The model space is defined as a so called S-system model. The S-system formalism (Savageau 1976, Voit 2000) is based on approximating kinetic laws with multivariate power-law functions. A model consists ofa n non-linear ODEs and the generic form of equation i reads
Xi'(t) = αi ∏j=1..n Xj(t)gij - βi ∏j=1..n Xj(t)hij
where X is a vector (length n) of dependent variables, α and β are vectors (length n) of non-negative rate constants and g and h are matrices (n*n) of kinetic orders, that can be negative as well as positive.
Data is presented in Ronen et al. (2002) and applied in Cho et al. (2006). Six variables are measured in time-series, uvrD (X1), lexA (X2), umuD (X3), recA (X4), uvrA (X5) and polB (X6).
ss_sosrepair1 is presented in Cho et al. (2006). Prior structure is assumed in form of non-zero hii's for all i. Since there is only one repetition available, standard deviations can not be estimated from data but are assumed equal to 10% of the measured value.
ss_sosrepair2 is similar to ss_sosrepair1, but here an initial structure based on information in Cho et al. (2006) is assumed known. All genes are assumed negatively regulated by lexA (X2).
Cho,D.Y., Cho,K.H.,Zhang,B.T. (2006) Identification of biochemical networks by S-tree based genetic programming. Bioinformatics, 22, 1631-40. PMID:16585066
Ronen,M., Rosenberg,R., Shraiman,B.I., Alon,U. (2002) Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci U S A., 99, 10555-60. PMID:12145321
Savageau,M.A. (1976) Biochemical systems analysis: a study of function and design in molecular biology (Addison-Wesley, Reading, Mass).
Voit,E.O. (2000) Computational analysis of biochemical systems. A practical guide for biochemists and molecular biologists. Cambridge University Press, Cambridge, 176-184.