\documentclass[journal,compsoc,10pt]{IEEEtran}

% Load some possibly useful packages. You can remove the ones you don't need or
% add other packages that you need in your paper.
\usepackage{graphicx}                   % required to include graphics
\usepackage{amsfonts,amssymb,amsmath}   % mathsymbols etc
\usepackage{mathtools}                  % includes some fixes to amsmath, and adds convenience macros
\usepackage{bm}                         % make any letter boldface in math
\usepackage{algpseudocode}              % aka `algorithmicx`: same look `algorithmic`, but more flexible
\usepackage{array}                      % for better looking arrays
\usepackage{booktabs}                   % for better looking tables
\usepackage[usenames]{xcolor}           % colors for highlighting etc.
\usepackage{url}                        % for urls
\usepackage[%pdftitle=,                 % define the PDF metadata
            %pdfauthor=,
            colorlinks=true, linkcolor=purple, urlcolor=blue, citecolor=cyan,
            anchorcolor=black   % make links/references 'clickable' without ugly frames
            ]{hyperref}
\usepackage{cleveref}                   % smart references to figures, equations etc.

% some packages which may be useful when drafting, but should be removed before submission
\usepackage{todonotes}

% You can define your own commands. This is useful for shorthands, for example
\newcommand{\EE}{\mathbb{E}}
\newcommand{\RR}{\mathbb{R}}
\newcommand{\eE}{\mathcal{E}}
\newcommand{\gG}{\mathcal{G}}
\newcommand{\nN}{\mathcal{N}}
\newcommand{\lnorm}[1]{\ell_{#1}\text{-norm}}

% Commands are also useful to ensure standardized notation, such as how to display vectors and matrices.
% The point is to replace formatting commands with semantic ones.
% This both makes the source more semantic, and also makes it easier to change formatting choices later
% IMPORTANT: In TeX, all commands share a global namespace. You need to be careful therefore not to overwrite an existing command.
%            Use \newcommand to ensure you don't accidentally overwrite an important macro
%            Use \renewcommand if you *do* want to overwrite a macro, have checked what the original does,
%            and have made sure the redefinition is safe.
\newcommand{\T}{\mathsf{T}}            % transpose
\renewcommand{\vec}[1]{\bm{#1}}        % redefine \vec to produce boldface instead of adding an arrow
\newcommand{\mat}[1]{\bm{#1}}          % define \vec to produce boldface
\newcommand{\ones}{\bm{1}}             % all-ones vector
\newcommand{\eye}{\bm{I}}              % identity matrix
\newcommand{\ei}{\bm{e}_i}             % standard basis vector e_i
\newcommand{\ej}{\bm{e}_j}             % standard basis vector e_j
    % TIP: Resist the temptation to be too clever with macros
    %   - \ei and \ej are easier to type than e.g. \ee[i]  (note that \e is a low-level command and should not be redefined)
    %   - While you can define macros in terms of other macros  (eg we could define \ei in terms of \vec),
    %     many journals won’t accept this. Recursive macros also produce more frequent and more complicated compilation errors

% Commands like \sin and \exp ensure proper fonts and spacing for math operators.
% Use the dedicated \DeclareMathOperator to define new operators
\DeclareMathOperator{\diag}{diag}

\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}



\section{Boolean networks}
Explain Boolean network and what an update scheme is using the synchronous/parallel scheme.

\subsection{Notation}
Define clear notation used throughout the paper



\section{Update Schemes}
Explain different update schemes including characteristics for behavior especially chaotic behavior.
\subsection{Synchronous scheme}
all nodes update at the same time
\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}
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}
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=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{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*}

\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`
\bibliographystyle{unsrt}
\bibliography{IEEEabrv,references}

\end{document}