reproducible research approach

manuscript/manuscript.Rmd

@@ -1100,6 +1100,9 @@ provide a probabilistic output.
 
 # Appendix / Supplemental Material
 
+
+## Distribution of GOSe in validation folds
+
 ```{r marginal-GOSe-folds, echo=FALSE, fig.cap="Marginal GOSe distribution per validation fold."}
 df_ground_truth %>% 
     ggplot(aes(Outcomes.DerivedCompositeGOSE)) +
@@ -1115,6 +1118,21 @@ df_ground_truth %>%
 ```
 
 
+## Reproducible Research Strategy
+
+CENTER-TBI is commited to reproducible research. 
+To this end, the entire source code to run the analyses is publicly available
+at https://git.center-tbi.eu/kunzmann/gose-6mo-imputation.
+Scripts for automatically downloading the required data from the central
+access restricted 'Neurobot' (https://neurobot.incf.org/) database at 
+https://center-tbi.incf.org/ are provided.
+The analysis is completely automated using the workflow managment tool 'snakemake'
+[@koster2012snakemake] and a singularity [@kurtzer2017singularity] container image
+containing all required dependencies is publicly available from zenodo.org
+at https://zenodo.org/record/2600385#.XJzZwEOnw5k (DOI: 10.5281/zenodo.2600385).
+Detailed step-bz-step instructions on how to reproduce the analysis are provided 
+in the README.md file of the GitLab repository. 
+
 
 
 ```{r zip-figures, include=FALSE}

manuscript/references.bib

@@ -9,6 +9,18 @@
   publisher={Lippincott Williams and Wilkins}
 }
 
+@article{kurtzer2017singularity,
+  title={Singularity: Scientific containers for mobility of compute},
+  author={Kurtzer, Gregory M and Sochat, Vanessa and Bauer, Michael W},
+  journal={PloS one},
+  volume={12},
+  number={5},
+  pages={e0177459},
+  year={2017},
+  publisher={Public Library of Science}
+}
+
+
 @article{mcmillan2016glasgow,
   title={The Glasgow Outcome Scale—40 years of application and refinement},
   author={McMillan, Tom and Wilson, Lindsay and Ponsford, Jennie and Levin, Harvey and Teasdale, Graham and Bond, Michael},
@@ -49,6 +61,17 @@
   publisher={Springer Science \& Business Media}
 }
 
+@article{koster2012snakemake,
+  title={Snakemake—a scalable bioinformatics workflow engine},
+  author={K{\"o}ster, Johannes and Rahmann, Sven},
+  journal={Bioinformatics},
+  volume={28},
+  number={19},
+  pages={2520--2522},
+  year={2012},
+  publisher={Oxford University Press}
+}
+
 
 @article{msm2011,
 author = {Jackson, Christopher H.},