The BioMASS module for Julia

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

Features

BioMASS.jl supports:

• parameter estimation of ODE/DDE models
• visualization of simulation results
• bifurcation analysis

Usage

using BioMASS

model = load_model("./examples/fos_model");

# Estimate unknown model parameters against experimental observations.
optimize(model, 1, max_generation=20000, allowable_error=0.5)

# Save simulation results to figure/ in the model folder
visualize(model, viz_type="best", show_all=true)

Convert optimized parameters to BioMASS format

param2biomass("./examples/fos_model")

Installation

The package is a registered package, and can be installed with Pkg.add.

julia> using Pkg; Pkg.add("BioMASS")

or through the pkg REPL mode by typing

] add BioMASS

References

• Nakakuki, T. et al. Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell141, 884–896 (2010). https://doi.org/10.1016/j.cell.2010.03.054

• Inoue, K. et al. Oscillation dynamics underlie functional switching of NF-κB for B-cell activation. npj Syst. Biol. Appl.2, 16024 (2016). https://doi.org/10.1038/npjsba.2016.24

• Yao, G., Lee, T. J., Mori, S., Nevins, J. R. & You, L. A bistable Rb-E2F switch underlies the restriction point. Nat. Cell Biol.10, 476–482 (2008). https://doi.org/10.1038/ncb1711

• Barr, A. R., Heldt, F. S., Zhang, T., Bakal, C. & Novák, B. A Dynamical Framework for the All-or-None G1/S Transition. Cell Syst.2, 27–37 (2016). https://doi.org/10.1016/j.cels.2016.01.001

• Rata, S. et al. Two Interlinked Bistable Switches Govern Mitotic Control in Mammalian Cells. Curr. Biol.28, 3824-3832.e6 (2018). https://doi.org/10.1016/j.cub.2018.09.059