Changeset 18 for liacs/pnbm/project/report.tex
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- Dec 1, 2009, 11:27:26 PM (15 years ago)
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liacs/pnbm/project/report.tex
r12 r18 47 47 proteins (figure: blue) are leading in a second process of the creation of 48 48 gradients which also needs modeling. We assume a 1:1 mapping between the amount 49 of proteins and gradients -this taken into consideration- ones an $INITIAL$ 50 protein is used in this process it get called $ACTIVATED$. We assume that the 51 proteins to gradients process is starting at an certain time from the start of 52 the process. 49 of proteins and gradients -this taken into consideration- ones an \texttt{INITIAL} 50 protein is 'used' (e.g. has on posterisation counterpart) in this process it 51 get called \texttt{ACTIVATED}. We assume that the proteins to posterisation 52 process is taking place at the same time as the proteins distribution. And in a 53 special format (figure: object B). It tries to matches the posterisation to the 54 same level as the proteins present. But the moment the protein level lowers, 55 the posterisation will remain the same. In pseudo-code: 56 \begin{verbatim} 57 if numPos < numProteins then 58 numPos = numPos + 1 59 endif 60 \end{verbatim} 61 \texttt{numProteins} is the proteins available and \texttt{numPos} is the 62 posterisation present. 53 63 54 64 The connectors between the cells (the membrams) has a special properly. One 55 65 can see them as pressure valves others as sighons (see Fig~\ref{fig:pressure}). 56 66 The moment the 'volume' at complies with the following properly $A / 2 < B$ 57 then the pressure closes, else it passes volume from A to B at an certain rate. 67 then the pressure closes, else it passes volume from A to B at an certain rate 68 (\texttt{flowSpeed}). This rate could depend on the difference, actual value present 69 or something else. 70 58 71 For the case there exists no standard PetriNet 'component', hence this require 59 72 the creation of a new property (figure: $2:1$), with the following properties: 60 73 61 74 \begin{verbatim} 62 flowSpeed = 275 flowSpeed = n 63 76 if A > 2 * B then 64 77 A = A - flowSpeed … … 72 85 Planar signaling could theoretically start in every cell, by 73 86 inserting some amount of protiens. In our model represented as a bunch of 74 $INITIAL$tokens beeing put in a random cell.87 \texttt{INITIAL} tokens beeing put in a random cell. 75 88 76 89 \begin{figure}[htp] 77 90 \centering 78 91 \caption{Planar signaling model} 79 \includegraphics[width= 60mm]{planar-signaling-model.eps}92 \includegraphics[width=100mm]{planar-signaling-model.eps} 80 93 \label{fig:model} 81 94 \end{figure} … … 96 109 workaround for this (see Fig~\ref{fig:CPNplanar}) we used a 'dump' gradation 97 110 function. In our case it simply take 3 tokens and pushes 1 forward and 98 converting 2 directly to $ACTIVATED$. This does not take in consideration if 99 the amount get changed in 'further-up', by some external source. 111 converting 2 directly to \texttt{ACTIVATED}. This does not take in 112 consideration if the amount get changed in 'further-up', by some external 113 source. 100 114 101 115 Secondly it is missing a possibility to for easy random initialisation for … … 109 123 Also it should be noted that it missing a notion of timed firing sequences; 110 124 meaning firing sequences which will occur at an certain time. This could for 111 example used to 'trigger' a timmed activation of the $INITIAL$ to $ACTIVATED$ 112 process as modeled in fig~\ref{fig:model}. 125 example used to 'trigger' a timmed activation of the \texttt{INITIAL} to 126 \texttt{ACTIVATED} process as modeled in fig~\ref{fig:model}. An initial idea 127 is shown at fig\ref{fig:time-idea} in appendix 1. 128 113 129 114 130 \begin{figure}[htp] … … 139 155 140 156 \end{thebibliography} 157 \section{*Appendix} 158 159 \begin{figure}[htp] 160 \centering 161 \caption{Timed transition idea} 162 \includegraphics[width=0.5\textwidth]{timer-proposal.eps} 163 \label{fig:time-idea} 164 \end{figure} 141 165 \end{document}
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