Statistical analysis and BEST method of Kruschke for python applied on citation data in Systems Biology
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). Also the bayesian multiple comparison analysis can be found in the BEST_method_python_Kruschke2012.py file.
The results of the statistical analysis, including histograms of the data and full posterior and Posterior Predicitive Distributional (PPD) information is added in a results folder. Diagnostics according to the Bayesian Analysis Reporting Guidelines of Kruschke 2021 were added for every bayeisan estimation, including the multiple period comparison.
Methodical details can be found in the methods section of the publication.
SEEK ID: https://fairdomhub.org/assays/2009
Modelling analysis
Projects: Working Group Nicole Radde
Investigation: hidden item
Study: Bayesian hypothesis testing reveals that reproducible models in systems biology get more citations
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: No organisms
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Created: 29th Sep 2022 at 13:12
Last updated: 11th Jan 2023 at 15:31
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Projects: Working Group Nicole Radde, SteaPKMod
Institutions: University of Stuttgart
https://orcid.org/0000-0002-5300-0915
Currently I focuse on the integration of data into multi-scale models with statistical methods and uncertainty tracking in the research unit QuaLiPerF.
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 ...
Projects: de.NBI-SysBio, ExtremoPharm, ZucAt, Kinetics on the move - Workshop 2016, Example use cases, MIX-UP, Working Group Nicole Radde, MPIEvolBio-SciComp, SABIO-VIS
Web page: http://www.denbi.de
The group around Nicole Radde specializes in the modeling, analysis, and simulation of biochemical systems. This especially includes parameter optimization and identification.
Programme: de.NBI Systems Biology Service Center (de.NBI-SysBio)
Public web page: https://www.ist.uni-stuttgart.de/research/group-of-nicole-radde/
Start date: 11th Feb 2020
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 ...
Submitter: Sebastian Höpfl
Investigation: 1 hidden item
Assays: Statistical analysis and BEST method of Kruschke for python applied on c...
The Results of the analysis are structured in three parts:
- The results of the main analysis
- The results with a broader prior (Sensitivity analysis)
- The Results of the multiple period comparison
For each part, full posterior traces for all analysis and visualizations of the paper are avalable.
Furthermore the diagnostics and traces were added for the different analysis. The trace for the mulitple comparison was to large to upload it and is available on request.
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 ...
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.
There is a class for the BEST method according to Kruschke and a class für the BEST multiple comparison.
A conda environment file with all libraries that are necessary to perform the analysis, including the package version was created. It can be easily installed via conda env create -f pymc_env.yml
Creator: Sebastian Höpfl
Submitter: Sebastian Höpfl
Model type: Not specified
Model format: Not specified
Environment: Not specified
