User:Daniela A. Garcia S./Notebook/Modeling UNAMGenomics Mexico/2010/08/21
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Modeling: PoPS mathematical protocol1) Raw data was processed by first subtracting the appropriate backgrounds. A_{corrected} = A_{raw}  A_{media} G_{corrected} = G_{raw}  G_{media} 2) The data was then converted to absolute units (CFU/well and GFP molecules/well) using the calibration method. CFU = 3.1E8A_{corrected}  1.6E6 GFP = 7.0E8G_{corrected} + 6.0E11 3) Mean synthesis rates of GFP per cell, S_{cell}, were calculated by assuming the total GFP synthesis rate, S_{total}, to be equal to the time differential of GFP. S_{total} = dGFP/dt S_{cell} = S_{total}/CFU 4) To interpret the behavior: the input is defined as the time dependent rate of mRNA synthesis, PoPS(t) (mRNA per cell per sec). The output is the synthesis rate of mature GFP, S_{cell} (GFP molecules per cell per sec). [M] = PoPS(t)  γ_{M}[M], concentration of mRNA per cell [I] = ρ[M]  (α + γ_{I}[I]), the level of immature GFP S_{cell} = α[I]
5) Steady state relationship to calculate the specific output.
Transient output in the response time experiments. It relates the time dependent PoPS output to measured values of S_{cell}.
