DYNAMO

These are codes associated to the article:

Santolini,M. and Barabasi,A.-L. (2018) Predicting perturbation patterns from the topology of biological networks. Proc Natl Acad Sci USA, 169, 201720589. (pdf)

A test model BIOMD0000000404.xml corresponding to bacterial chemotaxis is provided.

Jacobian computation

First compute the Jacobian using compModelSensitivityAndJacobian.m. It is a Matlab code and it requires the library libSBML to be installed (http://sbml.org/Software/libSBML/Downloading_libSBML#MATLAB). In the paper, SBML Toolbox 4.1.0 was used. The key libSBML functions that are used in our context are in the subfolder codes_libSBML.

Computation of DYNAMO accuracies

The core of the DYNAMO computation and accuracy evaluation are done in compAccuracies.R (reproduces figure 4b).

Comparison between model accuracy and network features

The code plotAccuracyVsFeatures.R computes the association between model accuracy and network features once DYNAMO has been used for several BioModels (reproduces figure 2G).