BioMASS.jl

This module provides a Julia interface to the BioMASS parameter estimation.

The open access publication describing BioMASS is available here:

• Imoto, H., Zhang, S. & Okada, M. A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway. Cancers 12, 2878 (2020). https://doi.org/10.3390/cancers12102878

Installation

] add BioMASS

• Parameter Estimation
• • Core functions
  • • Model(path_to_model::String)
    • scipy_differential_evolution(model::Model, ix_id::Int, kwargs...)
    • run_simulation(model::Model, viz_type::String, show_all::Bool=false, stdev::Bool=false)
  • Estimate unknown model parameters
  • Simultaneous parameter optimization
  • • Using module Distributed
    • Calling multiple bash scripts
  • How to track optimization process
  • Visualization of simulation results
• Bifurcation Analysis
• • Procedure for stability analysis at fixed points
  • Usage
  • • Prepare name2idx/ to define model species and parameters
    • Create set_model.jl
    • Run create_diffeq function
    • Load requirements
    • Calculate fixed points and analyze their stability
    • Plot results
    • Run all functions defined above