Changeset 18 for liacs/pnbm/project/report.tex

Timestamp:

Dec 1, 2009, 11:27:26 PM (15 years ago)

Author:

Rick van der Zwet

Message:

Revised model

File:

• liacs/pnbm/project/report.tex (modified) (5 diffs)

liacs/pnbm/project/report.tex

@@ -47 +47 @@
 proteins (figure: blue) are leading in a second process of the creation of
 gradients which also needs modeling. We assume a 1:1 mapping between the amount
-of proteins and gradients -this taken into consideration- ones an $INITIAL$
-protein is used in this process it get called $ACTIVATED$. We assume that the
-proteins to gradients process is starting at an certain time from the start of
-the process.
+of proteins and gradients -this taken into consideration- ones an \texttt{INITIAL}
+protein is 'used' (e.g. has on posterisation counterpart) in this process it
+get called \texttt{ACTIVATED}. We assume that the proteins to posterisation
+process is taking place at the same time as the proteins distribution. And in a
+special format (figure: object B). It tries to matches the posterisation to the
+same level as the proteins present. But the moment the protein level lowers,
+the posterisation will remain the same. In pseudo-code:
+\begin{verbatim}
+if numPos < numProteins then
+    numPos = numPos + 1
+endif
+\end{verbatim}
+\texttt{numProteins} is the proteins available and \texttt{numPos} is the
+posterisation present.
 
 The connectors between the cells (the membrams) has a special properly. One
 can see them as pressure valves others as sighons (see Fig~\ref{fig:pressure}).
 The moment the 'volume' at complies with the following properly $A / 2 < B$
-then the pressure closes, else it passes volume from A to B at an certain rate.
+then the pressure closes, else it passes volume from A to B at an certain rate
+(\texttt{flowSpeed}). This rate could depend on the difference, actual value present
+or something else.
+
 For the case there exists no standard PetriNet 'component', hence  this require
 the creation of a new property (figure: $2:1$), with the following properties:
 
 \begin{verbatim}
-flowSpeed = 2
+flowSpeed = n
 if A > 2 * B then
   A = A - flowSpeed
@@ -72 +85 @@
 Planar signaling could theoretically start in every cell, by
 inserting some amount of protiens. In our model represented as a bunch of
-$INITIAL$ tokens beeing put in a random cell.
+\texttt{INITIAL} tokens beeing put in a random cell.
 
 \begin{figure}[htp]
 \centering
 \caption{Planar signaling model}
-\includegraphics[width=60mm]{planar-signaling-model.eps}
+\includegraphics[width=100mm]{planar-signaling-model.eps}
 \label{fig:model}
 \end{figure}
@@ -96 +109 @@
 workaround for this (see Fig~\ref{fig:CPNplanar}) we used a 'dump' gradation
 function. In our case it simply take 3 tokens and pushes 1 forward and
-converting 2 directly to $ACTIVATED$. This does not take in consideration if
-the amount get changed in 'further-up', by some external source.
+converting 2 directly to \texttt{ACTIVATED}. This does not take in
+consideration if the amount get changed in 'further-up', by some external
+source.
 
 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;
 meaning firing sequences which will occur at an certain time. This could for
-example used to 'trigger' a timmed activation of the $INITIAL$ to $ACTIVATED$
-process as modeled in fig~\ref{fig:model}.
+example used to 'trigger' a timmed activation of the \texttt{INITIAL} to
+\texttt{ACTIVATED} process as modeled in fig~\ref{fig:model}. An initial idea
+is shown at fig\ref{fig:time-idea} in appendix 1.
+
 
 \begin{figure}[htp]
@@ -139 +155 @@
 
 \end{thebibliography}
+\section{*Appendix}
+
+\begin{figure}[htp]
+\centering
+\caption{Timed transition idea}
+\includegraphics[width=0.5\textwidth]{timer-proposal.eps}
+\label{fig:time-idea}
+\end{figure}
 \end{document}