Table 1

Equations and threshold inequalities used to simulate the TOL network

PL equations for the TOL model

Description


1

dupper/dt = k0upper * s+ (XylR, θXylR) * s+ (mxyl, θmxyl) - gupper * upper

Upper pathway expression

2

dXylS/dt = k0XylS + k1XylS * s+ (XylR, θXylR) * s+ (mxyl, θmxyl) - gXylS * XylS

XylS expression

3

dmeta/dt = k0meta * s+ (XylS, θ2XylSh) + k1meta * s+ (XylS, θ1XylSi) * s+ (upper, θupper) * s+ (mxyl, θmxyl)

- gmeta * meta

Meta pathway expression

4

dXylR/dt = k0XylR - gXylR * XylR

XylR expression


Parameter inequalities


zeroupper upper < k0upper/gupper < maxupper

Parameter inequalities for equation 1

zeroXylS < θ1XylSi < k0XylS/gXylS < θ2XylSh < (k0XylS + k1XylS)/gXylS < maxXylS

Parameter inequalities for equation 2

zerometa < θmeta< k0meta/gmeta < k1meta/gmeta < (k0meta + k1meta)/gmeta < maxmeta

Parameter inequalities for equation 3

zeroXylRXylR < k0XylR/gXylR < maxXylR

Parameter inequalities for equation 4


Alternative parameter inequalities


zeroXylS < θ1XylSi < k0XylS/gXylS < (k0XylS + k1XylS)/gXylS < θ2XylSh < maxXylS

No XylS hyper-expression condition (for eq. 2)

zeroupper < k0upper/gupper upper < maxupper

No XylSa condition (for eq. 1)


Silva-Rocha et al. BMC Systems Biology 2011 5:191   doi:10.1186/1752-0509-5-191

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