main.tex

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\title{\rightline{\HUGE StochSS: Stochastic Simulation Service}}
\date{}
\renewcommand{\maketitlehookb}{\vspace{-0.4cm}{\rightline{\LARGE User Guide and Tutorial}}\vspace{11.3cm}}

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\begin{document}
\maketitle

\tableofcontents

%\chapter{Introduction}

%\input{intro.tex}

\input{Install.tex}
\input{T1/tutorial1.tex}
\input{T2/tutorial2.tex}
\input{T3/tutorial3.tex}
\input{T4/tutorial4.tex}
\input{T6/tutorial6.tex}
\input{PSweep/psweep.tex}
\input{Vis/vis.tex}
%\input{T7/tutorial7.tex}
\input{custommesh.tex}



\begin{thebibliography}{9}

\bibitem{dan}
  D.T. Gillespie.
  \textit{Exact stochastic simulation of coupled chemical reactions}.
  J. Phys. Chem., 81(25), 2340-2361 (1977)

\bibitem{sundials}
  A. C. Hindmarsh et al.,
  \textit{SUNDIALS: Suite of nonlinear and differential/algebraic equation solvers}.
  ACM Trans. Math. Softw., 31(3), 363-396 (2005)
  
  \bibitem{scale}
  W. A. Link and P. F. Doherty Jr.,
  \textit{Scaling in sensitivity analysis}.
  Ecology, 83(12), 3299-3305 (2002)
  
  \bibitem{calib}
  M. C. Hill,
  \textit{Methods and guidelines for effective model calibration}. 
  U.S. Geol. Surv. Water Resour. Invest. Rep. 98-4005 (1998)
  
  \bibitem{bernie}
  B.J. Daigle et al.
  \textit{Accelerated maximum likelihood parameter estimation for stochastic biochemical systems}.
  BMC Bioinformatics, 13, 68 (2012)
  
  \bibitem{caffo}
  B.S. Caffo et al.
  \textit{Ascent-based Monte Carlo expectation-maximization}. 
  J. Royal Statistical Society Series B, 67(2), 235-251 (2005)
  
  \bibitem{nsm}
  J. Elf and M. Ehrenberg,
  \textit{Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases}. IEEE Systems Biology, 1, 230-6 (2004)
  
 \bibitem{urdme}
 B. Drawert, S. Engblom and A. Hellander, 
 \textit{URDME: {A} modular framework for stochastic simulation
of reaction-transport processes in complex geometries}. BMC Systems Biology, 6(76) (2012)
  
  \bibitem{wiki-michaelis-menten}
  Michaelis-Menten kinetics. 
  \url{http://en.wikipedia.org/wiki/Michaelis-Menten_kinetics}
  
  \bibitem{congote}
  Congote, John and Segura, Alvaro and Kabongo, Luis and Moreno, Aitor and Posada, Jorge and Ruiz, Oscar.
  \textit{Interactive Visualization of Volumetric Data with WebGL in Real-time}
  In Proceedings of the 16th International Conference on 3D Web Technology (Web3D '11). ACM, New York, NY, USA, 137-146.
  \url{http://dx.doi.org/10.1145/2010425.2010449}
  
\end{thebibliography}


\end{document}