Splcing_PolII.nb

<<myPadRight.m ; <<cellerator.m ; <<kMech.m ; Off[General :: "spell1"] ; Off[General :: "spell"] ;

(* Start Transcription/RNA Splcing Coupling Simulation *)(* NE1 : RNA polymera ... , kf10, kr11, kcat12}},  {{Overscript[mRNA⇄NMP, NEd], kf13, kr14, kcat15}} ]

{{$Complex$NE1$DNA$NTP$DNA + NE1 + premRNA, kcat3}, {$Complex$NEs$premRNA$mRNA ... P, NEd], kf7, kr8, kcat9}, {Overscript[$Complex$NEs$premRNA$⇄NMP, NEd], kf10, kr11, kcat12}}

{myODEs,myVars}=interpret[mRNASplcing]

${{DNA^′[t]  -kf1 DNA[t] NE1[t] NTP[t] + kcat3 $Complex$NE1$DNA$NTP$[t] + kr2 $Co ... $NE1$DNA$NTP$, $Complex$NEs$premRNA$, $Complex$premRNA$NEd$, $Complex$$Complex$NEs$premRNA$$NEd$}}$

Lamda = 1 ;  RowBox[{myKs, =, RowBox[{{, , , RowBox[{RowBox[{KmNE1$DNA ... 2754;Kf[KmNEd$mRNA, kcat15, Lamda], ,, , kr14Kr[kcat15, Lamda]}], , }}]}]

$RowBox[{{, RowBox[{RowBox[{kf1, , 2.5*10^-6}], ,, kr20, ,, RowBox[{kf4, ᢃ ... , , 0.001}], ,, kr110, ,, RowBox[{kf13, , 0.001}], ,, kr140}], }}]$

RowBox[{RowBox[{myICs, =, RowBox[{{, , RowBox[{DNA[0] 12, ,, , NTP[0] ... s$premRNA$$NEd$[0] 0, ,, , $Complex$mRNA$NEd$[0] 0}], , }}]}], ;}]

RowBox[{{, RowBox[{{, RowBox[{RowBox[{DNA, , TagBox[RowBox[{InterpolatingFunction, [, ... x[{{, RowBox[{0., ,, 165.}], }}], }}], ,, <>}], ]}], False, Editable -> False]}]}], }}], }}]

orderedVars={DNA,NTP,premRNA,mRNA,NMP,NE1,NEs,NEd,$Complex$NE1$DNA$NTP$,
$Complex$NEs$premRNA$,$Complex$premRNA$NEd$,$Complex$mRNA$NEd$};

Show[GraphicsArray[
    Partition[
      Map[Plot[#[t]/.mySolution,{t,0,tmax},PlotLabel→#,
            PlotRange→All,DisplayFunction→Identity]&,orderedVars],3]
    ]
  ];

[Graphics:HTMLFiles/Splcing_PolII_15.gif]

$RowBox[{RowBox[{FormalPlot[varName_, displayTime_, YplotRange_], :=, , RowBox[{Plot, [ ... ,, RowBox[{AxesStyle, , RowBox[{{, RowBox[{Thickness, [, 0.0006, ]}], }}]}]}], ]}]}], ;}]$

RowBox[{RowBox[{P1, =, RowBox[{DotPlot, [, RowBox[{mRNA, ,, tmax, ,, RowBox[{{, RowBox[{0, ,, ... , RowBox[{{, RowBox[{0, ,, 0.1}], }}]}], ,, DisplayFunction$DisplayFunction}], ]}], ;}]

<<Graphics`MultipleListPlot`(* Time points (min) : 15, 40, 65, 90, 115, ... ,, RowBox[{AxesStyle, , RowBox[{{, RowBox[{Thickness, [, 0.0006, ]}], }}]}]}], ]}]}], ;}]

[Graphics:HTMLFiles/Splcing_PolII_20.gif]

[Graphics:HTMLFiles/Splcing_PolII_23.gif]

[Graphics:HTMLFiles/Splcing_PolII_25.gif]

[Graphics:HTMLFiles/Splcing_PolII_27.gif]

Created by Mathematica (December 16, 2004)