Model parameters based on biological literature are summarized in Table 1.
A set of adequately selected parameters based on biological processes may deliver accurate all-round tumor classification for grouping of uniform tumors for treatment allocation, prediction of treatment response or distinction of patient groups with a different prognosis.
Table 1 summarises estimates of the model parameters based on values reported in the biological literature; these are discussed further in the "Biological Parameter Estimates" section of Additional file 1. Parameters used for both the stochastic and deterministic models.
Furthermore, it is also useful for simulation tools that can consider the concentration of the molecules and adjust parameters based on the type of biological event.
To identify possible plant miRNAs in the viruses genomes we used strict parameters based on experimentally valid miRNA:target pairings to ensure potential biological activity.
The approach of developing a generic disease progression submodel and calibrating its parameters based on outcomes data was taken because of the lack of biological data needed to directly estimate these parameters.
We chose three sets of parameters based on two criteria: representation of a high diversity of the replication phenotype, g ¯, and biological plausibility.
Motivation: Computational models of biological signalling networks, based on ordinary differential equations (ODEs), have generated many insights into cellular dynamics, but the model-building process typically requires estimating rate parameters based on experimentally observed concentrations.
To gain mechanistic insight, we have used parameters based on the hard and soft, acids and bases (HSAB) theory to profile the different aldehyde subclasses with respect to electronic character (softness, hardness), electrophilic reactivity (electrophilic index), and biological nucleophilic targets.
Relationships between mRNA levels of the different target genes, and comparisons between median target gene mRNA levels and clinical, histological and biological parameters were based on nonparametric tests – namely the Mann–Whitney test (link between one qualitative parameter and one quantitative parameter) and the Spearman rank correlation test (link between two quantitative parameters).
