IGEM:Melbourne/2008/BioClock/Version2/Stage1 Modelling

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Okay, here goes the first model for Di's binary clock bit1.

A couple of things to note:

  • parameters such as reaction rates are arbitrary.
  • all components are hypothetical.

bit1 biochemical pathway

Di, I still think the inhibition from InhibitOff should act on the self-promotion loop of Off since without the production of B1, the pathway from Tr1P to Off does not exist, therefore the only thing to repress is the self-promotion of Off. In addition, to achieve the modelling of a stronger promotion from Tr1P and a weaker self-promotion from Off, in relation to the Inhibition from InhibitOff, this shall be the way to represent their pathways.

Input Signal pulse
Input Signal pulse
Output reporter molecule
Output reporter molecule
Signalling molecule for bit2
Signalling molecule for bit2

As we can see, Sg1 does not follow the pulsing pattern, which should be due to parameter settings in the model. This shall be improved after a parameter test is taken.

In addition, the oscillation of B1 and On1 is not completely satisfying since their minimum values are still within ranges of their effectivity. However, these should again be taken as the results of inaccurate parameter assignment.

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