CANAlization: Control & Redundancy in Boolean Networks

This package implements a series of methods used to study control, canalization and redundancy in Boolean Networks.

If you are using this package, please consider citing the following papers:

[GRBCR21] “A.J. Gates, R.B. Correia, X. Wang, & L.M. Rocha [2021]. “The effective graph reveals redundancy, canalization, and control pathways in biochemical regulation and signaling”. Proceedings of the National Academy of Sciences (PNAS), 118 (12). doi: 10.1073/pnas.2022598118”

[CGWR18] “R.B. Correia, A. Gates, X. Wang and L.M. Rocha [2018]. “CANA: A python package for quantifying control and canalization in Boolean Networks.” Frontiers in Physiology, 9: 1046. doi: 10.3389/fphys.2018.01046.”

[GR16] “A. Gates and L.M. Rocha. [2016] “Control of complex networks requires both structure and dynamics.” Scientific Reports 6, 24456. doi: 10.1038/srep24456.”

[GR14] “A. Gates and L.M. Rocha [2014]. “Structure and dynamics affect the controllability of complex systems: a Preliminary Study”. Artificial Life 14: Proceedings of the Fourteenth International Conference on the Synthesis and Simulation of Living Systems: 429-430, MIT Press.”

[MPR13] “M. Marques-Pita and L.M. Rocha [2013]. “Canalization and control in automata networks: body segmentation in Drosophila Melanogaster”. PLoS ONE, 8 (3): e55946. doi:10.1371/journal.pone.0055946.”

Documentation:

Tutorials: For examples of utilization pleasee see tutorials in github.com/rionbr/CANA.

Table of Contents:

• API Reference
  • Node
    • Boolean Node
  • Network
    • Boolean Network
    • BNS Attractors Interface
  • Canalization
    • Boolean Canalization
  • Control
    • Dynamics based control
    • Structure based control
  • Datasets
    • Boolean Nodes
    • Biological Boolean Networks
    • Network Motifs
  • Ensemble Methods
    • Random Boolean Network
  • Utilities
• Appendix
  • R
• Bibliography

Indices and tables

• Index

• Module Index

• Search Page