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main.aux
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\relax
\providecommand*{\memsetcounter}[2]{}
\@writefile{toc}{\contentsline {chapter}{Contents}{2}}
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\@writefile{toc}{\contentsline {chapter}{\chapternumberline {1}Installation}{4}}
\@writefile{toc}{\contentsline {section}{\numberline {1.1}Try StochSS}{4}}
\@writefile{toc}{\contentsline {section}{\numberline {1.2}Install StochSS}{4}}
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\@writefile{toc}{\contentsline {chapter}{\chapternumberline {2}Basic Introduction}{5}}
\newlabel{chapter1}{{\M@TitleReference {2}{Basic Introduction}}{5}}
\@writefile{toc}{\contentsline {section}{\numberline {2.1}Creating Administrator and Standard User Accounts}{5}}
\@writefile{lof}{\contentsline {figure}{\numberline {2.1}{\ignorespaces Administrator login page}}{5}}
\newlabel{fig:admin}{{\M@TitleReference {2.1}{Administrator login page}}{5}}
\@writefile{toc}{\contentsline {section}{\numberline {2.2}Importing a Model}{6}}
\@writefile{toc}{\contentsline {subsection}{Importing an existing model}{6}}
\@writefile{toc}{\contentsline {section}{\numberline {2.3}Creating a New Model}{7}}
\newlabel{eq:tut1-reac1}{{\M@TitleReference {2.1}{Creating a New Model}}{7}}
\@writefile{lof}{\contentsline {figure}{\numberline {2.2}{\ignorespaces Dimerization reaction}}{7}}
\newlabel{fig:reaction2}{{\M@TitleReference {2.2}{Dimerization reaction}}{7}}
\@writefile{lof}{\contentsline {figure}{\numberline {2.3}{\ignorespaces Decay reaction}}{8}}
\newlabel{fig:reaction1}{{\M@TitleReference {2.3}{Decay reaction}}{8}}
\@writefile{toc}{\contentsline {section}{\numberline {2.4}Running a Simulation and Visualizing results}{8}}
\@writefile{toc}{\contentsline {subsection}{Converting a concentration model to population}{8}}
\citation{dan}
\@writefile{toc}{\contentsline {section}{\numberline {2.5}Backup and Transfer your Data}{9}}
\@writefile{toc}{\contentsline {subsection}{Exporting data from an old version of StochSS (1.2 or previous)}{10}}
\citation{sundials}
\citation{wiki-michaelis-menten}
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\@writefile{toc}{\contentsline {chapter}{\chapternumberline {3}Sensitivity Analysis}{11}}
\@writefile{toc}{\contentsline {section}{\numberline {3.1}Example: Michaelis-Menten}{11}}
\citation{bernie}
\citation{bernie}
\@writefile{lof}{\addvspace {10pt}}
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\@writefile{toc}{\contentsline {chapter}{\chapternumberline {4}StochOptim: Parameter Estimation}{12}}
\newlabel{chapter-stochoptim}{{\M@TitleReference {4}{StochOptim: Parameter Estimation}}{12}}
\@writefile{toc}{\contentsline {section}{\numberline {4.1}Example: Estimate parameters of a birth-death model}{12}}
\@writefile{toc}{\contentsline {subsection}{StochOptim input file format}{13}}
\citation{urdme}
\citation{nsm}
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\@writefile{toc}{\contentsline {chapter}{\chapternumberline {5}Spatial Stochastic Simulations}{14}}
\@writefile{toc}{\contentsline {section}{\numberline {5.1}Example: Annihilation of two species in a cylinder}{14}}
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\@writefile{toc}{\contentsline {chapter}{\chapternumberline {6}Cloud Computing}{16}}
\newlabel{sec:cc}{{\M@TitleReference {6}{Cloud Computing}}{16}}
\@writefile{toc}{\contentsline {section}{\numberline {6.1}Credentials}{16}}
\@writefile{toc}{\contentsline {subsection}{Setting Credentials in StochSS}{16}}
\@writefile{lof}{\contentsline {figure}{\numberline {6.1}{\ignorespaces Cloud Computing page - Credentials section}}{16}}
\newlabel{fig:1}{{\M@TitleReference {6.1}{Cloud Computing page - Credentials section}}{16}}
\@writefile{toc}{\contentsline {subsection}{Launching and Shutting Down Nodes}{17}}
\@writefile{lof}{\contentsline {figure}{\numberline {6.2}{\ignorespaces Cloud Computing page - Compute nodes default setting section}}{17}}
\newlabel{fig:2}{{\M@TitleReference {6.2}{Cloud Computing page - Compute nodes default setting section}}{17}}
\@writefile{toc}{\contentsline {section}{\numberline {6.2}Job Reproduction}{17}}
\@writefile{toc}{\contentsline {subsection}{An Example on Job Reproduction}{17}}
\@writefile{lof}{\contentsline {figure}{\numberline {6.3}{\ignorespaces Job summary page - reproduction available}}{18}}
\newlabel{fig:3}{{\M@TitleReference {6.3}{Job summary page - reproduction available}}{18}}
\@writefile{toc}{\contentsline {section}{\numberline {6.3}Cost Analysis}{18}}
\@writefile{lof}{\contentsline {figure}{\numberline {6.4}{\ignorespaces Cost Analysis page}}{19}}
\newlabel{fig:cost-analysis}{{\M@TitleReference {6.4}{Cost Analysis page}}{19}}
\@writefile{toc}{\contentsline {subsection}{An Example on Job Reproduction}{19}}
\@writefile{lof}{\addvspace {10pt}}
\@writefile{lot}{\addvspace {10pt}}
\@writefile{toc}{\contentsline {chapter}{\chapternumberline {7}Parameter Sweeps}{20}}
\@writefile{lof}{\contentsline {figure}{\numberline {7.1}{\ignorespaces A two-parameter sweep is visualized as a heat map. We have performed a sweep over the two parameters $k1$ and $k2$ of the \emph {lotkavolterra\_concentration\_oscil} model. The \emph {mapper} performs the initial analysis on the output---in this case simply taking the value of each solution at the final time point. The \emph {reducer} performs some analysis on the output of the mapper---in this case taking the average of the final time points. Note that this model is deterministic, and the average simply is the value of the ODE solution at the final time point.}}{21}}
\newlabel{psweep-fig1}{{\M@TitleReference {7.1}{A two-parameter sweep is visualized as a heat map. We have performed a sweep over the two parameters $k1$ and $k2$ of the \emph {lotkavolterra\_concentration\_oscil} model. The \emph {mapper} performs the initial analysis on the output---in this case simply taking the value of each solution at the final time point. The \emph {reducer} performs some analysis on the output of the mapper---in this case taking the average of the final time points. Note that this model is deterministic, and the average simply is the value of the ODE solution at the final time point.}}{21}}
\@writefile{lof}{\addvspace {10pt}}
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\@writefile{toc}{\contentsline {chapter}{\chapternumberline {8}Visualization}{22}}
\@writefile{toc}{\contentsline {section}{\numberline {8.1}Surface Renderings with Domain Clipping}{22}}
\@writefile{lof}{\contentsline {figure}{\numberline {8.1}{\ignorespaces Surface rendering of cylindrical domain. The actual stochastic simulation is run on the dual of the shown mesh, so the color at each node corresponds to the concentration in the corresponding voxel of the dual mesh. Colors are interpolated linearly between nodes. The color scale is not shown for brevity. }}{22}}
\newlabel{surface}{{\M@TitleReference {8.1}{ Surface rendering of cylindrical domain. The actual stochastic simulation is run on the dual of the shown mesh, so the color at each node corresponds to the concentration in the corresponding voxel of the dual mesh. Colors are interpolated linearly between nodes. The color scale is not shown for brevity. }}{22}}
\@writefile{lof}{\contentsline {figure}{\numberline {8.2}{\ignorespaces Surface rendering of cylindrical domain clipping along the X dimension. It is now possible to see concentrations of voxels inside the cylinder. }}{22}}
\newlabel{clipx}{{\M@TitleReference {8.2}{ Surface rendering of cylindrical domain clipping along the X dimension. It is now possible to see concentrations of voxels inside the cylinder. }}{22}}
\citation{congote}
\@writefile{toc}{\contentsline {section}{\numberline {8.2}Colorized Wireframe Meshes}{23}}
\@writefile{lof}{\contentsline {figure}{\numberline {8.3}{\ignorespaces Wireframe rendering of cylindrical domain. The colors are handled similarly to in Figure 8.1\hbox {}. }}{23}}
\newlabel{wireframe}{{\M@TitleReference {8.3}{ Wireframe rendering of cylindrical domain. The colors are handled similarly to in Figure 8.1\hbox {}. }}{23}}
\@writefile{lof}{\contentsline {figure}{\numberline {8.4}{\ignorespaces Wireframe rendering of cylindrical domain clipped in the Y direction. }}{23}}
\newlabel{clipy}{{\M@TitleReference {8.4}{ Wireframe rendering of cylindrical domain clipped in the Y direction. }}{23}}
\@writefile{toc}{\contentsline {section}{\numberline {8.3}Volume Rendering}{23}}
\@writefile{toc}{\contentsline {section}{\numberline {8.4}Visualization in Interactive Jupyter Notebook}{23}}
\@writefile{lof}{\contentsline {figure}{\numberline {8.5}{\ignorespaces This is the volume rendering of the same data shown above. The idea behind volume rendering is to color darkly areas with high concentrations and leave volumes with low concentrations transparent. The transparency makes it possible to see inside a volume rendering, and so the slicing as shown in the surface and wireframe renderings is not used. }}{24}}
\newlabel{fig:volume}{{\M@TitleReference {8.5}{ This is the volume rendering of the same data shown above. The idea behind volume rendering is to color darkly areas with high concentrations and leave volumes with low concentrations transparent. The transparency makes it possible to see inside a volume rendering, and so the slicing as shown in the surface and wireframe renderings is not used. }}{24}}
\@writefile{lof}{\contentsline {figure}{\numberline {8.6}{\ignorespaces Default Notebook for custom postprocessing.}}{24}}
\newlabel{vis-jupyter}{{\M@TitleReference {8.6}{Default Notebook for custom postprocessing.}}{24}}
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\@writefile{toc}{\contentsline {chapter}{\chapternumberline {9}Import a custom mesh}{25}}
\@writefile{toc}{\contentsline {section}{\numberline {9.1}Mesh library}{25}}
\@writefile{toc}{\contentsline {section}{\numberline {9.2}Using DOLFIN Built-In Geometry with Subdomains Outside of Mesh Library}{25}}
\@writefile{toc}{\contentsline {section}{\numberline {9.3}Advanced mesh generation}{27}}
\@writefile{toc}{\contentsline {section}{\numberline {9.4}References}{28}}
\bibcite{dan}{1}
\bibcite{sundials}{2}
\bibcite{scale}{3}
\bibcite{calib}{4}
\bibcite{bernie}{5}
\bibcite{caffo}{6}
\bibcite{nsm}{7}
\bibcite{urdme}{8}
\bibcite{wiki-michaelis-menten}{9}
\bibcite{congote}{10}
\@writefile{toc}{\contentsline {chapter}{Bibliography}{29}}
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