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> ]
(v1.5) pkg> add LikelihoodProfilerQuick 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.