Jupyter software inside the root directory of the repository instead and locate to the programming language that shall be tested.
diff --git a/_Data/Fig. 5_MG63_19.07.2016_PPAAm_n1.xlsx b/_Data/Fig. 5_MG63_19.07.2016_PPAAm_n1.xlsx
diff --git a/_Data/Fig. 5_MG63_19.07.2016_PPAAm_n2.xlsx b/_Data/Fig. 5_MG63_19.07.2016_PPAAm_n2.xlsx
diff --git a/_Data/Fig. 5_MG63_19.07.2016_PPAAm_n3.xlsx b/_Data/Fig. 5_MG63_19.07.2016_PPAAm_n3.xlsx
diff --git a/_Data/Fig. 5_MG63_19.07.2016_Ti_n1.xlsx b/_Data/Fig. 5_MG63_19.07.2016_Ti_n1.xlsx
diff --git a/_Data/Fig. 5_MG63_19.07.2016_Ti_n2.xlsx b/_Data/Fig. 5_MG63_19.07.2016_Ti_n2.xlsx
diff --git a/_Data/Fig. 5_MG63_19.07.2016_Ti_n3.xlsx b/_Data/Fig. 5_MG63_19.07.2016_Ti_n3.xlsx
diff --git a/_Data/Fig. 5_MG63_Col_n1.xlsx b/_Data/Fig. 5_MG63_Col_n1.xlsx
diff --git a/_Data/Fig. 5_MG63_Col_n2.xlsx b/_Data/Fig. 5_MG63_Col_n2.xlsx
diff --git a/_Data/Fig. 5_MG63_Col_n3.xlsx b/_Data/Fig. 5_MG63_Col_n3.xlsx
diff --git a/_Data/Fig. 5_MG63_IBIDI_n1.xlsx b/_Data/Fig. 5_MG63_IBIDI_n1.xlsx
diff --git a/_Data/Fig. 5_MG63_IBIDI_n2.xlsx b/_Data/Fig. 5_MG63_IBIDI_n2.xlsx
diff --git a/_Data/Fig. 5_MG63_IBIDI_n3.xlsx b/_Data/Fig. 5_MG63_IBIDI_n3.xlsx