• John Zobolas's PhD Thesis
  • Acknowledgements
  • Abstract
  • Paper list
    • Primary
    • Additional
  • Abbreviations
  • Summary
    • One for all
    • Dots and lines
    • Knowledge from a stack of papers
    • Biological Dictionaries aid in the curation of complex knowledge
    • Sharing causal interactions with PSICQUIC
    • Biological modeling: a Prelude
    • Clean Code
    • Get the right rules
    • Discussion & Future Perspectives
  • Appendix
  • Links to software, documentation and data analyses
    • GitHub organizations
    • Documentation
    • DrugLogics software modules
    • R community packages
    • Miscellaneous data analyses and repositories
  • References
  • Published with bookdown

Software implementations allowing new approaches toward data analysis, modeling and curation of biological knowledge for Systems Medicine

Links to software, documentation and data analyses

GitHub organizations

  • UniBioDicts: https://github.com/UniBioDicts/
  • VSM: https://github.com/vsm
  • DrugLogics: https://github.com/druglogics
  • PSICQUIC: https://github.com/PSICQUIC

Documentation

  • DrugLogics software: https://druglogics.github.io/druglogics-doc/
  • VSM technology and related projects: https://vsm.github.io/
  • PSICQUIC: https://psicquic.github.io/

DrugLogics software modules

  • gitsbe: A Java module that defines Boolean models compliant with observed behavior (e.g. steady state or perturbation data) using an automated, model parameterization genetic algorithm
  • drabme: A Java module that performs a drug perturbation response analysis to the Boolean model ensembles generated by Gitsbe
  • druglogics-synergy: A Java module to execute serially Gitsbe and then Drabme
  • abmlog: A Java-based generator of all possible logical models with AND/OR-NOT link operators in their respective Boolean equations (Figure 7)
  • druglogics-roc: R Shiny web app to visualize the ROC and PR prediction performance of Drabme’s ensemble-wise predictions (Figure 6)
  • emba: R package for analysis and visualization of biomarkers in Boolean model ensembles [3]

R community packages

  • usefun: various useful R functions
  • rtemps: templates for reproducible data analyses with R [173]

Miscellaneous data analyses and repositories

All the following repositories have been authored exclusively by myself. Each repository has a README.md file with a brief description of the analysis and a link to online documentation and results (in the form of R Markdown documents or R GitBooks).

  • cascade: repository of the different versions of the CAncer Signaling CAusality DatabasE developed by the DrugLogics group
  • ags-paper: simulation results and data analyses related to Paper 3
  • sintef-obs-synergies: synergy assessment of the Flobak et al. (2019) [116] drug combination dataset using rbbt [174] and the CImbinator tool [117]
  • brf-bias: data analyses related to the study of truth density bias in standardized Boolean regulatory functions for Paper 5
  • gitsbe-model-analysis: several analyses using Boolean model ensemble datasets generated via Gitsbe and the emba R package to analyze them
  • bool-param-maps: visualization of model parameterization and node importance using UMAP and random forests on the CASCADE 1.0 Boolean model dataset generated by abmlog