Working Group Nicole Radde

The German Network for Bioinformatics Infrastructure - de.NBI offers first class bioinformatics services including training and education to users in basic and applied life sciences research. In this network 40 projects belonging to eight service centers provide services that cover a wide variety of methods (genomics, proteomics, ...) and applications (from plants to humans). de.NBI-SysBio is the Systems Biology Service Center of de.NBI. In collaboration with FAIRDOM, de.NBI-SysBio serves the ...

This study investigates the citations of reproducible vs. not reproducible papers and is based on 328 published models, classified by Tiwari et al. based on their reproducibility are analyzed in this study. Hypothese testing is performed using a flexible Bayesian approach for a complete assessment of posteriors. The approach handels outliers via a non-central t distribution. Results show that reproducible papers are significantly more citet between 2013 and 2020, i.e. 10 years after the introduction ...

Motivated by an increasing population and the desire to grow plants more efficiently, attention has turned to the use of Light Emitting Diodes (LEDs) to illuminate plants which are grown indoors. Indoor growing facilities enable closely controlled and mon- itored environmental conditions. More and more of these facilities exchange High Pressure Sodium (HPS) lamps for LED lighting since they provide more efficient lighting and the possibility to control light intensity and quality in order to ...

Motivated by an increasing population and the desire to grow plants more efficiently, attention has turned to the use of Light Emitting Diodes (LEDs) to illuminate plants which are grown indoors. Indoor growing facilities enable closely controlled and mon- itored environmental conditions. More and more of these facilities exchange High Pressure Sodium (HPS) lamps for LED lighting since they provide more efficient lighting and the possibility to control light intensity and quality in order to ...

The statistical analysis was performed in a jupyter notebook. This notebook contains the commands for all performed analyses (Statistical_analysis_of_FAIR_citations.ipynb)

The Bayesian Estimation Superseeds the t Test (BEST) method of Kruschke 2013 was used for the Bayesian significance testing. The method was implemented in a python class together with visualization and distributional analysis methods (BEST_method_python_Kruschke2012.py).

The results of the statistical analysis, including ...

The classification in reproducible and not reproducible models was made by Tiwari et al.

Citations were looked up in Scopus, Web of Science and Google Scholar.

The following journals had to be excluded, as Journal Impact Factors (JIF) were missing or papers were discontinued:

• Experientia was closed 1996 and continued as Cellular and Molecular Life Sciences 1997
• The American journal of physiology – split into fields 1977, further splits in 1980 and 1989
• IFAC Proceedings Volumes – last issue ...

Full posterior traces for all analysis are avalable.

Furthermore all visualizations of the paper are included.

The folder contains the jupyter notebook for the execution of all analyses of the study. The BEST method is used in the notebook and is added in a separate python skript.

The Folder contains:

• The MCMC and simulation results, as well as the synthetic data of the Chemical Reaction Network model (DoubleDecayIndep)
• The MCMC and simulation results, as well as the synthetic data of the Lotka-Volterra model (LotkaVolterraJoint)

Together with an executable ipynb script (Exe.ipynb) and the MCMC plotting and execution functions (MCMCFunctions.py).