Scholma - Biological networks 101 - Computational modeling for molecular biologists

Jetse Scholma, Stefano Schivo, Ricardo A. Urquidi Camacho, Jaco van de Pol, Marcel Karperien, Janine N. Post

Gene - 2013


Computationalmodeling of biological networks permits the comprehensive analysis of cells and tissues to define
molecular phenotypes and novel hypotheses. Although a large number of software tools have been developed,
the versatility of these tools is limited by mathematical complexities that prevent their broad adoption and
effective use by molecular biologists. This study clarifies the basic aspects ofmolecular modeling, howto convert
data into useful input, as well as the number of time points and molecular parameters that should be considered
for molecular regulatory models with both explanatory and predictive potential. We illustrate the necessary
experimental preconditions for converting data into a computational model of network dynamics. This model
requires neither a thorough background in mathematics nor precise data on intracellular concentrations, binding
affinities or reaction kinetics. Finally,we showhowan interactivemodel of crosstalk between signal transduction
pathways in primary human articular chondrocytes allows insight into processes that regulate gene expression.