Minnesota/22 June 2009

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|'''[[Minnesota/19 June 2009|Go to Previous Day (June 19)]]'''|| width=158|'''[[Minnesota/23 June 2009|Go to Next Day (June 23)]]'''
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|}
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'''Patrick'''<br>
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I figured out how to fix the issue with deleting reactions. Unfortunately, changing designGUI appears to be impossible. So a work-around needs to be established for the non-linear parameter variations.
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'''Ben'''<br>
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Here is the first incarnation of the TNN model (many future models will simply change this one):
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{| class="wikitable" style="text-align:center" border = "1"
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|-
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! Reaction
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! Forward Kinetic Constant
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! Reverse Kinetic Constant
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|-
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| RNAp + lacP + lacI4:lacO1 ->  RNAp:lacP||6.23E+05||
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|-
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| RNAp + lacP + lacO1 ↔ RNAp:lacP||1E+07|| 1
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|-
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|RNA:lacP -> RNAp:lacP* || .01 ||
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|-
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|RNAp:lacP* -> lacP + lacO1 + RNAp:DNAgfp||30||
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|-
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|RNAp:DNAgfp -> RNAp + gfp_mRNA||30||
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|-
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|gfp_mRNA + rib -> rib:gfp_mRNA||100000||
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|-
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|rib:gfp_mRNA -> rib:gfp_mRNA_1 + gfp_mRNA||33||
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|-
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|rib:gfp_mRNA_1 -> rib + gfp||33||
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|-
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|tetR2 + aTc ↔ tetR2:aTc||2E+09||4E-04
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|-
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|tetR2:aTc + aTc  ↔ tetR2:aTc2||1E+08||1E-03
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|-
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|tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc||1E+08||1
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|-
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|tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc2||1E+08||1E+05
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|-
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|tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc||1E+08||1E-03
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|-
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|tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc2||1E+08||1E-03
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|-
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|tetR2 -> Ø||2.89E-04||
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|-
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|tetR2:aTc -> aTc||2.89E-04||
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|-
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|tetR2:aTc2 -> 2 aTc||2.89E-04||
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|-
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|tetR2 + nsDNA ↔  tetR2:nsDNA||1000||3.2409
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|-
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|tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA||1000||3.2409
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|-
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|tetR2:aTc:nsDNA -> aTc + nsDNA||1.93E-04||
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|-
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|tetR2:nsDNA -> nsDNA||1.93E-04||
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|-
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|Ø -> tetR2||1E-11||
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|-
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|Ø -> aTc||3.3E-04||
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|-
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|gfp_mRNA -> Ø||1.16E-03||
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|-
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|gfp -> Ø||3.21E-05||
|}
|}

Latest revision as of 21:15, 29 July 2009

Back to Notebook Home
Go to Previous Day (June 19)Go to Next Day (June 23)

Patrick
I figured out how to fix the issue with deleting reactions. Unfortunately, changing designGUI appears to be impossible. So a work-around needs to be established for the non-linear parameter variations.

Ben
Here is the first incarnation of the TNN model (many future models will simply change this one):

Reaction Forward Kinetic Constant Reverse Kinetic Constant
RNAp + lacP + lacI4:lacO1 -> RNAp:lacP6.23E+05
RNAp + lacP + lacO1 ↔ RNAp:lacP1E+07 1
RNA:lacP -> RNAp:lacP* .01
RNAp:lacP* -> lacP + lacO1 + RNAp:DNAgfp30
RNAp:DNAgfp -> RNAp + gfp_mRNA30
gfp_mRNA + rib -> rib:gfp_mRNA100000
rib:gfp_mRNA -> rib:gfp_mRNA_1 + gfp_mRNA33
rib:gfp_mRNA_1 -> rib + gfp33
tetR2 + aTc ↔ tetR2:aTc2E+094E-04
tetR2:aTc + aTc ↔ tetR2:aTc21E+081E-03
tetR2:aTc + tetO1 ↔ tetR2:tetO1:aTc1E+081
tetR2:aTc2 + tetO1 ↔ tetR2:tetO1:aTc21E+081E+05
tetR2:tetO1 + aTc ↔ tetR2:tetO1:aTc1E+081E-03
tetR2:tetO1:aTc + aTc ↔ tetR2:tetO1:aTc21E+081E-03
tetR2 -> Ø2.89E-04
tetR2:aTc -> aTc2.89E-04
tetR2:aTc2 -> 2 aTc2.89E-04
tetR2 + nsDNA ↔ tetR2:nsDNA10003.2409
tetR2:aTc + nsDNA ↔ tetR2:aTc:nsDNA10003.2409
tetR2:aTc:nsDNA -> aTc + nsDNA1.93E-04
tetR2:nsDNA -> nsDNA1.93E-04
Ø -> tetR21E-11
Ø -> aTc3.3E-04
gfp_mRNA -> Ø1.16E-03
gfp -> Ø3.21E-05
Retrieved from "http://2009.igem.org/Minnesota/22_June_2009"