IGEM:Melbourne/2008/BioClock/Version2/Stage1 Modelling: Difference between revisions
No edit summary |
No edit summary |
||
| (One intermediate revision by the same user not shown) | |||
| Line 5: | Line 5: | ||
Okay, here goes the first model for Di's binary clock bit1. | Okay, here goes the first model for Di's binary clock bit1. | ||
A | A couple of things to note: | ||
* parameters such as reaction rates are arbitrary. | * parameters such as reaction rates are arbitrary. | ||
| Line 11: | Line 11: | ||
* all components are hypothetical. | * all components are hypothetical. | ||
---- | ---- | ||
[[Image: | [[Image:Model.png|1000px|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. | 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. | ||
| Line 27: | Line 26: | ||
[[Image:On1.jpg|thumb|right|400px]] | [[Image:On1.jpg|thumb|right|400px]] | ||
[[Image: | [[Image:Sg1 updated.bmp|thumb|left|400px|Signalling molecule for bit2]] | ||
Latest revision as of 17:53, 28 January 2008
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.
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.
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.
