diff --git a/4bit BN.png b/4bit BN.png new file mode 100644 index 0000000..f8d5cb3 Binary files /dev/null and b/4bit BN.png differ diff --git a/paper.pdf b/paper.pdf index aed09ff..2189e35 100644 Binary files a/paper.pdf and b/paper.pdf differ diff --git a/paper.tex b/paper.tex index ba201d6..efe9dac 100644 --- a/paper.tex +++ b/paper.tex @@ -70,21 +70,29 @@ \section{Introduction} - +Possible points to mention here: +\begin{itemize} + \item Explain shortly gene regulatory networks (GRN) + \item Explain why boolean networks are used to model GRN + \item Maybe mention history of boolean networks + \item Set the focus to the update scheme as it seems to be rarely covered in the field of GRNs + \item Possible open question about which update scheme might be best to model GRNs. Answer to this must follow in the conclusion +\end{itemize} \section{Boolean networks} -Explain Boolean network and what an update scheme is using the synchronous/parallel scheme. +Explain Boolean network and what an update scheme is using the synchronous/parallel scheme. Also use figure, e.g. \cref{fig:boolean_example} to further visualize and create a better understanding of boolean networks. Also explain what chaotic behavior is due its relevance for the update schemes. \subsection{Notation} -Define clear notation used throughout the paper +Define clear notation used throughout the paper. Position of this subsection could change to be part of the Introduction instead. \section{Update Schemes} -Explain different update schemes including characteristics for behavior especially chaotic behavior. +Explain different update schemes including characteristics for behavior especially chaotic behavior. These will mostly focus on boolean networks only. Maybe mention of use-cases for each update scheme. + \subsection{Synchronous scheme} -all nodes update at the same time +The Synchronous (also known as Parallel) update scheme assumes that every node is updated at once. \subsection{Sequential scheme} close to synchronous. the nodes update in a specific order and take into account the updated input node if that node had been updated before/is positioned earlier in the sequence \subsection{Block-sequential scheme} @@ -96,26 +104,30 @@ same as asynchronous deterministic with the slight change that within the sequen \section{Relevance for Gene Regulatory Networks} +\label{sec:relevance_grn} Tie the update schemes and their different outcomes or behavior to GRN. Emphasizing the drawbacks of asynchronous models when applied to GRN e.g. it takes way to long to update a GRN using asynchronous deterministic for it to have an effect; assuming that one update takes a few minutes, when the whole process can take days to complete.\cite{schwab2020concepts} \section{Conclusion} +Not yet included: robustness! might be covered for each update scheme individually. + References: \cite{schwab2020concepts}\cite{aracena2009robustness}\cite{bornholdt2008boolean}\cite{goles2010block}\cite{helikar2011boolean} -\begin{figure*} % The starred version uses both columns; unstarred only one column +\begin{figure} % The starred version uses both columns; unstarred only one column \centering - % \includegraphics[width=5in]{edge_vs_hyperedge.png} + \includegraphics[width=3in]{4bit BN.png} % TIP: Ensure the original image file has approximately the right dimensions % (if using matplotlib, specify correct figure size) so that the image is not rescaled too brutally. - \caption{Boolean example. - % NB: The '~' inserts a non-breaking space, ensuring 'Ref.' is never separated from its number - Simple boolean network example; a graph of the network and most likely a table as well for the updated states $x(t) \rightarrow x(t+1)$ - } -\end{figure*} + \caption{Boolean example (image will be changed!). + % NB: The '~' inserts a non-breaking space, ensuring 'Ref.' is never separated from its number + Simple boolean network example; a graph of the network and most likely a table as well for the updated states $x(t) \rightarrow x(t+1)$ (currently missing) + } +\label{fig:boolean_example} +\end{figure} \begin{figure*} % The starred version uses both columns; unstarred only one column \centering