README.md
In CNORode: ODE add-on to CellNOptR

CNORode: a logic based ordinary differential equation add-on for CellNOptR

This version of CNORode is a continuation of the CNORode2017 package. CNORode2017 was lamor equivalent to CNORode with some added features, such as the sparsity enforcing regularisation and parameter uncertainty analysis based on bootstrapping. Maintaining two packages are time consuming, therefore we decided to merge the packages and continue with CNORode2017.

The older version of CNORode can be downloaded from release_v1.23

We refer to the vignette for learning usage of the classic CNORode.

The added features of the CNORode2017 are summarised on the main site of CNORode2017.

For more general information about the CellNOpt project visit: http://www.cellnopt.org/.

CNORode requires CellNOptR and MEIGOR which are available in Bioconductor and can be installed typing:

source("https://bioconductor.org/biocLite.R")
biocLite("CellNOptR")
biocLite("MEIGOR")

Alternatively, you can obtain the most recent version of CellNOptR from our GitHub repository:

library(devtools)
install_github("saezlab/CellNOptR")

CNORode can be installed from this repository by typing:

library(devtools)
install_github("saezlab/CNORode")

Install the developement version of CNORode:

library(devtools)
install_github("saezlab/CNORode",ref="crossval", build_vignettes = TRUE)

For an introduction on logic based ODE we recommend reading the original publication (Wittmann et al., BMC Syst Biol., 2009). Briefly, logic based ODE are ordinary differential equations (ODE) derived from logic rules using continuous update function (Bi), which allows to have a continuous description of the behaviour of the species of interest both in time and in state. Each species xi is described by an ODE:

d(xi)/dt=τi(Bi(f(xi1), f(xi2), ..., f(xiN))-xi)

where τi is the life-time of the species and xi1, xi2, ... xiN are its N regulators. Each regulation is described by a transfer function f(xij) which can be, for example, a linear relationsip or a sigmoidal (Hill like) curve.

Please visit CNORode2017.