Difference between revisions of "Model Overview"
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default [[Welcome to the In-Silico Model of γ-butyrolactone regulation in Streptomyces coelicolor|Go back to overview]] | default [[Welcome to the In-Silico Model of γ-butyrolactone regulation in Streptomyces coelicolor|Go back to overview]] | ||
</imagemap> | </imagemap> | ||
+ | |||
+ | == Model scripts == | ||
+ | |||
+ | The model scripts for the different scenarios can be found in pdf form here: [[File:GBL_Models.pdf]] | ||
== List of Model Reactions == | == List of Model Reactions == | ||
− | <sup>*1</sup> Reactions taking place only in the | + | <sup>*1</sup> Reactions taking place only in the scenarios which includes the activating complex <math>AR_{2}</math> |
− | <sup>*2</sup> Reactions taking place only in the | + | <sup>*2</sup> Reactions taking place only in the scenarios which includes the antisense RNA interactions |
+ | |||
+ | <sup>*3</sup> Reactions taking place only in the scenarios which include the activation of ''scbA'' by <math>R_{2}</math> | ||
{|class="wikitable" | {|class="wikitable" | ||
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! Reactions | ! Reactions | ||
|- | |- | ||
− | |<math>O_{R} + R_{2} \rightleftharpoons O_{R} | + | |<math>O_{R} + R_{2} \rightleftharpoons O_{R} \bullet R_{2}</math> |
− | <math>O_{R} | + | <math>O_{R}\bullet R_{2} + R_{2} \rightleftharpoons O_{R}\bullet 2R_{2}</math> |
− | <math>O_{A} + R_{2} \rightleftharpoons O_{A} | + | <math>O_{A} + R_{2} \rightleftharpoons O_{A}\bullet R_{2}</math> |
− | <math>O_{A} | + | <math>O_{A}\bullet R_{2} + R_{2} \rightleftharpoons O_{A}\bullet 2R_{2}</math> |
<math>A + R_{2} \rightleftharpoons AR_{2}</math> <sup>*1</sup> | <math>A + R_{2} \rightleftharpoons AR_{2}</math> <sup>*1</sup> | ||
− | <math>2C + R_{2} \rightleftharpoons C_{2} | + | <math>2C + R_{2} \rightleftharpoons C_{2}\bullet R_{2}</math> |
− | <math>O_{A} + AR_{2} \rightleftharpoons O_{A} | + | <math>O_{A} + AR_{2} \rightleftharpoons O_{A}\bullet AR_{2}</math> <sup>*1</sup> |
− | <math>O_{A} | + | <math>O_{A}\bullet R_{2} + AR_{2} \rightleftharpoons O_{A}\bullet R_{2}\bullet AR_{2}</math> <sup>*1</sup> |
− | <math>O_{A} | + | <math>O_{A}\bullet 2R_{2} + AR_{2} \rightleftharpoons O_{A}\bullet 2R_{2}\bullet AR_{2}</math> <sup>*1</sup> |
− | <math>O_{A} | + | <math>O_{A}\bullet AR_{2} + R_{2} \rightleftharpoons O_{A}\bullet R_{2}\bullet AR_{2}</math> <sup>*1</sup> |
− | <math>O_{A} | + | <math>O_{A}\bullet R_{2}\bullet AR_{2} + R_{2} \rightleftharpoons O_{A}\bullet 2R_{2}\bullet AR_{2}</math> <sup>*1</sup> |
<math>S \xrightarrow{A} C</math> | <math>S \xrightarrow{A} C</math> | ||
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<math>O_{A} \rightarrow O_{A} + a</math> | <math>O_{A} \rightarrow O_{A} + a</math> | ||
− | <math>O_{A} | + | <math>O_{A}\bullet AR_{2} \rightarrow O_{A}\bullet AR_{2} + a</math> <sup>*1</sup> |
+ | |||
+ | <math>O_{A}\bullet R_{2} \rightarrow O_{A}\bullet R_{2} + a</math> <sup>*3</sup> | ||
+ | |||
+ | <math>O_{A}\bullet 2R_{2} \rightarrow O_{A}\bullet 2R_{2} + a</math> <sup>*3</sup> | ||
+ | |||
+ | <math>O_{A}\bullet R_{2}\bullet AR_{2} \rightarrow O_{A}\bullet R_{2}\bullet AR_{2} + a</math> <sup>*3</sup> | ||
− | <math>a + r \rightleftharpoons r | + | <math>O_{A}\bullet 2R_{2}\bullet AR_{2} \rightarrow O_{A}\bullet 2R_{2}\bullet AR_{2} + a</math> <sup>*3</sup> |
+ | |||
+ | <math>a + r \rightleftharpoons r\bullet a</math> <sup>*2</sup> | ||
<math>r \rightarrow r + R</math> | <math>r \rightarrow r + R</math> | ||
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<math>C\rightarrow \varnothing</math> | <math>C\rightarrow \varnothing</math> | ||
− | <math>C_{2} | + | <math>C_{2}\bullet R_{2}\rightarrow \varnothing</math> |
<math>AR_{2}\rightarrow \varnothing</math> <sup>*1</sup> | <math>AR_{2}\rightarrow \varnothing</math> <sup>*1</sup> | ||
− | <math>r | + | <math>r\bullet a\rightarrow \varnothing</math> <sup>*2</sup> |
<math>C_{e}\rightarrow \varnothing</math> | <math>C_{e}\rightarrow \varnothing</math> | ||
+ | |||
+ | <math>O_{R}\bullet R_{2} \rightarrow O_{R}\bullet R_{2} + O_{R}</math> | ||
+ | |||
+ | <math>O_{R}\bullet 2R_{2} \rightarrow O_{R}\bullet 2R_{2} + O_{R}</math> | ||
+ | |||
+ | <math>O_{A}\bullet R_{2} \rightarrow O_{A}\bullet R_{2} + O_{A}</math> | ||
+ | |||
+ | <math>O_{A}\bullet 2R_{2} \rightarrow O_{A}\bullet 2R_{2} + O_{A}</math> | ||
+ | |||
+ | <math>O_{A}\bullet AR_{2} \rightarrow O_{A}\bullet AR_{2} + O_{A}</math> | ||
+ | |||
+ | <math>O_{A}\bullet R_{2}\bullet AR_{2} \rightarrow O_{A}\bullet R_{2}\bullet AR_{2} + O_{A}</math> | ||
+ | |||
+ | <math>O_{A}\bullet 2R_{2}\bullet AR_{2} \rightarrow O_{A}\bullet 2R_{2}\bullet AR_{2} + O_{A}</math> | ||
|} | |} | ||
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|−4.6234 | |−4.6234 | ||
|1.0539 | |1.0539 | ||
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|} | |} | ||
− | == Parameters for cell | + | == Parameters for cell growth == |
{|class="wikitable" | {|class="wikitable" | ||
<table border='1' style="text-align:center"> | <table border='1' style="text-align:center"> | ||
! Parameter | ! Parameter | ||
− | ! | + | ! Range of values |
! Units | ! Units | ||
|- | |- | ||
− | | <math>\ | + | |<math>K</math> |
− | |<math> | + | |<math>7.14 \cdot 10^{12} - 9\cdot 10^{12}</math> |
− | |<math> min </math> | + | |cells |
+ | |- | ||
+ | |<math>N_0</math> | ||
+ | |<math>5 \cdot 10^{10} - 2\cdot 10^{11}</math> | ||
+ | |cells | ||
+ | |- | ||
+ | |<math>\mu_{max}</math> | ||
+ | |<math>0.003368 - 0.007499</math> | ||
+ | |<math>min^{-1}</math> | ||
|- | |- | ||
− | | <math> | + | |<math>v</math> |
− | |<math> 0. | + | |<math>0.001482 - 0.5814</math> |
− | |<math> - </math> | + | |<math>min^{-1}</math> |
|- | |- | ||
− | | <math> | + | |<math>m</math> |
− | |<math> | + | |<math>0.47 - 2.46</math> |
− | | | + | |n.a. |
|- | |- | ||
− | |<math> | + | |<math>\lambda</math> |
− | |<math> | + | |<math>330.52 - 883</math> |
− | |<math> | + | |<math>min</math> |
|} | |} | ||
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== Differential equations == | == Differential equations == | ||
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Latest revision as of 17:10, 16 October 2019
Contents
Model scripts
The model scripts for the different scenarios can be found in pdf form here: File:GBL Models.pdf
List of Model Reactions
*1 Reactions taking place only in the scenarios which includes the activating complex
*2 Reactions taking place only in the scenarios which includes the antisense RNA interactions
*3 Reactions taking place only in the scenarios which include the activation of scbA by
Reactions |
---|
*1
*1 *1 *1 *1 *1
*1 *3 *3 *3 *3 *2
*1 *2
|
Parameters for model reactions
Reaction | Parameter | Values in literature | Units | Mode | Spread | Location
parameter (μ) |
Scale
parameter (σ) |
---|---|---|---|---|---|---|---|
Binding of R2 to OR operator | 0.005−5.8 | 0.299 | 6.8 | 0.15471 | 1.1661 | ||
0.09−0.846 | 0.489 | 1.98 | −0.37642 | 0.58225 | |||
Binding of R2 to OA operator | 0.005−5.8 | 0.299 | 6.8 | 0.15471 | 1.1661 | ||
0.09−0.846 | 0.489 | 1.98 | −0.37642 | 0.58225 | |||
Binding of R2 to A | 10.02 | 13.192 | 1.2977 | ||||
1879.7 | 23.13 | 9.9423 | 1.5503 | ||||
Binding of R2 to C | 1.58 | 730.63 | 5.9389 | 2.3412 | |||
0.816 | 244 | 4.2872 | 2.119 | ||||
Binding of A-R2 to OA' operator | 0.005−5.8 | 0.299 | 6.8 | 0.15471 | 1.1661 | ||
0.09−0.846 | 0.489 | 1.98 | −0.37642 | 0.58225 | |||
Synthesis of C | 0.00315−85.5 | 0.094 | 60.49 | 0.87914 | 1.8017 | ||
Transcription of r | 0.16−8.24 | 0.8346 | 3.55 | 0.63056 | 0.90076 | ||
18.2−33 | 20.7 | 1.34 | 3.1107 | 0.28276 | |||
0.0518-14.5 | 0.867 | 4.09 | 0.78694 | 0.96428 | |||
Transcription of a | 0.001−0.2 | 0.0037 | 10.93 | −3.8324 | 1.3259 | ||
0.11−5.65 | 0.572 | 3.5 | 0.2514 | 0.89956 | |||
0.039-8.82 | 0.587 | 3.875 | 0.35255 | 0.94054 | |||
Antisense interaction between r and a | 0.4−89 | 7.8 | 7.27 | 3.4665 | 1.1882 | ||
0.006−6 | 0.223 | 4.8 | −0.43359 | 1.0326 | |||
Translation of R | 0.165−5.86 | 0.744 | 3.2 | 0.42952 | 0.85176 | ||
Translation of A | 0.11−4 | 0.5 | 3.2 | 0.053356 | 0.85327 | ||
Formation of homo-dimer R2 | 2.58-42.9 | 3.89 | 1.9 | 1.6716 | 0.55779 | ||
0.144-51.2 | 1.1997 | 21.7 | 2.5303 | 1.5324 | |||
Degradation of r | 0.03−0.365 | 0.14 | 2.06 | −1.5916 | 0.60824 | ||
Degradation of R | 1.78 | −6.2837 | 0.50981 | ||||
Degradation of R2 | 1.78 | −6.2837 | 0.50981 | ||||
Degradation of a | 0.03−0.365 | 0.14 | 2.06 | −1.5916 | 0.60824 | ||
Degradation of A | 1.78 | −6.2837 | 0.50981 | ||||
Degradation of C | 5.1 | −4.6234 | 1.0539 | ||||
Degradation of C2-R2 | 1.78 | −6.2837 | 0.50981 | ||||
Degradation of A-R2 | 1.78 | −6.2837 | 0.50981 | ||||
Degradation of r-a | 0.35−69.3 | 4.9 | 14.1 | 2.5669 | 0.98835 | ||
Diffusion of C and Ce | 0.1−24 | 2.8 | 4.27 | 1.9947 | 0.98233 | ||
Degradation of Ce | 5.1 | −4.6234 | 1.0539 |