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paper.tex
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@@ -15,7 +15,7 @@
%pdfauthor=, %pdfauthor=,
colorlinks=true, linkcolor=purple, urlcolor=blue, citecolor=cyan, colorlinks=true, linkcolor=purple, urlcolor=blue, citecolor=cyan,
anchorcolor=black % make links/references 'clickable' without ugly frames anchorcolor=black % make links/references 'clickable' without ugly frames
]{hyperref} ]{hyperref}
\usepackage{cleveref} % smart references to figures, equations etc. \usepackage{cleveref} % smart references to figures, equations etc.
% some packages which may be useful when drafting, but should be removed before submission % some packages which may be useful when drafting, but should be removed before submission
@@ -69,49 +69,52 @@
\end{abstract} \end{abstract}
\section{Introduction}00 \section{Introduction}
\subsection{Notation}
\section{Boolean networks} \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} \section{Update Schemes}
Explain different update schemes: Explain different update schemes including characteristics for behavior especially chaotic behavior.
\begin{itemize} \subsection{Synchronous scheme}
\item Synchronous scheme - all nodes update at the same time all nodes update at the same time
\item Sequential - 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{Sequential scheme}
\item block sequential - mix of synchronous and sequential. predefined blocks update sequentiall, inside a block the update follows the synchronous 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
\item asynchronous deterministic - one node is updated per tick following a specific sequence \subsection{Block-sequential scheme}
\item asynchronous generalized - same as asynchronous deterministic with the slight change that within the sequence nodes may appear multiple times. mix of synchronous and sequential. predefined blocks update sequential, inside a block the update follows the synchronous scheme
\subsection{Asynchronous deterministic}
\end{itemize} 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} \section{Relevance for Gene Regulatory Networks}
Tie the update schemes and their different outcomes or behavior to GRN. Tie the update schemes and their different outcomes or behavior to GRN.
\section{Conclusion} 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 \begin{figure*} % The starred version uses both columns; unstarred only one column
\centering \centering
% \includegraphics[width=5in]{edge_vs_hyperedge.png} % \includegraphics[width=5in]{edge_vs_hyperedge.png}
% TIP: Ensure the original image file has approximately the right dimensions % 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. % (if using matplotlib, specify correct figure size) so that the image is not rescaled too brutally.
\caption{Boolean example. \caption{Boolean example.
% NB: The '~' inserts a non-breaking space, ensuring 'Ref.' is never separated from its number % 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 $x(t) \rightarrow x(t+1)$ 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*} \end{figure*}
\begin{figure*} % The starred version uses both columns; unstarred only one column \begin{figure*} % The starred version uses both columns; unstarred only one column
@@ -120,18 +123,18 @@ Tie the update schemes and their different outcomes or behavior to GRN.
\caption{ \caption{
graph of all possible states for a boolean network using a synchronous update scheme graph of all possible states for a boolean network using a synchronous update scheme
} }
\end{figure*} \end{figure*}
\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 \centering
% \includegraphics[width=5in]{edge_vs_hyperedge.png} % \includegraphics[width=5in]{edge_vs_hyperedge.png}
% TIP: Ensure the original image file has approximately the right dimensions % 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. % (if using matplotlib, specify correct figure size) so that the image is not rescaled too brutally.
\caption{ \caption{
example graph of boolean network showcasing grouping of specific nodes. example graph of boolean network showcasing grouping of specific nodes.
} }
\end{figure*} \end{figure*}

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references.bib
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@@ -19,18 +19,32 @@
publisher={Episciences. org} publisher={Episciences. org}
} }
@article{helikar2011boolean,
title={Boolean modeling of biochemical networks},
author={Helikar, Tomas and Kochi, Naomi and Konvalina, John and A Rogers, Jim},
journal={The Open Bioinformatics Journal},
volume={5},
number={1},
year={2011}
}
@article{ARACENA20091, @article{schwab2020concepts,
title = {On the robustness of update schedules in Boolean networks}, title={Concepts in Boolean network modeling: What do they all mean?},
journal = {Biosystems}, author={Schwab, Julian D and K{\"u}hlwein, Silke D and Ikonomi, Nensi and K{\"u}hl, Michael and Kestler, Hans A},
volume = {97}, journal={Computational and structural biotechnology journal},
number = {1}, volume={18},
pages = {1-8}, pages={571--582},
year = {2009}, year={2020},
issn = {0303-2647}, publisher={Elsevier}
doi = {https://doi.org/10.1016/j.biosystems.2009.03.006}, }
url = {https://www.sciencedirect.com/science/article/pii/S0303264709000471},
author = {J. Aracena and E. Goles and A. Moreira and L. Salinas}, @article{bornholdt2008boolean,
keywords = {Boolean network, Update schedule, Robustness, Attractor, Dynamical cycle}, title={Boolean network models of cellular regulation: prospects and limitations},
abstract = {Deterministic Boolean networks have been used as models of gene regulation and other biological networks. One key element in these models is the update schedule, which indicates the order in which states are to be updated. We study the robustness of the dynamical behavior of a Boolean network with respect to different update schedules (synchronous, block-sequential, sequential), which can provide modelers with a better understanding of the consequences of changes in this aspect of the model. For a given Boolean network, we define equivalence classes of update schedules with the same dynamical behavior, introducing a labeled graph which helps to understand the dependence of the dynamics with respect to the update, and to identify interactions whose timing may be crucial for the presence of a particular attractor of the system. Several other results on the robustness of update schedules and of dynamical cycles with respect to update schedules are presented. Finally, we prove that our equivalence classes generalize those found in sequential dynamical systems.} author={Bornholdt, Stefan},
} journal={Journal of the Royal Society interface},
volume={5},
number={suppl\_1},
pages={S85--S94},
year={2008},
publisher={The Royal Society}
}