LikelihoodProfiler

LikelihoodProfiler is a Julia language package for identifiability analysis and confidence intervals estimation.

See documentation.

Use cases

Notebooks with use cases can be found in a separate repository: https://github.com/insysbio/likelihoodprofiler-cases

Case	Ref
PK model with saturation in elimination
Local optim methods comparison
TGF-β Signaling Pathway Model
SIR Model. A simple model used as an exercise in identifiability analysis.
Cancer Taxol Treatment Model
STAT5 Dimerization Model

Installation

julia> ]

(v1.7) pkg> add LikelihoodProfiler

Quick start

using LikelihoodProfiler

# testing profile function
f(x) = 5.0 + (x[1]-3.0)^2 + (x[1]-x[2]-1.0)^2 + 0*x[3]^2

# Calculate parameters intervals for first parameter component, x[1]
res_1 = get_interval(
  [3., 2., 2.1], # starting point
  1,             # parameter component to analyze
  f,             # profile function
  :LIN_EXTRAPOL; # method
  loss_crit = 9. # critical level of loss function
  )
#

# Plot parameter profile x[1]
using Plots
plotly()
plot(res_1)

License

MIT Public license

How to cite

Borisov I, Metelkin E (2020) Confidence intervals by constrained optimization—An algorithm and software package for practical identifiability analysis in systems biology. PLoS Comput Biol 16(12): e1008495.

Ref: https://doi.org/10.1371/journal.pcbi.1008495