Technical Notes

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Choosing Ranges for transsys Numeric Parameters

transsys programs include the following seven types of parameters:

  • decay rate (in decay statements of factor declarations)
  • diffusibility (in diffusibility statements of factor declarations)
  • constitutive expression rate (in constitutive promoter elements)
  • activation specificity (in activate promoter elements)
  • maximal activation (in activate promoter elements)
  • repression specificity (in repress promoter elements)
  • maximal repression (in repress promoter elements)

When given a set of target gene expression levels and the task to choose parameters for a transsys program to match these levels, the following rules may prove useful.

Decay Rates

The decay rates determine the time scale of gene expression dynamics, and particularly the number of time steps required for gene expression levels to equilibrate. The number of time steps should therefore be at least 10 * 1.0 / d, where d is the smallest decay rate.

From this perspective it is reasonable to use a lower limit for the decay rate. As a coarse estimate we will assume that the average is 2 * d.

Constitutive Expression Rates

Maximal Activation and Repression Rates

Activation and Repression Specificities