BONITA

BONITA (Boolean Omics Network Invariant-Time Analysis) is a software tool for pathway analysis of high-throughput omics data. It addresses the limitations of existing methods by incorporating signal flow and integration represented by pathway topology. The key features and functionalities of BONITA are:

1. Discrete state network modeling: BONITA models cellular heterogeneity using discrete state dynamics, simplifying parameterization for large-scale data analysis.

2. Signal propagation: The tool propagates binary signals repeatedly across networks, modeling heterogeneity in transcriptomic data due to intercellular heterogeneity rather than intracellular stochasticity.

3. Signal integration: Logic rules defining signal integration are inferred by a genetic algorithm and refined by local search. These rules determine the impact of each node in a pathway.

4. Pathway scoring: BONITA scores the probability of a pathway's modulation by chance based on the impact of each node.

Topic

Molecular interactions, pathways and networks;Transcriptomics;Drug discovery

Detail

  • Operation: Enrichment analysis;Pathway or network analysis;Network simulation

  • Software interface: Command-line user interface

  • Language: Python

  • License: Not stated

  • Cost: Free of charge

  • Version name: 1.0.0

  • Credit: National Institutes of Health, National Library of Medicine, National Institute of Allergy and Infectious Disease.

  • Input: -

  • Output: -

  • Contact: Juilee Thakar juilee_thakar@urmc.rochester.edu

  • Collection: -

  • Maturity: -

Publications

  • Executable pathway analysis using ensemble discrete-state modeling for large-scale data.
  • Palli R, et al. Executable pathway analysis using ensemble discrete-state modeling for large-scale data. Executable pathway analysis using ensemble discrete-state modeling for large-scale data. 2019; 15:e1007317. doi: 10.1371/journal.pcbi.1007317
  • https://doi.org/10.1371/JOURNAL.PCBI.1007317
  • PMID: 31479446
  • PMC: PMC6743792

Download and documentation

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