In dkaschek/dMod: Dynamic Modeling and Parameter Estimation in ODE Models

PEtab is a data format thought for the straight forward exchange of models between tools with regard to parameter estimation. It covers SBML models along with their data, observable, parameter and condition specifications. PEtab2dMod is a tool to import such PEtab files in dMod. Basic functions are provided for import, visualization and further processing.

knitr::opts_chunk$set(echo = TRUE, fig.width = 10, fig.height = 3.5)

Installation

The usage of PEtab2dMod requires libSBML. The libSBML R source package can be downloaded as tar.gz file provided by SBML and installed as R package. PEtab2Mod is delivered along with the current version of dMod?!

Loading a model

In order to use PEtab2dMod and import a model, data, observable, condition and parameter files have to meet the requirements specified by PEtab.

As a first step, we have to load dMod, which includes all necessary PEtab2dMod functions as well as a collection of Benchmark models.

library(dMod)
library(PEtab2dmod) # hopefully not necessary anymore

Now import and plotting functions are available. As an example we will import and plot Boehm_JProteomeRes2014, which is a STAT5 activation model in BaF3-EpoR cells.

importPEtabSBML(modelname = "Boehm_JProteomeRes2014", path2model = "../BenchmarkModels/") 

plotPEtabSBML(name%in%names(observables))

Happy PEtab import!!

dkaschek/dMod documentation built on April 23, 2024, 5:18 p.m.