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\begin{document}

\title{Influence of update schemes on gene regulatory networks}

% author information
% COMMENT OUT THESE LINES FOR YOUR CONFERENCE SUBMISSION!
\author{Tom Zuidberg \\ 455969}

\maketitle
\thispagestyle{plain}
\pagestyle{plain}

\begin{abstract}
    In this paper we will introduce boolean networks (BN) and their relevance to gene regulatory networks (GRN). We will have a closer look on update schemes. Specifically, synchronous, sequential and asynchronous update schemes and their effect on the behavior of BN and GRN respectively.
\end{abstract}


\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. 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. 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. These will mostly focus on boolean networks only. Maybe mention of use-cases for each update scheme.

\subsection{Synchronous scheme}
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}
mix of synchronous and sequential. predefined blocks update sequential, inside a block the update follows the synchronous scheme
\subsection{Asynchronous deterministic}
one node is updated per tick following a specific sequence
\subsection{Asynchronous generalized}
same as asynchronous deterministic with the slight change that within the sequence nodes may appear multiple times.


\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
	\centering
	\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 (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

	\caption{
		graph of all possible states for a boolean network using a synchronous update scheme
	}

\end{figure*}

\begin{figure*}  % The starred version uses both columns; unstarred only one column
	\centering
	% \includegraphics[width=5in]{edge_vs_hyperedge.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{
		example graph of boolean network showcasing grouping of specific nodes.
	}

\end{figure*}


% The list of references is provided as `references.bib`
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\bibliography{IEEEabrv,references}

\end{document}
